Search for motifs of 1577 Regulatory Elements (REs) was performed by NSITE program [http://www.softberry.com]; version 3.2009 SET of REs: REGSITE DB: Plant Transcription Regulatory Sites [Last Update: March 15, 2009] For NSITE programs | Only one of identical REs (regardless RE NAME and GROUP) is presented in this Set Search Parameters: Expected Mean Number : 0.01 or less Statistical Siginicance Level : 0.95 Level of homology between known RE and motif: 90% or higher Variation of Distance between RE Blocks : 20% ============================================================ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698A04.33|complement(1152095..1155249) |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +90 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.16 T - 0.37 C - 0.22 1 agctgccggc ttacttctac ttccttgtct tcttctgaaa acctttgcaa 51 agatcactat aattttggtc aaattcaact atatgctggg acattctaat 101 ttttttaacc gaatactacc ttttcttttc gatccgcgta tttgaATTGA 151 cttgtagcat atgaggcTAT AAATAtgcat ctcatttcat ttcatctcac 201 CCAAGGTTGT TCCAAAAATT TGGGAGTTCG AACTTCGAAC GACTCGGCGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00301 Mean Expected Number 0.008 +strand -155 : -149 TGCAAAG AC RSP00383 Mean Expected Number 0.008 +strand -134 : -128 GGTCAAA AC RSP00839 Mean Expected Number 0.001 -strand -63 : -70 CGCGGATC AC RSP01296 Mean Expected Number 0.003 +strand -34 : -26 CTATAAATA Totally 4 motifs of 4 different REs have been found Description of REs found 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 368. Group TF: WRKY1 /AC: RSP00383//OS: Petroselinum crispum /GENE: WRKY1/RE: WA /TF: WRKY1 784. Group RE: OCT /AC: RSP00839//OS: Arabidopsis thaliana /GENE: H4A748/RE: OCT /TF: unknown ||Identical REs AC: RSP00845 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.14|complement(1214121..1214918) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +355 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.11 T - 0.29 C - 0.27 1 acaactaatg ttatcttgac caaaactatc ctggatgcca caatgtctga 51 acttttgcag aaaaaaaatg ataggtaatc acacggaatc agccattgga 101 acgttcttgc cacgcgtttt tttatttttt ttaaattttt tttgccaaca 151 acgacgcact atataTATAA ACCcaagcaa ccagcccaag ctccaaatca 201 ATCAAATCGC ATTCCACCAA TTCTCCACTC TCCATCCTCC TCTAAAATCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00961 Mean Expected Number 0.005 -strand -142 : -149 TGCAAAAG AC RSP01007 Mean Expected Number 0.003 -strand -125 : -131 ACCTATC Totally 2 motifs of 2 different REs have been found Description of REs found 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 932. Group TF: PtMYB1; PtMYB4 /AC: RSP01007//OS: Pinus sylvestris /GENE: PsGS1b/RE: GS1b AC box 2 (AC-I) /TF: PtMYB1; PtMYB4 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0037C04.16|complement(1344452..1345525) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +41 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.22 T - 0.23 C - 0.23 1 catatggaag aaagcgtcaa attaattaat cagcactgat atagtagtgg 51 caaagccagg aagaagggaa tcagagtaga cagatgcgtg gcaaatgggg 101 cctccacgtg ctcttatcct catgcaagtc agcatttgtg ATTGGgtagt 151 atgggttgct cgatctttcT ATAAATAata acgctactca gtactcaccc 201 ATCACAAGCA CCCACACCAA CCAAAGATGA GCAACACCAC CATGGCTATT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00085 Mean Expected Number 0.001 +strand -35 : -20 TTTCTATAAATAaTAA AC RSP00085 Mean Expected Number 0.001 -strand -20 : -35 TTAtTATTTATAGAAA AC RSP00231 Mean Expected Number 0.010 -strand -56 : -62 CCAATCA AC RSP00681 Mean Expected Number 0.002 +strand -178 : -170 TAATTAATC AC RSP00817 Mean Expected Number 0.003 +strand -98 : -89 TcCACGTGCT AC RSP00889 Mean Expected Number 0.006 -strand -110 : -116 CCACGCA AC RSP01076 Mean Expected Number 0.004 +strand -118 : -109 gATGCGTGGC AC RSP01296 Mean Expected Number 0.003 +strand -32 : -24 CTATAAATA AC RSP01470 Mean Expected Number 0.006 +strand -81 : -72 TCATGCAaGT Totally 9 motifs of 8 different REs have been found Description of REs found 83. Group TF: AGL3 /AC: RSP00085//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AGL3-BE /TF: AGL3 224. Group RE: CCAAT box 1 /AC: RSP00231//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CCAAT box 1 /TF: unknown 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 763. Group TF: ACE-binding TF /AC: RSP00817//OS: Arabidopsis thaliana /GENE: CFI/RE: ACE-core (AtCFI) /TF: ACE-binding TF 821. Group RE: GC motif /Group TF: bZIP TF /AC: RSP00889//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: GC motif /TF: bZIP TF 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0037C04.37|1430798..1433611 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.18 T - 0.31 C - 0.20 1 tacatgcatg gtgtaccatc tacttaacat aacatgcata tatagtgctc 51 atcacaaaaa agtgcaaagg atgatcggtg tacatttgga ggcacattat 101 ttcctgtctc ttgagagtct ttgacacaca cagcactagt tcaccacttg 151 atggctcaag cacactacaT ATATATCctt gttttttcaa caaaaaagat 201 ATGGATTTTT TGTACTACTA CTTATGAAGA AGCTATGCAT AATGCAGAGG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -198 : -191 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -191 : -198 CATGCATG AC RSP00159 Mean Expected Number 0.001 -strand -63 : -71 TAGTGCTGT AC RSP00522 Mean Expected Number 0.010 +strand -57 : -51 CCACTTG AC RSP01071 Mean Expected Number 0.007 -strand -113 : -122 CAAAtGTACA AC RSP01237 Mean Expected Number 0.009 -strand -154 : -163 CaCTATATAT AC RSP01470 Mean Expected Number 0.009 -strand -190 : -199 cCATGCATGT AC RSP01641 Mean Expected Number 0.005 +strand -99 : -90 TCcTGTCTCT Totally 8 motifs of 7 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 154. Group RE: D4-core /AC: RSP00159//OS: Glycine max /GENE: GmAux28/RE: D4-core /TF: unknown 498. Group TF: DPBF-1; DPBF-2 /AC: RSP00522//OS: Daucus carota /GENE: Dc3/RE: E2-core /TF: DPBF-1; DPBF-2 989. Group TF: PvAlf /AC: RSP01071//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1c /TF: PvAlf ||Identical REs AC: RSP01153 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.14|1483202..1485699 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +222 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.18 T - 0.35 C - 0.26 1 ttgctagaat gcacagctta tttttttcag tttgtttaat tagtttaggt 51 tgggttggcc gtctccaact aactattcag cttgttgcgt cgtcggtcga 101 tcgatccatc catccatcca tctcgctgtc ctgcacgttt agacgtttac 151 ttactcagtc tcatccTATA AATAcatgcc catctcagat tgccaagatc 201 ATCATCAGTC GTGTGTCTCT CGTGTGTTAG CCACACGCCA CTGTCTAATT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00230 Mean Expected Number 0.006 -strand -145 : -154 AACCcAACCT AC RSP00230 Mean Expected Number 0.006 -strand -150 : -159 AACCTAAaCT AC RSP00808 Mean Expected Number 0.010 -strand -128 : -134 GTTAGTT AC RSP00934 Mean Expected Number 0.006 -strand -125 : -134 ATAgTTAGTT AC RSP00960 Mean Expected Number 0.003 +strand -135 : -128 CAACTAAC AC RSP01081 Mean Expected Number 0.000 +strand -96 : -85 TCCAtCCATCCA AC RSP01081 Mean Expected Number 0.000 +strand -92 : -81 TCCAtCCATCCA AC RSP01296 Mean Expected Number 0.001 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.008 +strand -35 : -26 CTATAAATAC Totally 9 motifs of 7 different REs have been found Description of REs found 223. Group TF: PcMYB1 /AC: RSP00230//OS: Petroselinum crispum /GENE: CHS-1/RE: MRECHS /TF: PcMYB1 761. Group TF: Pti4 /AC: RSP00808//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: Myb1 /TF: Pti4 ||Identical REs AC: RSP00810 RSP00812 RSP00813 863. Group RE: AT-2b /AC: RSP00934//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2b /TF: unknown 885. Group TF: HvGAMYB /AC: RSP00960//OS: Hordeum vulgare /GENE: ITR1/RE: MYB BS /TF: HvGAMYB 999. Group TF: DcMYB1 /AC: RSP01081//OS: Daucus carota /GENE: DcPAL1/RE: box-L3 /TF: DcMYB1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.21|1512637..1513516 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +39 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.21 T - 0.25 C - 0.27 1 tgagcaaacg agggaacatc cttaagggaa cattattaag ggattagaat 51 agtttcccta gttcagtcgt gtttcccgtg ttctgacaag tggggacagc 101 gccacgtgcg cgctcgctct tctccacatc tcgtggactc gttcgtgggc 151 cccgttgctg ccttcctggt cTATAAATAc acacactact atcacactct 201 GCATCTCAAA CCCAACTTCT TAAAGAACAA AAAACGATCA GCCATGAAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.006 -strand -91 : -100 CGCACGTGgC AC RSP00052 Mean Expected Number 0.002 -strand -92 : -102 GcACGTGGCGC AC RSP00056 Mean Expected Number 0.005 -strand -107 : -116 cCCACTTGTC AC RSP00057 Mean Expected Number 0.009 +strand -78 : -69 TCCACaTCTC AC RSP00065 Mean Expected Number 0.001 -strand -94 : -102 ACGTGGCGC AC RSP00075 Mean Expected Number 0.009 -strand -92 : -101 GcACGTGGCG AC RSP00175 Mean Expected Number 0.003 -strand -93 : -100 CACGTGGC AC RSP01296 Mean Expected Number 0.001 +strand -30 : -22 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -30 : -21 CTATAAATAC Totally 9 motifs of 9 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 51. Group RE: ABRE /AC: RSP00052//OS: Oryza sativa; /GENE: Rab-16A/RE: ABRE /TF: unknown 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 64. Group TF: EmBP-1 /AC: RSP00065//OS: Triticum aestivum /GENE: Em/RE: Em1a /TF: EmBP-1 74. Group TF: TAF-1 /AC: RSP00075//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: Iwt /TF: TAF-1 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.9|1695004..1699892 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +244 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.27 C - 0.20 1 cctaatacta ctttgtatat atatatatat atatattgcg aggattgtta 51 taataaaagt tgatttattt aaatctaata ccccgattgg tgatgcgcta 101 gtatcacagt atcactcagc tggaccccct gtcagtcata gcgacagagc 151 actccgattg gatatggggc cTATAAAACa gagaaaaaaa gcgccccatc 201 CAATGAACAT GCATGCCACT CAATGCATGC AGTGCAGTAG AGGAGGAGTA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00022 Mean Expected Number 0.007 +strand -151 : -143 ATAATAAAA AC RSP00108 Mean Expected Number 0.003 +strand +8 : +15 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand +15 : +8 CATGCATG AC RSP00157 Mean Expected Number 0.003 +strand -138 : -127 ATTTATtTAAAT AC RSP00157 Mean Expected Number 0.003 -strand -127 : -138 ATTTAaATAAAT AC RSP00566 Mean Expected Number 0.009 +strand -190 : -181 CtTTGTATAT AC RSP00713 Mean Expected Number 0.009 -strand -79 : -85 CAGCTGA AC RSP01074 Mean Expected Number 0.001 +strand +7 : +16 ACATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand +16 : +7 GCATGCATGt Totally 9 motifs of 6 different REs have been found Description of REs found 21. Group TF: PCF1 /AC: RSP00022//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX1 /TF: PCF1 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 542. Group RE: TATA P /AC: RSP00566//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: TATA P /TF: unknown 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.31|1899543..1901704 |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +157 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.14 T - 0.22 C - 0.41 1 gcgacgttga cctctgcgag cccatgacat ggcaccatta catcactctc 51 tctctctcgc tcgctcgcta ctccagactg aagcaacctc cttcgtctcg 101 ccttcccgga atcttcctcc caacttccat cctctcactg ttcgaaccgc 151 cattgcggct gcagTATAAA TCgagccgtc cgcacactgc aactcctcct 201 ACGCAAACCA CCCCAACCTG CACAACCTCT CCTCACCGAA CCAAAATCTC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00460 Mean Expected Number 0.002 -strand -168 : -177 GcCATGTCAT AC RSP00695 Mean Expected Number 0.006 +strand -36 : -30 TATAAAT AC RSP00864 Mean Expected Number 0.004 -strand -144 : -152 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 -strand -146 : -154 AGAGAGAGA Totally 4 motifs of 3 different REs have been found Description of REs found 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.49|1930919..1931726 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +130 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.16 T - 0.18 C - 0.40 1 ccaccaacgg acgcgccgtc gatcagctct agagatctcg cgccacaccc 51 agcacccgct gcttgccata tgccggtgac ctccagaaca agcaggaaac 101 ctcatcactc acccactcct cgacccttca cgacgcatcc aacccatcct 151 cacttctcaa ctgattctcg TATAAATCca cccccctcga acaccggatc 201 ATCGGTCGCC AAAAATCACA CAAACCTGCG TGCAAAGCCA TCTTGATCCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00301 Mean Expected Number 0.008 +strand +31 : +37 TGCAAAG AC RSP00320 Mean Expected Number 0.002 +strand -4 : +7 GATCATCGgTC AC RSP00695 Mean Expected Number 0.006 +strand -30 : -24 TATAAAT AC RSP00735 Mean Expected Number 0.006 +strand +11 : +18 AAAAATCA AC RSP00837 Mean Expected Number 0.008 -strand -176 : -185 tGATCGACGG Totally 5 motifs of 5 different REs have been found Description of REs found 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 698. Group TF: DET1; CCA1 /AC: RSP00735//OS: Arabidopsis thaliana /GENE: CAB2/RE: CCA1 BS /TF: DET1; CCA1 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.1|1937813..1938679 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +137 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.24 T - 0.22 C - 0.30 1 agaagaagaa ggaatggcgc cgatcgccgc cgtcgatcgg tgggaggaag 51 gtgaagccgt gcccgagctt tcgtcgtctc tcgttggaaa gctactgttt 101 tgacccgttc acaccactac gcttccagct ataggcagta tgtacggtgc 151 cacgcacggc tctcgtcctt taTATAAACC aactacctcg ccattgccac 201 CACCAGCAGC AGCTCGCCAT CCAAGCATCA AAGCTTCTAA ACTGAAGCTT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00122 Mean Expected Number 0.010 -strand -155 : -161 CTCCCAC AC RSP00146 Mean Expected Number 0.008 +strand -31 : -25 TTATATA AC RSP00146 Mean Expected Number 0.009 -strand -24 : -30 TTATATA AC RSP00837 Mean Expected Number 0.009 -strand -162 : -171 cGATCGACGG Totally 4 motifs of 3 different REs have been found Description of REs found 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.6|1948730..1949483 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +119 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.25 T - 0.18 C - 0.22 1 tgaaaatcat aaaacaagga gctccaggct ccagtaagcg ggagactagt 51 ctagaaaaga gtgggtcctg ctggacagag acaagggaaa taagctgatc 101 tggaaagaaa agagaacatc agagagtgga gatcactcga gatgcttcaa 151 gaccaagttc tgaagaaccT ATAAATAcgc ccaccttgca tcgcatctcc 201 GCATTCAAGG CAGAGCTAGT AGTGGTCACA TCGCCAATTC ACAGTCGAAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.002 +strand -32 : -24 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -32 : -23 CTATAAATAC Totally 2 motifs of 2 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.44|2068645..2070411 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +127 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.16 T - 0.24 C - 0.31 1 ttgccccttt gaccttggta gctgtaacgc ggcgcccaga catagtcgca 51 ctagctctcg cactcacatg cgcatccgct tcatcaaagc aaaaaagatt 101 aaattaattc ggtgataaga tcgattccgt ctagtaatcc aagctGCAAT 151 tccgattgat taccttcTAT AAATAcctca ccccacccct gagccctccc 201 AAATCCGAGC AAATCAACAA CACACGATCA ATCGATCGAT TAATCCTCTC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.004 -strand -167 : -173 CGCCGCG AC RSP00447 Mean Expected Number 0.006 +strand -118 : -109 AtCAAAGCAA AC RSP00536 Mean Expected Number 0.009 +strand -89 : -83 GTGATAA AC RSP00987 Mean Expected Number 0.002 -strand -177 : -186 CAGCTACCAa AC RSP01296 Mean Expected Number 0.002 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -34 : -25 CTATAAATAC AC RSP01351 Mean Expected Number 0.002 +strand -12 : -2 CTGaGCCCTCC Totally 7 motifs of 7 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 512. Group RE: LRE-TATA AA2 /AC: RSP00536//OS: Lycopersicon esculentum /GENE: rbcS3C/RE: LRE-TATA AA2 /TF: unknown 908. Group RE: H-box-like motif /AC: RSP00987//OS: Antirrhinum majus /GENE: CHS/RE: H-box-like motif /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1233. Group TF: CPRF1 /AC: RSP01351//OS: Arabidopsis thaliana /GENE: APX1/RE: DNase I footprint /TF: CPRF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.19|2773774..2778525 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +121 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.15 T - 0.24 C - 0.25 1 tcttgccatc caatcagtac agttgcgtca agcattcaac ttctgaattt 51 ccatctgata agtaattact actccagctt tgagtcgtta aaaatatagt 101 actagaaaca atccaagtta gaacaagctc tatagaatcA TTGGccagct 151 ggacagacag tcactaaaTA TAAATAtcca agtgtctcaa gcacacaagc 201 CACCCAACAC CACAGTGCGA CAAGCTCTCG CCAAGTCGCT ATCCAAGAAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00314 Mean Expected Number 0.001 -strand -79 : -89 TCtAACTTGGA AC RSP00340 Mean Expected Number 0.004 +strand -24 : -15 TCCAaGTGTC Totally 2 motifs of 2 different REs have been found Description of REs found 300. Group TF: RSG /AC: RSP00314//OS: Arabidopsis thaliana /GENE: GA3/RE: rbe /TF: RSG 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.36|3028281..3029811 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +101 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.21 T - 0.21 C - 0.30 1 gacgtggggc ccaaggttgt aacggattat tcacctcgga agaatgtaaa 51 atactcgcgg ttaaaaaaat taaaccgcgg gcgcacgagt tgtcagtgac 101 accgagagac ggtaattttc cgtgtcttca ccggcaagcc acatttcacc 151 tcgtccagca accttgtcTA TAAATTgcgt cctcgtcttc atctccatcc 201 AAACCGCCAC ACACACGCGC GCGGAAAACA CTCCCAATCC CAAACCGAAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00566 Mean Expected Number 0.005 +strand -39 : -30 CCTTGTcTAT Totally 1 motifs of 1 different REs have been found Description of REs found 542. Group RE: TATA P /AC: RSP00566//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: TATA P /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.14|complement(3097096..3102031) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +2501 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.20 T - 0.25 C - 0.33 1 atactagtag tagtaaaagg gactttttat ataggagtat ttggatcgtg 51 gagttccatg tgtgggcgca gagccgtggg ccccaatccg cacgcgatgc 101 gcttccgctt ctccgccccc gattccttcc tctccacccc gcccatctct 151 tcctcttcTA TAAATAcgag agccctttcc atccccatct cctcttcccc 201 TTCTACTCCA CACCGCACAG ACAAATACTC TACGAGAGAG AGAGAGAGAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00161 Mean Expected Number 0.008 +strand -189 : -179 AGTAAAAGGGA AC RSP00313 Mean Expected Number 0.001 -strand -139 : -149 CACATGGaACT AC RSP00509 Mean Expected Number 0.000 +strand -42 : -31 TATAAATACgAG AC RSP00695 Mean Expected Number 0.010 +strand -42 : -36 TATAAAT AC RSP00864 Mean Expected Number 0.000 +strand +35 : +43 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 +strand +37 : +45 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 +strand +39 : +47 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 +strand +41 : +49 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 +strand +43 : +51 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 +strand +34 : +50 GAGAGAGAGAGAGAGAg AC RSP01296 Mean Expected Number 0.001 +strand -43 : -35 CTATAAATA AC RSP01301 Mean Expected Number 0.007 +strand -43 : -34 CTATAAATAC Totally 12 motifs of 8 different REs have been found Description of REs found 156. Group TF: Dof1 /AC: RSP00161//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof1 BSopt /TF: Dof1 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.26|complement(3133122..3137020) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +120 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.41 G - 0.14 T - 0.19 C - 0.26 1 cgtcgtgtag cgaaagtcca cggccacaat acctctcatc tcgactcatc 51 ccataataat cctacgtagt acatacagca tgcgccactt gtttctagaa 101 attcaaaaac aaatcagaaa cattttttcc acgcaaaaac aaaaaaaaaa 151 gaagcaaaaa tccatcgTAT AAATTgcatc cgttgccatc cactggcctc 201 CAACTGTCCG ACACGCCGAG AAGAAAAAAA AAAGAAAAAA AAGCAACGAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00056 Mean Expected Number 0.002 +strand -117 : -108 GCCACTTGTt AC RSP00129 Mean Expected Number 0.006 -strand -194 : -199 CACGAC AC RSP00522 Mean Expected Number 0.009 +strand -116 : -110 CCACTTG AC RSP01017 Mean Expected Number 0.000 -strand -105 : -112 AGAAACAA AC RSP01343 Mean Expected Number 0.009 +strand -198 : -193 TCGTGT Totally 5 motifs of 5 different REs have been found Description of REs found 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 127. Group RE: R-motif /AC: RSP00129//OS: Zea mays /GENE: Bronze2/RE: R-motif /TF: unknown 498. Group TF: DPBF-1; DPBF-2 /AC: RSP00522//OS: Daucus carota /GENE: Dc3/RE: E2-core /TF: DPBF-1; DPBF-2 942. Group TF: AEF /AC: RSP01017//OS: Arabidopsis thaliana /GENE: GapA/RE: AE box 2 /TF: AEF 1227. Group RE: TCGTGT motif /AC: RSP01343//OS: Daucus carota /GENE: Dc3/RE: TCGTGT motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.39|complement(3185917..3187133) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.20 T - 0.34 C - 0.22 1 cgcagtcttt tgactcactc taggctgata tttctcttct caacagaggc 51 gtccgtggaa caacatctca ggtgtgctct gtcaaaagca aaattcgctc 101 ttgttttgac ctgtaagcaa aaATTGTttc tttttgacta gtataagcag 151 atacagagat actccattgc cTATAAATCa cacgtactaa ctggcggggt 201 TGTGTCATCT TGTCTATGGT AGTTCAGCAA TCCTCTGCTT TTGTCAGTTG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00459 Mean Expected Number 0.004 +strand -67 : -58 TTGACTAGTA AC RSP01711 Mean Expected Number 0.005 +strand -63 : -54 CTAGTATAAG Totally 2 motifs of 2 different REs have been found Description of REs found 437. Group TF: O2 /AC: RSP00459//OS: coix /GENE: alpha-coixin/RE: O2u /TF: O2 1519. Group TF: RIN /AC: RSP01711//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Others /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.8|complement(3355336..3357477) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +33 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.12 T - 0.27 C - 0.27 1 atgaagattc ttcaaactcc aattaacaac aaagattcct cagctcaatg 51 acttgatttc ctcttctaac aaccaagaat ccgctttacc aaaaattatg 101 ccgtgcttca ttagactcag tcatggatga gccaaaattt tatctgagga 151 accatcatct cttccatcTA TAAAACcaca ccaatactgg gatactccca 201 CATTGCAAAA CAAGCTCAAG TTTTCAACAA CGTAATGGCT CACAGCTTAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00038 Mean Expected Number 0.004 -strand -21 : -32 TGTGGTTtTATA AC RSP00416 Mean Expected Number 0.004 -strand -72 : -78 CATCCAT AC RSP01031 Mean Expected Number 0.006 -strand -190 : -197 AGAATCTT Totally 3 motifs of 3 different REs have been found Description of REs found 37. Group TF: GT-1 related TFs /AC: RSP00038//OS: Lycopersicon esculentum /GENE: LAT52; LAT56;/RE: 52/56 box /TF: GT-1 related TFs 398. Group RE: Box-1 /AC: RSP00416//OS: Hordeum vulgare /GENE: EPB-1/RE: Box-1 /TF: unknown 956. Group TF: AEF /AC: RSP01031//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 2 /TF: AEF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.9-1|complement(3358864..3364461) |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1362 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.24 T - 0.16 C - 0.42 1 gacacaggcg agccgtacac actgtagtta tgtggtgcac tggtcggttc 51 cgctgaccac ccgtgactct taccacgacc ccgtccccgg tgtggcccca 101 cctaccagcg acacacgcag gcggcttctt ctcgtgagct cgcggtgaac 151 ccgaccaccc gccgctaTAT AAACGtcgcc ccccttgcca cgacacgcgc 201 TACGCCCACC CATCCACTCG CACCCCGCGC CGCACCAACA CACGCAGAGG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.008 -strand -28 : -33 TTTATA AC RSP00079 Mean Expected Number 0.003 +strand -104 : -95 CCCACCTACC AC RSP00146 Mean Expected Number 0.001 -strand -29 : -35 TTATATA AC RSP00147 Mean Expected Number 0.008 +strand -33 : -28 TATAAA Totally 4 motifs of 4 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0089K24.23|complement(3827294..3828648) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +66 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.25 T - 0.26 C - 0.29 1 actgcgtgga gtactggagc gtatgaatcc gcccccaaat ggtgccaaat 51 cgcagccggt ggatcgaccg atcgatcgat ctggagctag gttttctgac 101 ccgatcccgA TTGCgacgga gacggcgccc ccaaatcgat ccattttttg 151 cctcacttaa tctctcgcTA TAAATCcacc actctctctt gtgttgctct 201 CTCTTCACTT GGTTGGCGGC GGCGCTGCGG GAGCTAGTAG TAGATCAAGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.006 +strand -32 : -26 TATAAAT AC RSP01301 Mean Expected Number 0.004 +strand -33 : -24 CTATAAATcC Totally 2 motifs of 2 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0666G04.25|complement(4319378..4322984) |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1179 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.31 T - 0.18 C - 0.24 1 cgtcgtctta tggtggtggc agtggcagcg gcgcacgagg cccccgtgga 51 ccgggtgcag gtgggccggc ccaaactgtt tgggcctagg aatggaggcc 101 caaactacat gggccaccaa atggtggccc atttagagtc gtagcccaac 151 acgtctgtca tactgtacgg gTATAAATAc gggcgtacca tttcggaggg 201 GAGGCGGCAA GTGAACAAAC CAGAGTTCAA AAATTTCCCA AAAAAAAATA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.008 +strand -29 : -23 TATAAAT AC RSP01301 Mean Expected Number 0.004 +strand -30 : -21 gTATAAATAC Totally 2 motifs of 2 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0666G04.28|complement(4343830..4353110) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +100 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.16 T - 0.30 C - 0.20 1 gtatcaattt tcatgaccga ttataatcat gatggagtaa ctataaggtg 51 ttgataattt tgttcagaat gcgtgtgatg taaaagttcg agaagacttt 101 gtttttgttt tgtcttaatt tcctcgatga tatataataa tGCAATccct 151 tgtctctccc acacccTATA AACAtccgga tatcacacac attcacactc 201 ACACCTCACA AAAAAGCAAA CAAGACAGCG AAAATAATCA GAGAGAGAAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00029 Mean Expected Number 0.008 +strand -122 : -115 TGTAAAAG AC RSP00122 Mean Expected Number 0.007 +strand -45 : -39 CTCCCAC AC RSP00441 Mean Expected Number 0.008 -strand -98 : -107 AACAAAGTcT AC RSP00864 Mean Expected Number 0.001 +strand +40 : +48 AGAGAGAGA AC RSP01641 Mean Expected Number 0.004 +strand -53 : -44 cCTTGTCTCT Totally 5 motifs of 5 different REs have been found Description of REs found 28. Group RE: P-box 1 /AC: RSP00029//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 1 /TF: unknown 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: B1370C05.27|124644..127133 |SUPPORT| 6 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +227 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.26 T - 0.24 C - 0.19 1 agagagccaa acatagaggg gcgggttaat caggaggtaa gaacaagtgg 51 agaagacaag gataagagat gagaagagca atgagctatg tatcaataaa 101 ataATTGAtg acctggcagc ttagcttaat tagtgcagct ggaactgata 151 ggcgcgcgat tgatagctTA TAAATCgaag gagggggaag gcctcatctc 201 CGTGCATCTC GCTACCTAAC CTAGCTAACC TCCTCTCTTC TTCTTCTTCT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00230 Mean Expected Number 0.006 +strand +13 : +22 tACCTAACCT AC RSP00595 Mean Expected Number 0.001 +strand -77 : -69 GCTTAATTA AC RSP00913 Mean Expected Number 0.006 +strand -94 : -85 GATGACCTGG AC RSP01678 Mean Expected Number 0.001 +strand -107 : -96 CAATAAAATAaT AC RSP01751 Mean Expected Number 0.002 -strand -150 : -158 TCCACTTGT Totally 5 motifs of 5 different REs have been found Description of REs found 223. Group TF: PcMYB1 /AC: RSP00230//OS: Petroselinum crispum /GENE: CHS-1/RE: MRECHS /TF: PcMYB1 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 844. Group TF: Opaque-2 /AC: RSP00913//OS: Zea mays /GENE: b-32/RE: B1 /TF: Opaque-2 1496. Group TF: AT-Hook TFs /AC: RSP01678//OS: Catharanthus roseus /GENE: ORSA3/RE: JRE (Quant. Seq.) /TF: AT-Hook TFs 1557. Group TF: AREB2/ABF4 /AC: RSP01751//OS: Arabidopsis thaliana /GENE: COX5b-1/RE: distalB-like /TF: AREB2/ABF4 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1435_F07.31|complement(180352..183441) |SUPPORT| 3 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +86 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.21 T - 0.23 C - 0.31 1 cccatttatt tattatatat gcgcatgtga attaaaatga ctgggctgct 51 gcattacaat ctacaagtcg cgagcgtgtt gattgggccc atccatcatc 101 attgaacggc ccaccagaaa gcctaggcCC AATatggcaa aaaccctaag 151 gccgtgtgcg tcacccacct aTATAAAGCg gaaaacgcca ctcgtctcct 201 TCTTCCTTCT TCTTCCACGC CCCGCATCGC CGCCGCCGCC GGAGAGGGAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00056 Mean Expected Number 0.009 +strand -14 : -5 GCCACTcGTC AC RSP00231 Mean Expected Number 0.007 -strand -115 : -121 CCAATCA AC RSP00279 Mean Expected Number 0.002 -strand -52 : -60 TTAGGGTTT AC RSP00369 Mean Expected Number 0.002 +strand -60 : -52 AAACCCTAA AC RSP00792 Mean Expected Number 0.003 -strand -115 : -124 CCAAtCAACA AC RSP01303 Mean Expected Number 0.004 +strand -61 : -52 aAAACCCTAA Totally 6 motifs of 6 different REs have been found Description of REs found 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 224. Group RE: CCAAT box 1 /AC: RSP00231//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CCAAT box 1 /TF: unknown 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1212_C06.24|295323..299167 |SUPPORT| 2 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +168 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.30 C - 0.16 1 gtttgtgatt aaacagtgta acaacacgga aaggttcaag acgagcaaac 51 acgtcagcat gtacaaacgc agtgtatgag ttaattaatt atatggttag 101 cgtgtatcga cattctcgat accagtttaa aatatgtgat gatattatta 151 gaccttgcac cccTATAAAT Tagggccggt gaacaaaacc atcaacgcct 201 TAGTTTTTGA TTTTGAAGAA GAAATTGTTG TCAGCATCAT TAGATCTTGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00997 Mean Expected Number 0.002 -strand -143 : -152 GCTGACGTGT AC RSP01258 Mean Expected Number 0.002 -strand -145 : -152 TGACGTGT Totally 2 motifs of 2 different REs have been found Description of REs found 918. Group TF: Opaque-2 (O2) /AC: RSP00997//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-2 /TF: Opaque-2 (O2) 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0501G04.27|633586..635778 |SUPPORT| 4 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +56 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.23 T - 0.24 C - 0.31 1 tttcgttgac gggccgacgt cgctggctga aggtgaatgg aacagcccat 51 gttccattat attggcccag aacggaatcg taactattgg ttcctaatat 101 cggcCCAATc aattgcgttg gttatgaatg gcccatggaa gcccactatt 151 gctgctcccg tgctcccTAT AAATAgctag ggttttacgc cacttccccc 201 ATCTCCGCCG CCGCCGCCCC ACTCTCCAAC CCTAGCCGAG AGGAGCAGAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00548 Mean Expected Number 0.001 +strand -121 : -111 GTAACtATTGG AC RSP00695 Mean Expected Number 0.007 +strand -33 : -27 TATAAAT AC RSP00759 Mean Expected Number 0.008 +strand -145 : -139 ATTATAT AC RSP00950 Mean Expected Number 0.005 +strand +22 : +32 CTCtCCAACCC AC RSP01296 Mean Expected Number 0.000 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.005 +strand -34 : -25 CTATAAATAg AC RSP01708 Mean Expected Number 0.002 +strand -34 : -25 CTATAAATAG AC RSP01708 Mean Expected Number 0.002 -strand -25 : -34 CTATTTATAG Totally 8 motifs of 7 different REs have been found Description of REs found 524. Group RE: CAAT/13 Y /AC: RSP00548//OS: Lycopersicon esculentum /GENE: rbcS3C/RE: CAAT/13 Y /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 721. Group RE: submotif D /AC: RSP00759//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif D /TF: unknown 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0501G04.36|complement(667264..669054) |SUPPORT| 1 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +92 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.21 T - 0.24 C - 0.24 1 ttgttttaaa ttcagaccaa taatgcaccc attgttaatt cagaaagaaa 51 tcggtaagcc cagagagttc agacttcaga gagctgacag cgtgttcagg 101 ccgttcgatt ttggtgaggc cATTGCacca gcacgaatca cgaggcagat 151 attacaactt gagctctcTA TAAATAgccc cagcgatgcg cgatccaaag 201 CAAGCAACAG CAGCAGAAGT GCACTTTTGC ATTCTATTTC CAATCAATCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00860 Mean Expected Number 0.003 +strand -159 : -151 AGAAAGAAA AC RSP00961 Mean Expected Number 0.003 -strand +31 : +24 TGCAAAAG AC RSP01296 Mean Expected Number 0.002 +strand -33 : -25 CTATAAATA AC RSP01621 Mean Expected Number 0.004 +strand +20 : +29 TgCACTTTTG AC RSP01708 Mean Expected Number 0.006 +strand -33 : -24 CTATAAATAG AC RSP01708 Mean Expected Number 0.006 -strand -24 : -33 CTATTTATAG Totally 6 motifs of 5 different REs have been found Description of REs found 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1441. Group TF: GmDof4; GmDof22 /AC: RSP01621//OS: Glycine max /GENE: Synthetic OLIGO/RE: E4 /TF: GmDof4; GmDof22 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1399_H05.34|complement(767270..772099) |SUPPORT| 9 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +12 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.39 G - 0.18 T - 0.18 C - 0.25 1 aggacaaatt cgtattcgag ctcgaaaagg caaaaagaaa ccaaaaacag 51 aaaaaaaaaa gaaaaggaat ccggctgtgc ttggattgca ttggaagcaa 101 agttcgttta aaaaaaaaaa ctaaaactaa taaaccagtc cgtttcaaac 151 accaaaaccg cgaacgcTAT AAATTcggag ggaaaacctc tccgaatctc 201 CAAACTCCTC CAATGGCGAC CGCGCGCGTC TCCCTCATCC TCCTCGTCGT 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0088N06.21|complement(1103043..1104294) |SUPPORT| 1 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +106 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.24 T - 0.14 C - 0.38 1 cagcccacac gtgcgagtca cgggcccacg cgtcggtgtc cgaaccaagg 51 cccactcccc cacgaccgtc cagatcccgg tcgcgcgatc acggccgtcc 101 gatcaacccc catcccgcga gtcgtctccc ccccctctcg gctcgagttc 151 ctcgtatacc acgccgccgc cTATAAATAg agtctcccaa ggaaacagat 201 AAGATCGGGC ACACGCGTAG CGAGACGAGG GGAAAAAAAA ATCAATCAAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00095 Mean Expected Number 0.006 -strand -172 : -180 GTGGGCCCG AC RSP00695 Mean Expected Number 0.002 +strand -29 : -23 TATAAAT AC RSP00722 Mean Expected Number 0.007 +strand -3 : +4 GATAAGA AC RSP00735 Mean Expected Number 0.003 +strand +37 : +44 AAAAATCA AC RSP01250 Mean Expected Number 0.002 +strand +37 : +46 AAAAaTCAAT AC RSP01296 Mean Expected Number 0.000 +strand -30 : -22 CTATAAATA AC RSP01301 Mean Expected Number 0.003 +strand -30 : -21 CTATAAATAg AC RSP01497 Mean Expected Number 0.006 +strand -107 : -98 GCCGTCcGAT AC RSP01505 Mean Expected Number 0.001 -strand -97 : -105 GATCGGACG AC RSP01708 Mean Expected Number 0.001 +strand -30 : -21 CTATAAATAG AC RSP01708 Mean Expected Number 0.001 -strand -21 : -30 CTATTTATAG Totally 11 motifs of 10 different REs have been found Description of REs found 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 687. Group RE: I-box /AC: RSP00722//OS: Nicotiana plumbaginifolia /GENE: rbcS 8B/RE: I-box /TF: unknown 698. Group TF: DET1; CCA1 /AC: RSP00735//OS: Arabidopsis thaliana /GENE: CAB2/RE: CCA1 BS /TF: DET1; CCA1 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0575F10.17|1237099..1240160 |SUPPORT| 6 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +68 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.14 T - 0.28 C - 0.27 1 aatagctaat gtacctgtcc cataacagat accatatgat tcttatattt 51 tggtacgaga gtaagtagct aatgtaccag tccactaaca gacgccactc 101 tccgttgctt atgctgttat gcatgcttca tgcttccaac caacaaataa 151 ctgccactaa ccgctaTATA TATCgcatct cgcactgaca ctagctaacc 201 AACCATGCAT GTTAATTAAC TCGTGCACAT ACATACGCCA CGTACTAGCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00043 Mean Expected Number 0.003 -strand +44 : +37 TACGTGGC AC RSP00051 Mean Expected Number 0.007 +strand +37 : +46 GCCACGTACt AC RSP00052 Mean Expected Number 0.001 -strand +45 : +35 GTACGTGGCGt AC RSP00064 Mean Expected Number 0.007 -strand +46 : +37 AGTACGTGGC AC RSP00075 Mean Expected Number 0.006 -strand +45 : +36 GTACGTGGCG AC RSP00103 Mean Expected Number 0.007 +strand +25 : +34 GCACATACaT AC RSP00108 Mean Expected Number 0.003 +strand +4 : +11 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand +11 : +4 CATGCATG AC RSP00821 Mean Expected Number 0.004 +strand +37 : +46 GCCACGTaCT AC RSP01034 Mean Expected Number 0.009 -strand +43 : +37 ACGTGGC AC RSP01114 Mean Expected Number 0.009 -strand -148 : -154 CCAAAAT AC RSP01237 Mean Expected Number 0.008 +strand -39 : -30 CgCTATATAT AC RSP01237 Mean Expected Number 0.008 +strand -37 : -28 CTaTATATAT AC RSP01276 Mean Expected Number 0.005 -strand +45 : +38 GTACGTGG AC RSP01470 Mean Expected Number 0.007 +strand +3 : +12 cCATGCATGT Totally 15 motifs of 13 different REs have been found Description of REs found 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 50. Group RE: A3 /AC: RSP00051//OS: Hordeum vulgare /GENE: HVA22/RE: A3 /TF: unknown 51. Group RE: ABRE /AC: RSP00052//OS: Oryza sativa; /GENE: Rab-16A/RE: ABRE /TF: unknown 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 74. Group TF: TAF-1 /AC: RSP00075//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: Iwt /TF: TAF-1 101. Group RE: Z element /AC: RSP00103//OS: Agrobacterium tumefaciens /GENE: nos/RE: Z element /TF: unknown 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 1033. Group RE: CCAAT box-like motif 1 /AC: RSP01114//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 1 /TF: unknown 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1175. Group RE: Box III /AC: RSP01276//OS: Petroselinum crispum /GENE: CHS/RE: Box III /TF: unknown 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0482F12.1-1|1326921..1330305 |SUPPORT| 6 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +150 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.20 T - 0.18 C - 0.41 1 tcaatgcttg cgaaactgta gaagcttccg gaccggtcgc gccgcaccgc 51 accgcacccg cgttaaaacg caccgagcct tcgcgagaac tacccgaaca 101 atacccgccc gtttccttgc tcgcgaatcc actcgcgcgt gcgtgggccc 151 caccagcccc cacgcgcggg taTATAAACC cccccccccg cctcccctct 201 CATTCCTTTT TATCCGACGA TTCAAAAAAT TCGAAGCCAT CCACCAACGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.003 -strand -24 : -30 TTATATA AC RSP00660 Mean Expected Number 0.003 +strand -184 : -178 TGTAGAA AC RSP00889 Mean Expected Number 0.004 -strand -55 : -61 CCACGCA Totally 3 motifs of 3 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 632. Group RE: -300 box /AC: RSP00660//OS: Oryza sativa /GENE: Gt3/RE: -300 box /TF: unknown 821. Group RE: GC motif /Group TF: bZIP TF /AC: RSP00889//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: GC motif /TF: bZIP TF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0482F12.7|complement(1347163..1351336) |SUPPORT|12 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +149 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.24 T - 0.22 C - 0.31 1 gggcggcaag ggggccgcct gcaaatttcg ttgacggccg tcgcccgaga 51 gcgaacggcc gtctgccacg tcattttcgc cgccctctga gagggcggta 101 ggcgactact tccgTCAATt ttcaaaatgg aaaattattt ttgtaaaact 151 tttaataaaa aaatTATAAA TAaaaaaaat tcgtcgtctc ttgccgcccc 201 CAAGCGCAGC CGCAACTCCG CCGAGTTCGC CGCCTCCGCC TCCGCCTCCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00018 Mean Expected Number 0.007 +strand -64 : -58 ATTTTTG AC RSP00113 Mean Expected Number 0.001 -strand -128 : -136 TGACGTGGC AC RSP00214 Mean Expected Number 0.006 -strand -128 : -135 TGACGTGG AC RSP00215 Mean Expected Number 0.006 +strand -135 : -128 CCACGTCA AC RSP00695 Mean Expected Number 0.008 +strand -36 : -30 TATAAAT AC RSP00819 Mean Expected Number 0.006 +strand -136 : -127 GCCACGTCaT AC RSP00821 Mean Expected Number 0.007 +strand -136 : -127 GCCACGTCaT AC RSP00933 Mean Expected Number 0.000 -strand -31 : -43 TTTATAATTTTTT AC RSP01021 Mean Expected Number 0.007 -strand -45 : -51 ATTAAAA AC RSP01115 Mean Expected Number 0.007 -strand -58 : -64 CAAAAAT AC RSP01275 Mean Expected Number 0.006 +strand -136 : -127 gCCACGTCAT Totally 11 motifs of 11 different REs have been found Description of REs found 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 765. Group TF: ACE-binding TF /AC: RSP00819//OS: Arabidopsis thaliana /GENE: F3H/RE: ACE-core (AtF3H) /TF: ACE-binding TF 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0482F12.17|1397696..1398983 |SUPPORT| 4 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +33 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.19 T - 0.27 C - 0.24 1 ggtaactttc ccctcaaatg attcctgcct ctccaatgcc aggccaactc 51 tagcttcaaa tccaggggag gaatcaaaga ggaagggcag aaaaggcatt 101 agtaacataa aagtaaagga aggaatgcat tccaagcttg cattcctttt 151 cttctcctga actaTATAAA CAcactggtt cccacaaatc ttgtaagcaa 201 ACAGTCTGTT TTGCCCTCTT TGCTGGAACA ATCATGGGTC TTGCATTTAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00038 Mean Expected Number 0.002 -strand -27 : -38 TGTGtTTATATA AC RSP00642 Mean Expected Number 0.005 -strand +49 : +42 TAAATGCA Totally 2 motifs of 2 different REs have been found Description of REs found 37. Group TF: GT-1 related TFs /AC: RSP00038//OS: Lycopersicon esculentum /GENE: LAT52; LAT56;/RE: 52/56 box /TF: GT-1 related TFs 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0482F12.25|1427398..1428069 |SUPPORT| 1 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +92 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.12 T - 0.31 C - 0.28 1 aattagatag aagaaaatta attaactgat gaaaaccaag tgaaaattaa 51 tgcgaagccc tatttttagc aaaaactaaa cctattgatc acgcttgtcc 101 gggaacctct cgtagcctga catatgatca catctctcgt cattctccct 151 cctcctttct cacgtaTATA AACAccaccc tcccctccgg ttgatcgatc 201 ATCTCTTGCA TCGATCTTAA TTTCTCATCT TTTCGCTCTC GATCTCCTAC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00203 Mean Expected Number 0.004 -strand -33 : -42 TATACGTgAG AC RSP00320 Mean Expected Number 0.001 -strand +3 : -8 GATgATCGATC AC RSP00572 Mean Expected Number 0.006 -strand -76 : -83 ATATGTCA AC RSP00653 Mean Expected Number 0.010 +strand -58 : -48 TTCTCcCTCCT AC RSP01601 Mean Expected Number 0.002 -strand -156 : -163 TTTCACTT AC RSP01708 Mean Expected Number 0.008 +strand -141 : -132 CTATTTTTAG AC RSP01708 Mean Expected Number 0.008 -strand -132 : -141 CTAAAAATAG Totally 7 motifs of 6 different REs have been found Description of REs found 196. Group TF: ABI5 /AC: RSP00203//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.1 /TF: ABI5 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 548. Group RE: 3'/AT-rich J1 /AC: RSP00572//OS: Lycopersicon esculentum /GENE: rbcS1/RE: 3'/AT-rich J1 /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0482F12.26|1430329..1430839 |SUPPORT| 1 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +53 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.14 T - 0.27 C - 0.29 1 ataggagaga tagacaaaca ttaacacatt acatgagaaa gataacatga 51 tgaaaaccaa gtgaaaactt actgcgaagc catattttta gcaaacacat 101 actcacgctt gcccgggaac ctctcgtagc ctcacatctc gtcattcctc 151 cctcctcctt tctcacgtaT ATAAACAccc tcccctccgg gcgatcgatc 201 GTCTCTTGCA TCGATCTTAA TTTCTCTCTT CATCATCTCG CTATATACGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00203 Mean Expected Number 0.004 -strand -30 : -39 TATACGTgAG AC RSP01601 Mean Expected Number 0.003 -strand -135 : -142 TTTCACTT Totally 2 motifs of 2 different REs have been found Description of REs found 196. Group TF: ABI5 /AC: RSP00203//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.1 /TF: ABI5 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1007_D04.17|complement(1632049..1636773) |SUPPORT|10 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +64 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.15 T - 0.32 C - 0.16 1 aagtaactga aaaagattca tactcattta aattgggtat atactcaatt 51 tcaacaatgg tgcccggaca ccatggagca caaaacaaat ttactatata 101 tatatatata tatattattt ataaattatt ttatttGCAA Tcataccgaa 151 taagccatag agcccttatt TATAAATAag tttttcggaa aggactaaaa 201 TGTAAAAAAA ATATAGTCGT CGTGTTCCTC CGGCTCGGCG GCTGCATTGA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00006 Mean Expected Number 0.002 +strand -78 : -65 AAATTATTTTATtT AC RSP00021 Mean Expected Number 0.010 +strand -4 : +8 AAAAtGTAAAAA AC RSP00030 Mean Expected Number 0.001 -strand +43 : +37 AGCCGCC AC RSP00438 Mean Expected Number 0.003 +strand +37 : +42 GGCGGC AC RSP00807 Mean Expected Number 0.003 -strand +42 : +37 GCCGCC Totally 5 motifs of 5 different REs have been found Description of REs found 6. Group RE: ATRE /AC: RSP00006//OS: Glycine max /GENE: GS15/RE: ATRE /TF: unknown 20. Group TF: GT-1 /AC: RSP00021//OS: Catharantus roseus /GENE: TDC/RE: GT-1#Box7 /TF: GT-1 29. Group TF: EREBP /AC: RSP00030//OS: Nicotiana sylvestris /GENE: OLP/RE: ERRE /TF: EREBP ||Identical REs AC: RSP00082 RSP01344 RSP01523 RSP01764 RSP01775 418. Group RE: PR-box /AC: RSP00438//OS: Arabidopsis thaliana /GENE: PR-1/RE: PR-box /TF: unknown 760. Group RE: GCC box /Group TF: Pti4 /AC: RSP00807//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: GCC box /TF: Pti4 ||Identical REs AC: RSP00809 RSP00811 RSP00814 RSP00921 RSP01328 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0585B01.23|1848216..1848878 |SUPPORT| 1 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +70 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.25 C - 0.32 1 aagccgttgg acacattcct gcatgcaatg caaacgcaaa gcaagtgtga 51 tccatccatg cgtgaggatc ggagtacgtg tttatctgat ggaatccgca 101 gattcctccg gaatcagcag cgatttctcc ctccctcccg atgaatcgcc 151 gccatactct cctcccctct aTATAAACCc cacccgcggg actacgtcat 201 CATCCTGCCA CTCTACAAAG AGCTTAATTA GCTAGCTAGT CTCTTCGATC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00072 Mean Expected Number 0.008 +strand -127 : -121 GTACGTG AC RSP00447 Mean Expected Number 0.003 +strand -166 : -157 cGCAAAGCAA AC RSP00503 Mean Expected Number 0.003 +strand +32 : +39 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +39 : +32 CTAGCTAG AC RSP00595 Mean Expected Number 0.001 +strand +22 : +30 GCTTAATTA AC RSP01072 Mean Expected Number 0.005 +strand -128 : -119 AgTACGTGTT AC RSP01702 Mean Expected Number 0.003 -strand -119 : -128 AACACGTAcT Totally 7 motifs of 6 different REs have been found Description of REs found 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1511. Group RE: ACGT1 /AC: RSP01702//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0081C13.25|1949825..1953397 |SUPPORT|12 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +101 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.21 T - 0.27 C - 0.21 1 tggatgctcc acgcaactca gataagttat ccagacgagg agtggtgatg 51 gtagtcaaca ggtgggtgac cagaaattaa cgttaactac aatcatagct 101 taatccatgc aaatcaacat cttatcagct ttaattaATT GGcattataa 151 tgcaagcttg cttgctccaT ATAAATTggc acagagagaa gaaggatcag 201 GAGTGCACCT GGCTTACACT GATCGATGCT GTTCTCAGTT CTCACCACCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00889 Mean Expected Number 0.010 +strand -192 : -186 CCACGCA AC RSP00949 Mean Expected Number 0.005 +strand -149 : -142 TAGTCAAC Totally 2 motifs of 2 different REs have been found Description of REs found 821. Group RE: GC motif /Group TF: bZIP TF /AC: RSP00889//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: GC motif /TF: bZIP TF 878. Group RE: TAGTCAAC motif /AC: RSP00949//OS: Petroselinum crispum /GENE: 4CL-1/RE: TAGTCAAC motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0081C13.27|1967731..1972802 |SUPPORT| 8 exon(s)|Contig: NT_1071751.txt | -200:+51 from mRNA start|,5"-UTR: +431 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.17 C - 0.33 1 aaaaaacaca tgctaaacga cccataacga cggcattttt tgcgagagtg 51 ggaggtggtc ccacctcgag cgggcaagca aagcagcaac gagaaaagga 101 atctggacgc caccccacca caccaccact accccccact tGCAATctcc 151 cctctctctc cctttttaaA ATAAATCcgg ataacgcatc ggtgaaccct 201 GCGGATTAAC AGAGTAAACT GCAACAAACC ACGCGACCCC CAAACCTCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00122 Mean Expected Number 0.003 -strand -147 : -153 CTCCCAC AC RSP00680 Mean Expected Number 0.008 +strand +7 : +16 TAACAGAGTa AC RSP00865 Mean Expected Number 0.001 -strand -40 : -48 GGAGAGAGA AC RSP00895 Mean Expected Number 0.002 +strand -146 : -139 GTGGTCCC Totally 4 motifs of 4 different REs have been found Description of REs found 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 649. Group RE: GARE/Box 2 /AC: RSP00680//OS: Hordeum vulgare /GENE: Amy32b/RE: GARE/Box 2 /TF: unknown 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 826. Group RE: CLE-core /AC: RSP00895//OS: Geminiviruses (Nicotiana species); Pepper Huasteco Virus (PHV) /GENE: Intergenic Regions; PHV coat protein (CP)/RE: CLE-core /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1145_F01.11|complement(260580..262341) |SUPPORT| 2 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +113 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.30 C - 0.23 1 tttttttccc ctacactcac gtttatcttt ggatacagcg ggaccagata 51 gtattcaatt ttaaatgtaa agaaaataaa ataggtagcc cataaaccgc 101 tgccttgtat ttacatgtgt gacgccacgt cagacgtcat cgtgttcatc 151 tgcaagtcac aaatttttgg TATAAATTtg gttgcctcat ctcacttgcc 201 ACAGTATCAA AGACCAAAGC TATCGAGAGA TCGATCACTG CACGCCAGCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00113 Mean Expected Number 0.001 -strand -69 : -77 TGACGTGGC AC RSP00214 Mean Expected Number 0.003 -strand -69 : -76 TGACGTGG AC RSP00215 Mean Expected Number 0.003 +strand -76 : -69 CCACGTCA AC RSP00247 Mean Expected Number 0.004 +strand -77 : -68 GCCACGTcAG AC RSP00248 Mean Expected Number 0.004 +strand -77 : -68 GCCACGTCAG AC RSP00997 Mean Expected Number 0.005 -strand -60 : -69 GATGACGTcT AC RSP01034 Mean Expected Number 0.008 -strand -71 : -77 ACGTGGC AC RSP01106 Mean Expected Number 0.000 +strand -79 : -69 ACGCCACGTCA AC RSP01469 Mean Expected Number 0.009 +strand -90 : -81 TtACATGTGT AC RSP01654 Mean Expected Number 0.009 -strand -60 : -69 GATGACGTCT AC RSP01656 Mean Expected Number 0.000 -strand -67 : -78 TCTGACGTGGCg Totally 11 motifs of 11 different REs have been found Description of REs found 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 918. Group TF: Opaque-2 (O2) /AC: RSP00997//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-2 /TF: Opaque-2 (O2) 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 1024. Group RE: rHex /AC: RSP01106//OS: Spinacia oleracea /GENE: rps22/RE: rHex /TF: unknown 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 1474. Group TF: HY5 /AC: RSP01656//OS: Arabidopsis thaliana /GENE: ARF19 (At1g19220)/RE: C/G-box /TF: HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1145_F01.24|complement(308599..309869) |SUPPORT| 2 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +113 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.40 G - 0.11 T - 0.27 C - 0.22 1 aatgttaaaa aagaaaaaaa aatcacaacc tgaaatgtta aaacagcatt 51 tacgaaaacc gtaattctgg attatagaaa agaaaaagaa agagagaaga 101 aaaatgtatt aaatttattc aaagtattcc cctccaaaat tcacaaataa 151 atttcctaaa tTATAAATTa gagaggataa gtcgccaatc ctctctcttt 201 TGCCTTCACT ATCCATCCCT CCTCCGCTTC TTCCTCCTCA GCCTCTCATC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00530 Mean Expected Number 0.005 -strand -187 : -198 TCTTTTTTAACa AC RSP00861 Mean Expected Number 0.001 +strand -114 : -106 AGAAAGAGA Totally 2 motifs of 2 different REs have been found Description of REs found 506. Group RE: AT-rich F /AC: RSP00530//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich F /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0453H10.12|complement(451146..451781) |SUPPORT| 1 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +108 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.15 T - 0.23 C - 0.29 1 cagtccaatt aactaatcaa ccaatcaaat caaatcaaat taaattacta 51 gtggccacaa attaattaga gattaacctg ggagcagcac agcacagcac 101 acagtttagc ccagccacag tgtgatgaca gtgtgaccca ctcccatgca 151 tcctcttcct cctcccctaT ATAAACCaac cagctcagct cagttgcctc 201 ACATCACACC ACACTAGCTG ATTAGCTTAA GCTTAGCTGA GATTGATCAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01401 Mean Expected Number 0.001 +strand -74 : -64 GACAGTGTgAC Totally 1 motifs of 1 different REs have been found Description of REs found 1283. Group TF: TAC1 /AC: RSP01401//OS: Arabidopsis thaliana /GENE: BT2/RE: TAC1 BS /TF: TAC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0437H03.116|complement(555605..556452) |SUPPORT| 1 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.10 T - 0.32 C - 0.22 1 aataaggttt tttaatccag atgtgtcaat taataaagaa aaaaatatcc 51 tcaatgaaaa ttcatcagtg ccctatcagt cccggcaaat ccttaattaa 101 ttaattatgc atcatctatt ttgttttgaa taatggaaag acacccggtc 151 caaccctttg cttttgccac tcTATAAATA catcttcttc atccttaatc 201 CACCTGCAAA ATAAAAAATT CAGACTCAAC TCTCCTTAAT CTCATCAAAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00379 Mean Expected Number 0.002 -strand -122 : -131 CtGATAGGGC AC RSP00521 Mean Expected Number 0.007 +strand -60 : -54 ACACCCG AC RSP00525 Mean Expected Number 0.007 -strand -177 : -183 ACATCTG AC RSP01301 Mean Expected Number 0.002 +strand -29 : -20 CTATAAATAC Totally 4 motifs of 4 different REs have been found Description of REs found 364. Group RE: LS7 /AC: RSP00379//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS7 /TF: unknown 497. Group TF: DPBF-1; DPBF-2 /AC: RSP00521//OS: Daucus carota /GENE: Dc3/RE: E1-core /TF: DPBF-1; DPBF-2 501. Group TF: DPBF-1; DPBF-2 /AC: RSP00525//OS: Daucus carota /GENE: Dc3/RE: E5-core /TF: DPBF-1; DPBF-2 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0437H03.124|581303..584431 |SUPPORT|11 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +82 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.16 T - 0.26 C - 0.27 1 atctatgaat ttatcggcta attagctgac aagctgaaca gggctgagac 51 tgaatttctt catagtgact ctgccgtgtg agtgctgacg caatcaagat 101 ccaACAATtt taggcccaca taaactttcc aagcccaact catgaaaagc 151 ccaattcttt ttcaccttaT ATAAACCcga gcagcagcag catccgcctc 201 AGCTCAACGG TCAAAAATCT CTTCCAATTT GAATATCTCT CCTCCCAAAC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00501 Mean Expected Number 0.007 +strand -23 : -17 CGAGCAG AC RSP00698 Mean Expected Number 0.002 +strand -195 : -185 TGAATTtATCG AC RSP00996 Mean Expected Number 0.008 -strand +8 : -2 GTTGAGCTGA Totally 3 motifs of 3 different REs have been found Description of REs found 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0026H03.18-1|complement(891377..891993) |SUPPORT| 1 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +56 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.21 T - 0.30 C - 0.15 1 gtttcattaa ttaataattg aatatatttt ttataaactt agtcaaattt 51 gaaaccgtct ttataacctg aaacggagaa agtattgttg aggggtctat 101 gtgtataatt cttttataga aaataaaact ggagcattta ttacgagagg 151 aaataaaatA ATAAATCgcc tataaaaagc gcgcgagcga gacgactctc 201 AAGTCTCAAG TCGTCTTGGT GCTCATCGGC GGCGAGCAAA AGCGAGCTTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00438 Mean Expected Number 0.010 +strand +28 : +33 GGCGGC AC RSP00807 Mean Expected Number 0.010 -strand +33 : +28 GCCGCC AC RSP00891 Mean Expected Number 0.007 -strand -171 : -179 AAAATATAT AC RSP00953 Mean Expected Number 0.006 -strand -181 : -189 CAATTATTA Totally 4 motifs of 4 different REs have been found Description of REs found 418. Group RE: PR-box /AC: RSP00438//OS: Arabidopsis thaliana /GENE: PR-1/RE: PR-box /TF: unknown 760. Group RE: GCC box /Group TF: Pti4 /AC: RSP00807//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: GCC box /TF: Pti4 ||Identical REs AC: RSP00809 RSP00811 RSP00814 RSP00921 RSP01328 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family 880. Group TF: ATHB6 /AC: RSP00953//OS: Arabidopsis thaliana /GENE: ATHB6/RE: ATHB6 BS /TF: ATHB6 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0026H03.20-1|complement(902090..909014) |SUPPORT| 7 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +44 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.18 T - 0.27 C - 0.27 1 ggaaaaaaga attcatattt atccccagtt taaaccgatt taaaaccttt 51 ccctaactaa ttcgagcaat ctttgcaaca aatctcaaac ggaaatccgc 101 gcgatttacg aggaaaattt acgattttac aggaggcaca agaggctgtt 151 ctttgtaacg accttctcTA TAAATTcgcg agctcggggg aggtgttcga 201 CAGTGTACTC TCCCATCCTC TCCACCTCAA TCCCTCTCGC CGCCATGGCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00253 Mean Expected Number 0.003 +strand -107 : -100 AATCCGCG Totally 1 motifs of 1 different REs have been found Description of REs found 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0544H11.38|complement(1291003..1295727) |SUPPORT| 9 exon(s)|Contig: NT_1071771.txt | -200:+51 from mRNA start|,5"-UTR: +156 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.25 C - 0.28 1 agcgccttcg tttgtaccat gttttattta aaaaaaattg cctaaaaaaa 51 gattttattt tctcagaact ctttgtttcg taggagcagt atttttgtat 101 tgtgatCCAA Tccaattccg aattccacat gggccggcct cgcggcttcg 151 tttgcagcga gttcctcacc cTATAAACAc gcagccacac aagcagagca 201 CGAGGGAGAC CCAACCCAGC AAGCAAGCAA ACCCAAACCC ACCCACCTCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00063 Mean Expected Number 0.004 -strand -55 : -64 GCCGCGaGGC AC RSP00433 Mean Expected Number 0.003 -strand +50 : +39 GGAGGTgGGTGG AC RSP00441 Mean Expected Number 0.005 -strand -124 : -133 AACAAAGaGT AC RSP01073 Mean Expected Number 0.001 +strand -11 : -3 CAAGCAGAG AC RSP01210 Mean Expected Number 0.007 -strand -150 : -159 CTTTTTTTAG AC RSP01712 Mean Expected Number 0.000 +strand -159 : -150 CTAAAAAAAG Totally 6 motifs of 6 different REs have been found Description of REs found 62. Group RE: Motif III /AC: RSP00063//OS: Oryza sativa /GENE: rab16B/RE: Motif III /TF: unknown 413. Group TF: AtMYB84 /AC: RSP00433//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB84 BS /TF: AtMYB84 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1120. Group RE: EM2 /Group TF: MADS box TFs /AC: RSP01210//OS: Lepidium africanum /GENE: LaCRC/RE: EM2 /TF: MADS box TFs 1520. Group TF: RIN /AC: RSP01712//OS: Solanum lycopersicum /GENE: LeACS2/RE: RIN BS /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1371_D04.6|2053553..2057218 |SUPPORT| 4 exon(s)|Contig: NT_1071791.txt | -200:+51 from mRNA start|,5"-UTR: +52 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.39 G - 0.11 T - 0.20 C - 0.30 1 tttaacaaaa tatccacatc cttctacttc aatataacca atctatagag 51 gaccattttg taattaccac aacacccaga agtctaaaca gatagagtac 101 tggaggagta gtactactgc aaatccccac cccaaaaaaa taaaaaaaaa 151 atctgctctt aacaactccc TATAAAGCta ccactacgcc cccctaccgc 201 GGAGAAGCAA CCAATCCAAT TCCGAACAAG CAAGGCACCA AATCCCCCCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00749 Mean Expected Number 0.000 +strand -146 : -135 ATTTTGTAATTA AC RSP00858 Mean Expected Number 0.010 -strand -133 : -140 GGTAATTA AC RSP01637 Mean Expected Number 0.001 +strand -31 : -21 CTATAAAGCTA Totally 3 motifs of 3 different REs have been found Description of REs found 711. Group TF: GT-1 /AC: RSP00749//OS: Catharanthus roseus /GENE: STR/RE: BN /TF: GT-1 794. Group TF: DF1 /AC: RSP00858//OS: Pisum sativum /GENE: pra2/RE: GT2 /TF: DF1 1457. Group RE: TERE /AC: RSP01637//OS: Arabidopsis thaliana /GENE: XSP1/RE: TERE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0403C01.28|2164005..2166928 |SUPPORT| 6 exon(s)|Contig: NT_1071791.txt | -200:+51 from mRNA start|,5"-UTR: +43 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.22 T - 0.24 C - 0.19 1 gttatcatag tataacaaat cctaggtaga gaagacagat ccatcagacg 51 tacaccatcc tctggaaata ttttatagta tagtaataat cgtatctggc 101 cagccagtgg ccaaaataat ataatcttca ccgtcatcga tccattaatc 151 taagacctaa aggagaggtc aaatCATAAA TCctcggtag caggtagctt 201 GAGTTAGTAG GAGACACGGG AAGCTAGCAA GTAGCAAGCG GAGATGGAGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01065 Mean Expected Number 0.001 -strand -57 : -67 tGGATCGATGA AC RSP01480 Mean Expected Number 0.006 +strand -132 : -125 TATTTTAT AC RSP01678 Mean Expected Number 0.001 -strand -123 : -134 CtATAAAATATT Totally 3 motifs of 3 different REs have been found Description of REs found 984. Group RE: Fungus RE /Group TF: homeodomain TF /AC: RSP01065//OS: Arabidopsis thaliana /GENE: At5g64250/RE: Fungus RE /TF: homeodomain TF 1348. Group TF: AT-1SNBP /AC: RSP01480//OS: Glycine max /GENE: GS15/RE: AT-cm /TF: AT-1SNBP 1496. Group TF: AT-Hook TFs /AC: RSP01678//OS: Catharanthus roseus /GENE: ORSA3/RE: JRE (Quant. Seq.) /TF: AT-Hook TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0048K16.15|3247354..3250894 |SUPPORT| 3 exon(s)|Contig: NT_1071791.txt | -200:+51 from mRNA start|,5"-UTR: +168 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.17 T - 0.24 C - 0.29 1 aagacctcag atcagtgttc atcagttgat gatcaagtga caccatgatg 51 cagagttaca tgtttcactc aaggcaaacc agaaatctcg tcagaagctt 101 cacgtcctac atctgcacag gggcagcaaa accagaaatc tcctggtcat 151 caagtcctca actcaaggct TATAAATAga aaggccccag gcttctttgt 201 ATCCAAACAC CTCTTCACAT TTTTCCCTCC AAGAAACCGA CCCGCTCCAC 251 T Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1003_F04.33|complement(4120485..4123674) |SUPPORT| 4 exon(s)|Contig: NT_1071791.txt | -200:+51 from mRNA start|,5"-UTR: +1401 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.20 T - 0.21 C - 0.31 1 tcccgaggac ggtagtccgc ccccattgtg aatccgccgc tgcgcacgag 51 gaggtcaaca taacttattt ctttacaaga aaaaagaatt gcaaaaggag 101 tgaGCAATga tttgtggccc gttgtccacg ttgctgccga gtgtgaaaac 151 aaaaccacag gggtagtaca aTATAAACAa cacgtcagag atcagacacc 201 CACCTCTCCA CCTCCCTCCT CTCCTCTCCT ATCGTCCCCA CGCGCACTCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00189 Mean Expected Number 0.006 +strand -76 : -67 TCCACGTtGC AC RSP00232 Mean Expected Number 0.008 +strand -19 : -10 ACGTCAgAGA AC RSP00682 Mean Expected Number 0.004 -strand -67 : -76 GCaACGTGGA AC RSP00961 Mean Expected Number 0.004 +strand -111 : -104 TGCAAAAG AC RSP01258 Mean Expected Number 0.007 -strand -14 : -21 TGACGTGT Totally 5 motifs of 5 different REs have been found Description of REs found 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 225. Group RE: LS7 /Group TF: TGA2 & NPR1/NIM1 /AC: RSP00232//OS: Arabidopsis thaliana /GENE: PR-1/RE: LS7 /TF: TGA2 & NPR1/NIM1 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: B1469H02.30|373978..374680 |SUPPORT| 2 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.31 C - 0.25 1 tactgttgct ccagtagaat ctcgaattgt tagaatttct tttttttggt 51 ccacaatgca ttaggggcgg tgagctacca gcttagcaac atgtgaatca 101 ctctatagtt ttggatcatc gcagcttaaa cattaatttg ttctcgtctt 151 tattatctgg gttgccctaT ATAAACCcct cccgtccatc cgttgcccat 201 CAACCAAGAG CTAGCACAGC ACCGGTGGCA GTAGCAAAGT AGCAGCCTCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00058 Mean Expected Number 0.000 -strand +30 : +22 TGCCACCGG AC RSP01174 Mean Expected Number 0.003 +strand -25 : -15 CCcCTCCCGTC Totally 2 motifs of 2 different REs have been found Description of REs found 57. Group RE: CE1 /AC: RSP00058//OS: Hordeum vulgare /GENE: HVA22/RE: CE1 /TF: unknown 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1581_H09.2|680817..681921 |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +84 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.14 T - 0.29 C - 0.25 1 gattaattag gcttaaaaaa tttgtctcgt gaattagctt ttatttatgt 51 aattagtttt gtaagtagtc tatatttaat actctaaatt agtgtctaaa 101 gacagggact aaagttaagt ccctggatct aaacaccacc taaagacgag 151 caagtctaca tcaagtccat TATAAATCta tccggcgtgt ccctctcccc 201 ATCACCTCAA AACCTCTCAA ACCCCACAGG CACCGGACCA CCACCACCAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00681 Mean Expected Number 0.003 -strand -192 : -200 TAATTAATC AC RSP01191 Mean Expected Number 0.002 +strand +24 : +31 CCACAGGC Totally 2 motifs of 2 different REs have been found Description of REs found 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 1102. Group RE: A-box /Group TF: A factor /AC: RSP01191//OS: Nicotiana tabacum /GENE: Adhl/RE: A-box /TF: A factor ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0014E22.37|810239..819545 |SUPPORT|17 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +478 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.15 T - 0.26 C - 0.29 1 tgccccatat gagtgtccta tatatatata tatatatata tatatatata 51 tatatatata tatataaagc agaaagaaat acccgcgaat taacgtggtg 101 ggataaccgt aggccgtagc cgcgtccatc tcgccctcgc cccaccacct 151 accaaaattg atggacacca aAATAAATCc gcccccctcc tctcttcccc 201 CAATCCGATC CGATCAGACG CCTAGTTTAG GGTTTCAGAG CTTTCTCCCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00260 Mean Expected Number 0.005 +strand +26 : +32 TTTAGGG AC RSP00279 Mean Expected Number 0.000 +strand +27 : +35 TTAGGGTTT AC RSP00369 Mean Expected Number 0.000 -strand +35 : +27 AAACCCTAA AC RSP00492 Mean Expected Number 0.000 +strand -185 : -144 tccTATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 +strand -183 : -142 cTATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 +strand -181 : -140 ATATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 +strand -179 : -138 ATATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 +strand -177 : -136 ATATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 +strand -175 : -134 ATATATATATATATATATATATATATATATATATATATATAa AC RSP00492 Mean Expected Number 0.000 +strand -173 : -132 ATATATATATATATATATATATATATATATATATATATAaAg AC RSP00492 Mean Expected Number 0.000 +strand -171 : -130 ATATATATATATATATATATATATATATATATATATAaAgca AC RSP00492 Mean Expected Number 0.000 -strand -130 : -171 tgcTtTATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 -strand -132 : -173 cTtTATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 -strand -134 : -175 tTATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 -strand -136 : -177 ATATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 -strand -138 : -179 ATATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 -strand -140 : -181 ATATATATATATATATATATATATATATATATATATATATAT AC RSP00492 Mean Expected Number 0.000 -strand -142 : -183 ATATATATATATATATATATATATATATATATATATATATAg AC RSP00492 Mean Expected Number 0.000 -strand -144 : -185 ATATATATATATATATATATATATATATATATATATATAgga AC RSP00621 Mean Expected Number 0.003 +strand -17 : -9 CCCCTCCTC AC RSP00860 Mean Expected Number 0.001 +strand -130 : -122 AGAAAGAAA AC RSP01237 Mean Expected Number 0.006 +strand -183 : -174 CTaTATATAT AC RSP01237 Mean Expected Number 0.003 -strand -132 : -141 CTtTATATAT AC RSP01303 Mean Expected Number 0.001 -strand +36 : +27 gAAACCCTAA Totally 24 motifs of 8 different REs have been found Description of REs found 253. Group RE: RTBP1 BS /AC: RSP00260//OS: Oryza sativa /GENE: Synthetic OLIGO/RE: RTBP1 BS /TF: unknown 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 468. Group RE: Zc2 A/T-2 /AC: RSP00492//OS: Zea mays /GENE: Zc2/RE: Zc2 A/T-2 /TF: unknown 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1282_H11.17|1078990..1083364 |SUPPORT| 7 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +119 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.21 T - 0.22 C - 0.30 1 acattggaga ctgtacggcg gacaaagcgg agagttacat cacgctaaag 51 agttcgcttc catgaggaga aagcgtaata agcgttaata gtactaagcg 101 gaagcttcga gaacccttga gagagatccg acggcccacg ccacgccgca 151 acaatcatag tggtcgccga tttTATAAAA Cttcatcttc tccgagacct 201 TAATCCCCCA TCTAACCCCA GACTTTTCCT CCCCTCCTCC CTCTCCTCCG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00063 Mean Expected Number 0.009 -strand -52 : -61 GCgGCGTGGC AC RSP00621 Mean Expected Number 0.003 +strand +31 : +39 CCCCTCCTC AC RSP01185 Mean Expected Number 0.006 +strand +8 : +19 CCAtCTAACCCC AC RSP01497 Mean Expected Number 0.009 -strand -66 : -75 GCCGTCGGAT Totally 4 motifs of 4 different REs have been found Description of REs found 62. Group RE: Motif III /AC: RSP00063//OS: Oryza sativa /GENE: rab16B/RE: Motif III /TF: unknown 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 1097. Group RE: box 2 /AC: RSP01185//OS: Petunia hybrida /GENE: chsA/RE: box 2 /TF: unknown 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0030D07.27|1211276..1212980 |SUPPORT| 3 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +171 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.23 T - 0.26 C - 0.31 1 ggcctctcgc cgcggcgctt gactcatcac gatttcgctt aattaatttg 51 gatttggatg cggatccctc gcctcctcgc aatttagcaa cgtgatcggc 101 tgacttaacg gcccatgctt aacgcacaag ccgcctcgcg ctctctctgt 151 ctcttcggcg gcagtgtata TATAAAGCgc gcgcgcagct agcccccaca 201 CATATCTTTT GTACACGGGC GTACTACGTG TTACGGCTGA ACCAATCTAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.006 -strand -26 : -32 TTATATA AC RSP00595 Mean Expected Number 0.001 +strand -164 : -156 GCTTAATTA AC RSP01072 Mean Expected Number 0.006 +strand +23 : +32 AcTACGTGTT AC RSP01108 Mean Expected Number 0.006 +strand -161 : -155 TAATTAA AC RSP01108 Mean Expected Number 0.009 -strand -156 : -162 TAATTAA AC RSP01237 Mean Expected Number 0.001 -strand -24 : -33 CTtTATATAT AC RSP01260 Mean Expected Number 0.004 +strand +24 : +31 CTACGTGT AC RSP01640 Mean Expected Number 0.008 +strand -56 : -47 CTcTGTCTCT AC RSP01702 Mean Expected Number 0.003 -strand +32 : +23 AACACGTAgT Totally 9 motifs of 8 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1026. Group RE: rAT-1 /AC: RSP01108//OS: Spinacia oleracea /GENE: rps22/RE: rAT-1 /TF: unknown 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1162. Group TF: GBF1 /AC: RSP01260//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS7 /TF: GBF1 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown 1511. Group RE: ACGT1 /AC: RSP01702//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0012J10.30|1455171..1456146 |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +64 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.33 T - 0.13 C - 0.23 1 aacgctcggt cggcagcgca gctgcgcaaa gcaaagcttg gcgatcgacg 51 cgacgaagag gacatgcatg gcaaagcaga atggcaaaag gcagcagcag 101 caaatcgatc gatcaaatcg tgGCAATggg ccggtggtgc gtgagcgcga 151 tcggttgcct gtggacgcTA TAAATAgggg catggcacgg gacatccact 201 GCAAGTGCAA CACAAGTACG CAGAGCCAAG AAACAGAGCA AGAGTGAGTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.002 +strand -138 : -131 CATGCATG AC RSP00108 Mean Expected Number 0.002 -strand -131 : -138 CATGCATG AC RSP00695 Mean Expected Number 0.005 +strand -32 : -26 TATAAAT AC RSP01076 Mean Expected Number 0.007 +strand -138 : -129 CATGCaTGGC AC RSP01191 Mean Expected Number 0.003 -strand -37 : -44 CCACAGGC AC RSP01296 Mean Expected Number 0.000 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.003 +strand -33 : -24 CTATAAATAg AC RSP01470 Mean Expected Number 0.007 -strand -130 : -139 cCATGCATGT AC RSP01708 Mean Expected Number 0.001 +strand -33 : -24 CTATAAATAG AC RSP01708 Mean Expected Number 0.001 -strand -24 : -33 CTATTTATAG Totally 10 motifs of 8 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1102. Group RE: A-box /Group TF: A factor /AC: RSP01191//OS: Nicotiana tabacum /GENE: Adhl/RE: A-box /TF: A factor 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1112_F09.30|1832329..1834074 |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +105 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.14 T - 0.27 C - 0.32 1 agaaattcag ctcgccttat tttgtaggta ctggatactg atcgaaaatc 51 aacaacagtt cgtttagcct ttttccctac accaacttgt cacgttctca 101 CCAATaattc tcgaccggca gaatccctaa atttcttgcc acgtacgtct 151 gcatccctcc aaaaattccc TATAAATAcc ccttctcggc cactccctgc 201 AACTCACCCA AGAACACACT CGAGCTGAGC ACGTCTAGCT AGCTATATCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00043 Mean Expected Number 0.003 -strand -56 : -63 TACGTGGC AC RSP00051 Mean Expected Number 0.008 +strand -63 : -54 GCCACGTACg AC RSP00064 Mean Expected Number 0.008 -strand -54 : -63 cGTACGTGGC AC RSP00075 Mean Expected Number 0.010 -strand -55 : -64 GTACGTGGCa AC RSP00247 Mean Expected Number 0.004 +strand -63 : -54 GCCACGTAcG AC RSP00489 Mean Expected Number 0.001 -strand -171 : -180 TACCTACaAA AC RSP00503 Mean Expected Number 0.003 +strand +35 : +42 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +42 : +35 CTAGCTAG AC RSP00817 Mean Expected Number 0.002 -strand +37 : +28 TAgACGTGCT AC RSP01012 Mean Expected Number 0.003 -strand -172 : -178 ACCTACA AC RSP01109 Mean Expected Number 0.009 +strand -97 : -90 ATAATTCT AC RSP01276 Mean Expected Number 0.007 -strand -55 : -62 GTACGTGG AC RSP01296 Mean Expected Number 0.002 +strand -31 : -23 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -31 : -22 CTATAAATAC AC RSP01692 Mean Expected Number 0.002 -strand -155 : -162 TTCGATCA Totally 15 motifs of 14 different REs have been found Description of REs found 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 50. Group RE: A3 /AC: RSP00051//OS: Hordeum vulgare /GENE: HVA22/RE: A3 /TF: unknown 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 74. Group TF: TAF-1 /AC: RSP00075//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: Iwt /TF: TAF-1 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 465. Group RE: UVLRE2 /AC: RSP00489//OS: Glycine max /GENE: chs1/RE: UVLRE2 /TF: unknown 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 763. Group TF: ACE-binding TF /AC: RSP00817//OS: Arabidopsis thaliana /GENE: CFI/RE: ACE-core (AtCFI) /TF: ACE-binding TF 930. Group TF: PtMYB1; PtMYB4 /AC: RSP01012//OS: Pinus sylvestris /GENE: PsGS1b/RE: GS1b AC box 1 (AC-I) /TF: PtMYB1; PtMYB4 1027. Group RE: rAT-2 /AC: RSP01109//OS: Spinacia oleracea /GENE: rps22/RE: rAT-2 /TF: unknown 1175. Group RE: Box III /AC: RSP01276//OS: Petroselinum crispum /GENE: CHS/RE: Box III /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1509. Group RE: CARE J /AC: RSP01692//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE J /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0516F12.19|1988480..1989312 |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +99 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.26 C - 0.27 1 acattatcag cgtagatgta cgtacgattt gttaattaat ctacgagcct 51 tgctagggca ggtgttctgc cagccaatcc agatcgccct cgtatgcacg 101 ctcacatgat ggcagggcag ggttcacatg agctctaacg gtcgattaat 151 taatcccggg gctcgacTAT AAATAcctcc ctaatcccat gatcaaaacc 201 ATCTCAAGCA GCCTAATCAT CTCCAGCTGA TCAAGAGCTC TTAATTAGCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00681 Mean Expected Number 0.002 +strand -168 : -160 TAATTAATC AC RSP00681 Mean Expected Number 0.002 +strand -54 : -46 TAATTAATC AC RSP00681 Mean Expected Number 0.001 -strand -49 : -57 TAATTAATC AC RSP00698 Mean Expected Number 0.003 -strand -48 : -58 TtAATTAATCG AC RSP01296 Mean Expected Number 0.002 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -34 : -25 CTATAAATAC Totally 6 motifs of 4 different REs have been found Description of REs found 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1743_B12.30|complement(3496188..3499690) |SUPPORT| 5 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +117 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.18 T - 0.24 C - 0.36 1 aaacggcgac agtcatcgtc gagcgcgacg tctcggtgtg atgcacatac 51 ctaagaatac ctgtttgtga catcatgcga gcaagacacg cacgctcctc 101 cacctccctt ttgtgatctg cacatcctac tcacagtcgc agagccagct 151 agccagctgc agctgagctc TATAAATCcc agacctctct gctcagacac 201 AACCACTTCC ATAGATCCCC TCCTCTTCTT CCTCCTGCTC GGCTTCCTCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00103 Mean Expected Number 0.007 +strand -158 : -149 GCACATACcT AC RSP00426 Mean Expected Number 0.002 -strand -164 : -174 ACCGAGACGTc AC RSP00509 Mean Expected Number 0.000 +strand -30 : -19 TATAAATcCCAG AC RSP00695 Mean Expected Number 0.008 +strand -30 : -24 TATAAAT AC RSP00872 Mean Expected Number 0.003 +strand -137 : -128 TtTGTGACAT AC RSP01136 Mean Expected Number 0.008 -strand -129 : -135 TGTCACA AC RSP01233 Mean Expected Number 0.007 +strand -121 : -115 AGCAAGA AC RSP01301 Mean Expected Number 0.007 +strand -31 : -22 CTATAAATcC Totally 8 motifs of 8 different REs have been found Description of REs found 101. Group RE: Z element /AC: RSP00103//OS: Agrobacterium tumefaciens /GENE: nos/RE: Z element /TF: unknown 407. Group RE: DRE1/ABRE1 /AC: RSP00426//OS: Zea mays /GENE: rab17/RE: DRE1/ABRE1 /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown 1054. Group RE: TGTCACA motif /AC: RSP01136//OS: Cucumis melo /GENE: Cucumisin/RE: TGTCACA motif /TF: unknown 1138. Group RE: PLE-79 /AC: RSP01233//OS: Collettrichum lindemuthianum (bean pathogen) /GENE: CLPG2/RE: PLE-79 /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1111_E07.14|complement(<4010307..4017125) |SUPPORT| 7 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +2599 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.32 T - 0.17 C - 0.31 1 gcaccacgtt aaaaatgcgt acgcagagca ggtgtggtac ggtgcgcgtg 51 gtaaggcctg ggacgtgggc caaagcaccc cactccccca accaagcgcc 101 acgcatcctg gccgtcgcag cctagcgaaa catacggacg gccgtgatcg 151 cgagcgcttt tctcccttgT ATAAATAgcc gtcgacggct cggtcggcga 201 GTGCTTTCGC TCGATTTCGG GGGCGGATCA GACGGCCGCG AGCGAATCCG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00044 Mean Expected Number 0.007 -strand -93 : -103 GGAtGCGTGGC AC RSP00089 Mean Expected Number 0.001 +strand -166 : -155 TGGTAcGGTGCG AC RSP00566 Mean Expected Number 0.002 +strand -36 : -27 CCTTGTATAa AC RSP00695 Mean Expected Number 0.002 +strand -31 : -25 TATAAAT AC RSP01435 Mean Expected Number 0.007 +strand -116 : -107 cCCCCAACCA Totally 5 motifs of 5 different REs have been found Description of REs found 43. Group TF: ASF1 /AC: RSP00044//OS: Triticum aestivum /GENE: H3/RE: hex3 /TF: ASF1 87. Group RE: ARE 231/219 /AC: RSP00089//OS: Chlamydomonas reinhardtii /GENE: Nia1/RE: ARE 231/219 /TF: unknown 542. Group RE: TATA P /AC: RSP00566//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: TATA P /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1308. Group TF: RNFG2 /AC: RSP01435//OS: Oryza sativa /GENE: RSs1/RE: BoxII /TF: RNFG2 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1218_D07.28|4179208..4181944 |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +114 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.24 T - 0.21 C - 0.34 1 tcggcagcgt ctatctgtct ctctcgcgcg cggaggcacc cagctcggct 51 attctagcgc gtagtggtgg tgctagctac tagtagtagt agatttttgg 101 gcagcaagcg gccgcagaaa aggagagcga aacggaggag aaaccgggaa 151 actcagctcg cggccaatcT ATAAATAgct gccacccctc tcgcctttcc 201 CTCCACACCC CCCCCAACAA CACCACCGCC CATTTCCCTT TCTCTTCCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00018 Mean Expected Number 0.005 +strand -108 : -102 ATTTTTG AC RSP00254 Mean Expected Number 0.007 -strand -78 : -84 CCTTTTC AC RSP00629 Mean Expected Number 0.001 -strand -103 : -110 AAAAATCT AC RSP00653 Mean Expected Number 0.001 -strand -70 : -80 TTCgCTCTCCT AC RSP00695 Mean Expected Number 0.005 +strand -31 : -25 TATAAAT AC RSP00888 Mean Expected Number 0.000 -strand -103 : -111 AAAAATCTA AC RSP01115 Mean Expected Number 0.005 -strand -102 : -108 CAAAAAT AC RSP01296 Mean Expected Number 0.000 +strand -32 : -24 CTATAAATA AC RSP01301 Mean Expected Number 0.004 +strand -32 : -23 CTATAAATAg AC RSP01708 Mean Expected Number 0.001 +strand -32 : -23 CTATAAATAG AC RSP01708 Mean Expected Number 0.001 -strand -23 : -32 CTATTTATAG Totally 11 motifs of 10 different REs have been found Description of REs found 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 820. Group TF: CCA1 /AC: RSP00888//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: CCA1 motif (2) /TF: CCA1 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0724B10.24|complement(4209591..4211669) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +18 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.33 C - 0.20 1 tgatagttat ttatgattta tatttttaaa gtttgactta aaaattatcc 51 taaacgactt ctatgggtac ggagtgatta gtatctttat cacgaggtac 101 ttgtactatc tttcttcccg gtctagcacg aatctgaaag ggacagcctc 151 tcttagcaag agaggccttT ATAAATAgcc gcacggttaa tctcacaact 201 CAGTGCAGTA GTAGTAGCAT GCAAAGGATT TGCCCTGCTC ACTGCTCGGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00501 Mean Expected Number 0.008 -strand +48 : +42 CGAGCAG AC RSP01463 Mean Expected Number 0.001 +strand -185 : -173 ATTTATATtTTTA AC RSP01499 Mean Expected Number 0.006 +strand -86 : -77 TTCCCgGTCT Totally 3 motifs of 3 different REs have been found Description of REs found 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 1333. Group RE: AT-rich ELS /AC: RSP01463//OS: Glycine max /GENE: BiP6/RE: AT-rich ELS /TF: unknown 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0060O16.25-3|4456032..4458135 |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +402 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.19 T - 0.36 C - 0.15 1 atctattaga gtaactatct ggagtatttt tcatgtccac tttatgatga 51 atattgtgtc accagcattg acatgtaatg atatcattta gaatagtgta 101 ttggcaaaAT TGAttgcctc catccatatt tagacactat tcaagttact 151 ggtTATAAAA Caagatctgg tatttcatgt tatgcaggtg ttgatttgat 201 TAGTGGTGTC ACATGCGATG CTCCATATGA ATGGTCAGAC AAGACTGATT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00416 Mean Expected Number 0.010 +strand -80 : -74 CATCCAT AC RSP00996 Mean Expected Number 0.006 +strand -11 : -2 GTTGATTTGA Totally 2 motifs of 2 different REs have been found Description of REs found 398. Group RE: Box-1 /AC: RSP00416//OS: Hordeum vulgare /GENE: EPB-1/RE: Box-1 /TF: unknown 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ2056_H01.25|complement(4988441..4989037) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +132 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.21 T - 0.15 C - 0.40 1 ccaaaccaaa gcacacacac aacgtggacg cctctggctg cacgaaacgg 51 gagagatcac cgcgcgaagc cgcccgttca ccatgcacac atgcaggcac 101 gtacgcgagc ctccacatgg cggccactcg catccccgaa ttagcccccc 151 actaatcccg cTATAAATTg tccccgtccc cgcggctcat ctccctcctc 201 AGGCAAAGCG CAGCAGCAGC AGCAGCAGCA GTAGCCATCT CTTCTTCCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00683 Mean Expected Number 0.008 -strand -80 : -89 GCCAtGTGGA AC RSP00695 Mean Expected Number 0.003 +strand -39 : -33 TATAAAT AC RSP01734 Mean Expected Number 0.008 -strand -173 : -179 TCCACGT Totally 3 motifs of 3 different REs have been found Description of REs found 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1542. Group TF: CAMTA3 /AC: RSP01734//OS: Arabidopsis thaliana /GENE: CBF2/RE: CM4 /TF: CAMTA3 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1008_D06.10|5033864..5035914 |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +123 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.22 T - 0.20 C - 0.25 1 tgatgactgt cgactgatga agcacatgtt atgcatgagc tagcgtgaaa 51 caagacgacg cgcgtcgacg agaccacccg gccccgacca aggctgagag 101 aaacaagtca cagaaATTGT acgtacttgt aatggactta ttaaccgcca 151 acacaacctg ctggcccTAT AAATTgacaa gtactcgtgc tcttcagctg 201 CAAAGAGCCA CAGCGAACAA AAGCCATATA TTGTAACGAA TTACTACCTA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00143 Mean Expected Number 0.004 +strand -144 : -135 GACGCGcGTC AC RSP00143 Mean Expected Number 0.007 -strand -135 : -144 GACGCGcGTC AC RSP00713 Mean Expected Number 0.010 -strand -1 : -7 CAGCTGA Totally 3 motifs of 2 different REs have been found Description of REs found 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0685G12.16-1|5247972..5249664 |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +101 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.32 C - 0.23 1 ggaagagaca atcagtatag ttcagtacta accggcgtcc cttcggtttt 51 aaatgggggg gaagaacata cattgagcaa catacgtacc agctgaatag 101 ctgatggcgg tgcaaccact aaaacaccgt acccatctct ctctctcttt 151 ctctcTATAA ATTtgacaca ataaaaagag gggtcatcgt tgggtgctcc 201 TCATTTCTCT AGTGATCTTC TTTTTCTTTT CTTTTGTTTT CTGTCTCTAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00861 Mean Expected Number 0.003 -strand -49 : -57 AGAAAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -53 : -61 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -55 : -63 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -57 : -65 AGAGAGAGA Totally 4 motifs of 2 different REs have been found Description of REs found 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0072H09.7|5509275..5512957 |SUPPORT| 8 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +361 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.24 T - 0.27 C - 0.30 1 tccgtgttgc tccccatcgc cgcgccgccg ccgactcgtg tgttcgcgcg 51 ccttttggtt ggttctggag tttttagggc ttttggactc gagacgaaag 101 ctgtgtcacc tatggttagt gactgaaatg tgggaccacc tccatctagg 151 cccacctgtc agaagagcTA TAAATTaatt tttgagaaag aaaattcccc 201 CAAACCCTAC ACCCTCCTCG TTTCTCCCAG GCTTCAGAGT CGCCGCCGCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.008 -strand -40 : -47 TGACAGGT AC RSP00695 Mean Expected Number 0.007 +strand -32 : -26 TATAAAT AC RSP00860 Mean Expected Number 0.000 +strand -16 : -8 AGAAAGAAA AC RSP00879 Mean Expected Number 0.009 +strand -106 : -100 CGAAAGC AC RSP00895 Mean Expected Number 0.003 -strand -62 : -69 GTGGTCCC AC RSP01326 Mean Expected Number 0.010 -strand -14 : -20 TCTCAAA Totally 6 motifs of 6 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 815. Group RE: D2 /Group TF: Dof family /AC: RSP00879//OS: Hordeum vulgare /GENE: Al21/RE: D2 /TF: Dof family 826. Group RE: CLE-core /AC: RSP00895//OS: Geminiviruses (Nicotiana species); Pepper Huasteco Virus (PHV) /GENE: Intergenic Regions; PHV coat protein (CP)/RE: CLE-core /TF: unknown 1089. Group TF: ABF-2 /AC: RSP01326//OS: Pisum sativum /GENE: AB80/RE: AB1 heptamer /TF: ABF-2 ||Identical REs AC: RSP01326 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0684F11.21|complement(6083074..6084792) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +173 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.24 T - 0.19 C - 0.33 1 gcttgtgaag cagtaacgcc gatccatttt agccctaacg aaccaacccc 51 ggctctcggt cggtcgcggt cgcgttgcag gggagattaa cgcgtaagca 101 aagcgaaggc gacgacgcgg gacccgcata ttctaaaaaa acacggtggt 151 tttattggta aagccacatg TATAAATCtc ccccccgaaa aaacaaaccc 201 GGCGGATTCG ATCGCCTCCG CCCTCGCCCT CGCCTCGCCT CCGCCTCGCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00447 Mean Expected Number 0.005 +strand -104 : -95 AGCAAAGCgA AC RSP00695 Mean Expected Number 0.005 +strand -30 : -24 TATAAAT Totally 2 motifs of 2 different REs have been found Description of REs found 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0516G10.12-1|complement(6149157..6151088) |SUPPORT| 3 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +235 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.34 C - 0.22 1 atactaaatc tatattttta tggtacatca attttaatac gtaattttta 51 ccatagtttc ttcaaagtag atgttgtttt ataaatcgtg ggaagcggaa 101 gcgcatgcag cggccgcttg ccgttgttat gaacggatac gatacgtgta 151 ccactttgtg tgtgTATAAA TTgatagcag cgtgcctctc ttcttcttca 201 CTGTGGTCAC CTGCAGTTTG CCCCACAGCC ATTCCAAGCA CATATTCCCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00195 Mean Expected Number 0.002 +strand -58 : -48 TaCGTGTACCA AC RSP00880 Mean Expected Number 0.007 -strand -75 : -84 CAACGGCAAg AC RSP01000 Mean Expected Number 0.004 +strand +18 : +27 tTGCCCCACA AC RSP01072 Mean Expected Number 0.007 -strand -156 : -165 ATTACGTaTT AC RSP01274 Mean Expected Number 0.003 -strand -51 : -60 TaCACGTATC AC RSP01288 Mean Expected Number 0.005 +strand -59 : -52 ATACGTGT Totally 6 motifs of 6 different REs have been found Description of REs found 188. Group RE: Box II /AC: RSP00195//OS: Oryza sativa /GENE: Gt2/RE: Box II /TF: unknown 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1173. Group RE: ACE 1 /AC: RSP01274//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 1 /TF: unknown 1185. Group RE: Z-DNA-motif /AC: RSP01288//OS: Arabidopsis thaliana /GENE: cab1/RE: Z-DNA-motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0516G10.12-2|complement(6150220..6151091) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +239 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.35 C - 0.21 1 ttgatactaa atctatattt ttatggtaca tcaattttaa tacgtaattt 51 ttaccatagt ttcttcaaag tagatgttgt tttataaatc gtgggaagcg 101 gaagcgcatg cagcggccgc ttgccgttgt tatgaacgga tacgatacgt 151 gtaccacttt gtgtgtgTAT AAATTgatag cagcgtgcct ctcttcttct 201 TCACTGTGGT CACCTGCAGT TTGCCCCACA GCCATTCCAA GCACATATTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00195 Mean Expected Number 0.002 +strand -55 : -45 TaCGTGTACCA AC RSP00880 Mean Expected Number 0.007 -strand -72 : -81 CAACGGCAAg AC RSP01000 Mean Expected Number 0.004 +strand +21 : +30 tTGCCCCACA AC RSP01072 Mean Expected Number 0.007 -strand -153 : -162 ATTACGTaTT AC RSP01274 Mean Expected Number 0.003 -strand -48 : -57 TaCACGTATC AC RSP01288 Mean Expected Number 0.005 +strand -56 : -49 ATACGTGT Totally 6 motifs of 6 different REs have been found Description of REs found 188. Group RE: Box II /AC: RSP00195//OS: Oryza sativa /GENE: Gt2/RE: Box II /TF: unknown 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1173. Group RE: ACE 1 /AC: RSP01274//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 1 /TF: unknown 1185. Group RE: Z-DNA-motif /AC: RSP01288//OS: Arabidopsis thaliana /GENE: cab1/RE: Z-DNA-motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1734_E02.22-1|complement(6377761..6381189) |SUPPORT| 6 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +80 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.16 T - 0.24 C - 0.35 1 gctattactg taccgtgcgt cgattcgctt acctcctaat acacactgac 51 ggatgggcct tggatgcaaa ccggacccac atgtcactga ctgataagtc 101 gatcccaccc acatccgcgc tgatgttcta gaacctttcg taaacctcct 151 ctttctcaTA TAAATCgggc ccaaacgaaa actcccattc ctccgactcc 201 AATCCAATCC AACGCTTCCT TCCTCGCAAA GCCTCTGCGA ATCTCGCGCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00313 Mean Expected Number 0.003 +strand -123 : -113 CACATGtCACT AC RSP01046 Mean Expected Number 0.003 +strand +5 : +13 CAATCCAAC Totally 2 motifs of 2 different REs have been found Description of REs found 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 970. Group RE: NON /AC: RSP01046//OS: Nicotiana tabacum /GENE: histone genes (oligo)/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1734_E02.22-2|complement(6380191..6381195) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +86 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.16 T - 0.24 C - 0.35 1 acccgcgcta ttactgtacc gtgcgtcgat tcgcttacct cctaatacac 51 actgacggat gggccttgga tgcaaaccgg acccacatgt cactgactga 101 taagtcgatc ccacccacat ccgcgctgat gttctagaac ctttcgtaaa 151 cctcctcttt ctcaTATAAA TCgggcccaa acgaaaactc ccattcctcc 201 GACTCCAATC CAATCCAACG CTTCCTTCCT CGCAAAGCCT CTGCGAATCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00313 Mean Expected Number 0.003 +strand -117 : -107 CACATGtCACT AC RSP01046 Mean Expected Number 0.003 +strand +11 : +19 CAATCCAAC Totally 2 motifs of 2 different REs have been found Description of REs found 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 970. Group RE: NON /AC: RSP01046//OS: Nicotiana tabacum /GENE: histone genes (oligo)/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1734_E02.43|6449818..6453427 |SUPPORT| 5 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +117 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.23 T - 0.23 C - 0.28 1 cttatgctga ttaattaggg ctaatgagct atgcatgcaa gcactgtacc 51 cagtggtgct ccgacaagta ggcctgccta atcaaaaggc agtgaggact 101 gtaactacta gtacctgcca cctcccagtt gctcaggctt ctcaacctta 151 gctagctcga tctcccTATA AATActcctg ctcattacca caacgagcaa 201 GCGATCGACG GAGCGAGCGA GCTAGCCAGC CAGTGTTAGA GCTTGAGCTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.006 +strand -84 : -77 GCCACCTC AC RSP00200 Mean Expected Number 0.006 +strand -192 : -183 gATTAATTAG AC RSP00681 Mean Expected Number 0.001 -strand -184 : -192 TAATTAATC AC RSP00837 Mean Expected Number 0.007 +strand +2 : +11 cGATCGACGG AC RSP01296 Mean Expected Number 0.001 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.008 +strand -35 : -26 CTATAAATAC Totally 6 motifs of 6 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 193. Group TF: GmHdl56; GmHdl57 /AC: RSP00200//OS: Glycine max /GENE: vspB/RE: PRD motif 1 /TF: GmHdl56; GmHdl57 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0627E03.33|6989468..6991312 |SUPPORT| 2 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +79 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.12 T - 0.29 C - 0.28 1 tgctaataaa caaattcaat acctccatcc aagccaaatc ccaagacgtt 51 aaccacttaa tttgttcata ccacccatct tttttttttg aaagtgaggg 101 aaagatgttg actttttcat accacaaaca caaatATTGT ttgctttgcg 151 gcatttcctg cagctgcacT ATAAATAcga gttgtccagc gcccatatca 201 CGTACAAACT CACCAATTCG ACCACAGTCA CCACAGATCT TCTTCCTTCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00447 Mean Expected Number 0.005 -strand -51 : -60 cGCAAAGCAA AC RSP00509 Mean Expected Number 0.002 +strand -31 : -20 TATAAATACgAG AC RSP01296 Mean Expected Number 0.004 +strand -32 : -24 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -32 : -23 CTATAAATAC Totally 4 motifs of 4 different REs have been found Description of REs found 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0627E03.41|complement(7018653..7019845) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +119 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.18 T - 0.27 C - 0.29 1 taatcttcta gtgtcactcc aacagctcag caaagcctga attttcaaga 51 ttccgtgact ttgttaccgt gcagtggcta gctgtccctt gagatctgaa 101 caccatgctt agggaagcat ccaggaacgt gttagcagtc caactccagt 151 gatggcttct ctaacccTAT AAATAagcgg ctcatgactt cactttgctc 201 ACCACTCAGC ATCAGAACAC AAGCAAATCC AACACTTCTT CCTTGAGCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00680 Mean Expected Number 0.007 -strand -135 : -144 TAACAaAGTC AC RSP01296 Mean Expected Number 0.002 +strand -34 : -26 CTATAAATA Totally 2 motifs of 2 different REs have been found Description of REs found 649. Group RE: GARE/Box 2 /AC: RSP00680//OS: Hordeum vulgare /GENE: Amy32b/RE: GARE/Box 2 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0627E03.43|complement(7024039..7025260) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +110 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.22 T - 0.15 C - 0.27 1 tggccactga aataggagta ccaccagaaa ctgaaataaa ggcacagcgt 51 ctccaaaaag ggggatagaa aacagaggca cagccgcctc acagcccaag 101 ggccaaactg gaaggaagtg tgcacgaaac tgcaaccgtg gcatATTGGc 151 atgcaggaat cacaccTATA AATAtccact cccgtagcta ttcagaaacc 201 ACACAAAGAC ACACGTACTT GTATACACAG CTCTCGCACC AAGCAAGCGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00337 Mean Expected Number 0.003 -strand -26 : -34 ATATTTATA AC RSP01296 Mean Expected Number 0.001 +strand -35 : -27 CTATAAATA Totally 2 motifs of 2 different REs have been found Description of REs found 323. Group TF: SEF1 /AC: RSP00337//OS: Glycine max /GENE: beta-conglicinin (7S globulin) alpha' and beta subunits genes/RE: SEF1 BS /TF: SEF1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0471A11.32|7104346..7105899 |SUPPORT| 2 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.25 T - 0.22 C - 0.28 1 ggactaaaga tatcggccca tctgaattgt gcgttccgcc ggataaggga 51 taactgaagg cggcgctcag tcccgcgcct tctggaacct tcccgtggaa 101 ggggcataca gccttgcagc ggcagcttcc ggaagcttct gaattcttct 151 ccaagatttg ccgcgacGAT AAATCctctc gtttctccgc tcgctgattc 201 ATTCTCAACG CAAAATCCAA AAGATAAGCA CAGTTACGCA GCGAGAGCGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00166 Mean Expected Number 0.004 +strand -44 : -37 TTTGCCGC AC RSP00857 Mean Expected Number 0.008 +strand -183 : -174 CCATCTGAAt Totally 2 motifs of 2 different REs have been found Description of REs found 160. Group TF: E2F /AC: RSP00166//OS: Nicotiana tabacum /GENE: RNP2/RE: E2Fb /TF: E2F 793. Group RE: NON /AC: RSP00857//OS: Zea mays /GENE: H4C7/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0539D10.19|complement(7387917..7388827) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.21 T - 0.17 C - 0.36 1 aacagacaaa gaacccaatc gacatagtca taattaaaat ccagccgtcc 51 tagcccgtct ctcccttgtg ccgcaccagt tcccacccca cgatgagaac 101 gtgccccgcg agcccagcag ccgtcgtctc cgtgtgcgtc tcgctggaga 151 tgcaccgttt cgcaccagta TATAAACCga cccagagacc aaaccccatc 201 AGCCATCAGC AGCAGCGCCC GGATCACGAT AGCGCGCCAA CTTTTGCGTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.005 -strand -26 : -32 TTATATA AC RSP00404 Mean Expected Number 0.003 +strand +43 : +49 TTTGCGT AC RSP00701 Mean Expected Number 0.008 +strand +18 : +25 CCCGGATC AC RSP01021 Mean Expected Number 0.008 +strand -168 : -162 ATTAAAA AC RSP01108 Mean Expected Number 0.005 +strand -170 : -164 TAATTAA AC RSP01236 Mean Expected Number 0.003 +strand -179 : -170 aCATAGTCAT Totally 6 motifs of 6 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 386. Group RE: adja /AC: RSP00404//OS: Nicotiana tabacum /GENE: RNP2/RE: adja /TF: unknown 667. Group RE: Oct (d) /AC: RSP00701//OS: Triticum aestivum /GENE: H3/RE: Oct (d) /TF: unknown 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 1026. Group RE: rAT-1 /AC: RSP01108//OS: Spinacia oleracea /GENE: rps22/RE: rAT-1 /TF: unknown 1141. Group RE: 10 bp Z-BAC- /AC: RSP01236//OS: Phaseolus vulgaris /GENE: BAC/RE: 10 bp Z-BAC- /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0539D10.32|complement(7431821..7433667) |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +31 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.21 C - 0.31 1 aactctcaaa gtctcaaggc cattaaattg cctatgggct caccagccaa 51 taacaaactc cggctgttat ccatccaatc cagtgtccca aagcaacatt 101 caagcccagc caggcctcca aaagttgcaa gttgagcatg gcaaaatccc 151 cggcaattct cgacTATAAA TAcctgacca gacacaccca ggagcttcat 201 CAATCATCCA TCTCCGAAGT GTGTCTGCAG CATGCAGGTG CTGAACACCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00509 Mean Expected Number 0.001 +strand -36 : -25 TATAAATACCtG AC RSP01201 Mean Expected Number 0.003 -strand -2 : -9 TGAAGCTC AC RSP01224 Mean Expected Number 0.000 +strand -151 : -138 ATAACAAACTCCGG AC RSP01296 Mean Expected Number 0.002 +strand -37 : -29 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -37 : -28 CTATAAATAC Totally 5 motifs of 5 different REs have been found Description of REs found 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 1112. Group TF: NIT2 /AC: RSP01201//OS: Chlorella vulgaris /GENE: NR/RE: NIT2 BS II /TF: NIT2 1130. Group RE: GARE /AC: RSP01224//OS: Oryza sativa /GENE: Amy7 (Amy1A)/RE: GARE /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1004_A11.25|complement(7484025..7487474) |SUPPORT| 5 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +92 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.28 C - 0.24 1 cacggtttta tatatcatcg ttgatcggac tgatcacttt gaactggtta 51 attaaactca tccaagcttt gcactaatct catacgctaa ttggcagagt 101 tgacacggct aggtcagctg ctaATTGCgc ttatatgcct ctacctaatt 151 gcattgcatg accacttcta TATAAACAtc gctgtgcttc gacgtacggg 201 AAGAGCAACG AGCTGTGTCG ACGCTAGCTA AGCCAACACC AACGAAGATT 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1353_F08.4|complement(7697236..7700648) |SUPPORT| 4 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +122 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.22 T - 0.22 C - 0.33 1 cacgtcgccg gtattaatct ggaaaatgaa gaaaaaaaat ccggccgaat 51 ccccctagaa atcccatcgc gcgcctgcgc gtgtggtgac gccagctcgt 101 ggcctgcttg ggtccgtgca tgcatcagag cagaggcaac tactacgacc 151 tcgcgttcct cgtccctaTA TAAACCccag accaccacct ccactgcttc 201 CAAGAACAGA TGCCATCCTG AGCTTCTAGC TCGCGAGTGA TCTCTTCTTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00016 Mean Expected Number 0.009 -strand -79 : -85 CATGCAC AC RSP00146 Mean Expected Number 0.007 -strand -28 : -34 TTATATA AC RSP00350 Mean Expected Number 0.003 +strand -86 : -76 CGTgCATGCAT AC RSP01014 Mean Expected Number 0.003 +strand -178 : -169 aAAATGAAGA AC RSP01019 Mean Expected Number 0.008 +strand -175 : -169 ATGAAGA Totally 5 motifs of 5 different REs have been found Description of REs found 15. Group RE: RY /AC: RSP00016//OS: Glycine max /GENE: beta-conglycinin/RE: RY /TF: unknown 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 335. Group RE: VP1 RE /AC: RSP00350//OS: Zea mays /GENE: C1/RE: VP1 RE /TF: unknown 939. Group TF: GAPF /AC: RSP01014//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 2 /TF: GAPF 944. Group TF: GAPF /AC: RSP01019//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 1 /TF: GAPF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1353_F08.16-1|7743811..7746143 |SUPPORT| 3 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.24 T - 0.20 C - 0.25 1 taaaaaaatt ttcaaataag acgaacggtt aaagttagat gcggaaaacc 51 atggctgcac ttattttgag atgtaggaag taaggcatac cgcacaccac 101 gtcctggggg tcaggcagtc agcctagtga aaaagataac tgtgcaagct 151 agcttctcgc tctcgcgccT ATAAATTggg cgctcgccgc cggcctcaga 201 GTGCACACAC AGACACACAG ACGCACTCAC ACACTCAGCT TAAGCGAGCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00228 Mean Expected Number 0.001 -strand -64 : -75 ATCtTTTTCACT AC RSP00821 Mean Expected Number 0.004 +strand -105 : -96 aCCACGTCCT AC RSP01599 Mean Expected Number 0.003 +strand -191 : -184 TTTCAAAT Totally 3 motifs of 3 different REs have been found Description of REs found 221. Group TF: GT-1 /AC: RSP00228//OS: Pisum sativum /GENE: rbcS-3A/RE: BOX III /TF: GT-1 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1353_F08.18|complement(7750570..7753535) |SUPPORT| 3 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.16 G - 0.16 T - 0.17 C - 0.51 1 gcgcgccggt cgctctccct cgctcgcacg gccgcaccac ccacttcgcc 51 acgaacccga cgcgagcgcg acgtgcatct cccaacatcc ccgccatttc 101 ctccccaccc aaaaccaacc cgcccgcgtg cggctggccc actttacagc 151 gcctcacctc ccccaacCAT AAATCcccgc ccttttcccc ccctctccac 201 CACTCACCAC GCTCTCCACT ACACGACTCG TCGCCGTCTT GCTCTGCTGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00394 Mean Expected Number 0.008 -strand -53 : -59 TGTAAAG AC RSP00495 Mean Expected Number 0.001 -strand -53 : -60 TGTAAAGT AC RSP00654 Mean Expected Number 0.003 +strand -163 : -154 CACCCACTTC AC RSP00716 Mean Expected Number 0.001 +strand -91 : -83 CAAAACCAA AC RSP00869 Mean Expected Number 0.001 -strand -53 : -61 TGTAAAGTG AC RSP01233 Mean Expected Number 0.008 -strand +43 : +37 AGCAAGA Totally 6 motifs of 6 different REs have been found Description of REs found 377. Group TF: PBF-1 /AC: RSP00394//OS: Zea mays /GENE: gamma-27kDa zein/RE: P-box (s) /TF: PBF-1 ||Identical REs AC: RSP00396 RSP00429 RSP01402 471. Group RE: P-box 2 /AC: RSP00495//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 2 /TF: unknown ||Identical REs AC: RSP00686 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 805. Group RE: EM1 /AC: RSP00869//OS: Triticum aestivum /GENE: LMWG-1D1/RE: EM1 /TF: unknown 1138. Group RE: PLE-79 /AC: RSP01233//OS: Collettrichum lindemuthianum (bean pathogen) /GENE: CLPG2/RE: PLE-79 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1611_C08.37|complement(7869634..7870317) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +83 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.38 G - 0.16 T - 0.14 C - 0.31 1 cgcaggcagc tcgccacctc cttccttgca aagcaaatcc aaccaatcaa 51 atgaacgaag ctatccccca ccaagaaaaa caaaaaacaa aaacaaaaat 101 actacacttc accgcttgcg tacacgacca agaaaatccg aaacaacatg 151 cagtccggct cgagtctaTA TAAAGCgagc aaagcggaga ccgagatgac 201 CAAACACACA AGCTTTGATC GATCTCTCCC ACACGGCTCA AACGCGCATA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.007 +strand -188 : -181 GCCACCTC Totally 1 motifs of 1 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1448_G06.21|complement(7911937..7912838) |SUPPORT| 1 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +65 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.22 T - 0.23 C - 0.38 1 tcgacgcctc ggcggcggca cacgcgtcgc cgcgcggttc gtccgctctc 51 gcgtttcacc tcacctccct cgtgaaggaa tcgcggaatc cccctcccgc 101 caagtaaagc gcagctcaac tctctctctc tctcgcaagt gttgttattc 151 ctttctctcc cgccaaTATA AACCagcagc catctcgtct tctcccttgc 201 AGCTTCGGAC TTTCGTCCAT CGCCGGCAAG AACAGCAGCG CAGCAGGAGG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00862 Mean Expected Number 0.002 -strand -45 : -53 AGAAAGGAA AC RSP00864 Mean Expected Number 0.003 -strand -68 : -76 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand -70 : -78 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand -72 : -80 AGAGAGAGA AC RSP00988 Mean Expected Number 0.001 +strand -44 : -33 CTCCCGCCAAtA AC RSP00989 Mean Expected Number 0.008 +strand -45 : -37 TCTCCCGCC Totally 6 motifs of 4 different REs have been found Description of REs found 798. Group TF: BPC1 /AC: RSP00862//OS: Arabidopsis thaliana /GENE: STK/RE: GA-3 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 909. Group TF: E2F/DP /AC: RSP00988//OS: Zea mays /GENE: RBR3/RE: E2F/DP I /TF: E2F/DP 910. Group TF: E2F/DP /AC: RSP00989//OS: Zea mays /GENE: RBR3/RE: E2F/DP IV /TF: E2F/DP ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1316_E06.27|8642720..8644577 |SUPPORT| 5 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +1016 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.18 T - 0.41 C - 0.18 1 acctgctttc ttcatttccg tgttcagcag ctttgcaata atttctatgt 51 tcatttctag tcgtcttaat gtttatttga aaatttattt tccttctatg 101 tgcgaaATTG Atgttttttt tactgtgttc tcttgcagaa tagctctctt 151 tgtgaTATAA ATCtaaatgt tcacttgaag ctggaagtct ctgctgaagc 201 GTAGAATCGT AGATAATTCC TGCACTCAGT TTTGAGAAAA CTGGAGGTCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01458 Mean Expected Number 0.002 +strand -126 : -114 ATTTgAAAATTTA AC RSP01599 Mean Expected Number 0.009 -strand -119 : -126 TTTCAAAT Totally 2 motifs of 2 different REs have been found Description of REs found 1328. Group RE: AT-rich ELS /AC: RSP01458//OS: Glycine max /GENE: BiP9/RE: AT-rich ELS /TF: unknown 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0054K20.35|complement(8725354..8730027) |SUPPORT| 8 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +1084 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.27 T - 0.17 C - 0.31 1 tcagtggagc gacaggagca gcaggacgtc ggacatgagt tgaaggaggc 51 aaaatgaact tattccaaaa gaaaaatagg caacctgttg ggccgtgaag 101 cccacggaaa ttcatggata gcatccgcta ggcccatccg aggccacgcg 151 tgaaaccagc ggcccaaTAT ATATCggctc cgctcgacca ccacgctggc 201 CGCGTCACTC TCCTCCCCCT CGTATCGCTC GGGAGCGGAG GTCTCCTCGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00050 Mean Expected Number 0.001 -strand -50 : -61 ACGCGTGgCCTC AC RSP00282 Mean Expected Number 0.008 -strand -81 : -87 TATCCAT AC RSP01703 Mean Expected Number 0.003 -strand -169 : -178 CCGACGTCCT Totally 3 motifs of 3 different REs have been found Description of REs found 49. Group RE: Ce3 /AC: RSP00050//OS: Hordeum vulgare /GENE: HVA1 gene/RE: Ce3 /TF: unknown 273. Group RE: Amylase-element /AC: RSP00282//OS: Oryza sativa /GENE: Amy3D/RE: Amylase-element /TF: unknown ||Identical REs AC: RSP00675 1512. Group RE: ACGT2/DRE2 /AC: RSP01703//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT2/DRE2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1695_H09.10|8988511..8989977 |SUPPORT| 3 exon(s)|Contig: NT_1071811.txt | -200:+51 from mRNA start|,5"-UTR: +87 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.20 T - 0.20 C - 0.28 1 ggttagctgg gggttgtaaa tgagacgagg tgcaccgtgc acgcgcttaa 51 cgagttaatg gaaacctacc atccaaaccc aaatgaaacg aatcacgaaa 101 ctgggccaca aaatttctcc aaattttgaa ttccagaggc gaccagtccg 151 gctcgaaatc cccgcctTAT AAATTacgca cgccgacacg atacgccccc 201 ATCGAATTCA GGCGCAAAAA CCTCCAAAAC CTTTGCAATA TTCCTCGTAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00301 Mean Expected Number 0.010 -strand +37 : +31 TGCAAAG AC RSP00651 Mean Expected Number 0.007 +strand -137 : -127 ACCTACCAtCC AC RSP00755 Mean Expected Number 0.010 -strand +45 : +39 AGGAATA AC RSP01015 Mean Expected Number 0.009 +strand -121 : -112 CAAATGAAAc AC RSP01772 Mean Expected Number 0.008 +strand -146 : -140 TTAATGG Totally 5 motifs of 5 different REs have been found Description of REs found 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown 940. Group TF: GAPF /AC: RSP01015//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 3 /TF: GAPF 1572. Group TF: WOX11 /AC: RSP01772//OS: Oryza sativa /GENE: PR2/RE: WOX11 BS /TF: WOX11 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ9003_G05.27|complement(302000..304940) |SUPPORT| 4 exon(s)|Contig: NT_1071761.txt | -200:+51 from mRNA start|,5"-UTR: +47 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.20 T - 0.35 C - 0.16 1 tgcatgtgga ggcatatttt tcactgttcc tttcaaaatc attggcgaat 51 ccaagttaaa ttaccctgct ttttatactg catttttctc tcaaaaaata 101 gatttcgaac taagtttgaa gtaatctcac tctctgaaga aatgtctgtt 151 aagtaagctc aggacTATAA ATActagtgt atataagcgg ttcacttcac 201 AAGTTTTGAG TTGAGTTAAG TTGAGTTGAG TAGTCGAGTG GGCGGCAATG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00450 Mean Expected Number 0.002 -strand -178 : -189 TgAAAAATATGC AC RSP00509 Mean Expected Number 0.001 +strand -35 : -24 TATAAATACtAG AC RSP00943 Mean Expected Number 0.003 +strand -9 : +2 TCAcTTCACAA AC RSP01296 Mean Expected Number 0.003 +strand -36 : -28 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -36 : -27 CTATAAATAC AC RSP01596 Mean Expected Number 0.003 -strand +2 : -9 TTGTGAAgTGA Totally 6 motifs of 6 different REs have been found Description of REs found 429. Group RE: AIV /AC: RSP00450//OS: Phaseolus vulgaris /GENE: CHS/RE: AIV /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 872. Group TF: GBF /AC: RSP00943//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box III /TF: GBF 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1417. Group RE: Box III /AC: RSP01596//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ9003_G05.34|complement(324774..326565) |SUPPORT| 6 exon(s)|Contig: NT_1071761.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.23 T - 0.21 C - 0.39 1 tctgcttgtt tggcccatcc gcccctacag catgggctaa cctgggccgt 51 caattgccgt ccacaacatc ttggcccagc ccataacact cctggtccca 101 cttgcagcgg gagagttgga caccgctgct tccgcagcaa accctagccc 151 ccgcgccgcc gcgcccataT ATAAAGCtca ctcgctgctc cacccttccc 201 TCTTCTCTCG TGTCTCCGGC GGCGGCGAGC TCGTGATCTC AACGACCAGG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.009 -strand -26 : -31 TTTATA AC RSP00146 Mean Expected Number 0.002 -strand -27 : -33 TTATATA AC RSP00147 Mean Expected Number 0.009 +strand -31 : -26 TATAAA AC RSP01237 Mean Expected Number 0.000 -strand -25 : -34 CTtTATATAT Totally 4 motifs of 4 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0030G02.42|892651..893235 |SUPPORT| 2 exon(s)|Contig: NT_1071761.txt | -200:+51 from mRNA start|,5"-UTR: +40 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.12 T - 0.36 C - 0.26 1 attccatgcc ttgtttccat ttctaaaaga gaaacgaaac agtttccctt 51 cttttttccc cttctggttg gttctccctt agttgatgcc aaaccataac 101 ttctttccaa ctttaACAAT aaactcctcc acgccttatt ttccgataaa 151 tgtttcacct tacttgtccT ATAAATTggc atgccaacct accctaagat 201 TCTTTCTAAA TCTTATAGCA ACCGGCATAT AGGTTTCGGC ATGGTTTGCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01031 Mean Expected Number 0.006 -strand +3 : -5 AGAATCTT AC RSP01454 Mean Expected Number 0.003 -strand -129 : -135 ACCAACC Totally 2 motifs of 2 different REs have been found Description of REs found 956. Group TF: AEF /AC: RSP01031//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 2 /TF: AEF 1325. Group RE: AC-II /Group TF: PtMYB4 /AC: RSP01454//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-II /TF: PtMYB4 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0030G02.53|937275..940991 |SUPPORT| 3 exon(s)|Contig: NT_1071761.txt | -200:+51 from mRNA start|,5"-UTR: +248 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.13 T - 0.42 C - 0.21 1 ttcgtatttt tattgttgtt agatgataaa atatgattaa tattttatgc 51 gtgacttgtc tttttaatat ttttcgtaat tttttcaaat aagacgaatg 101 gtgaaacgtt gaacacgaaa atcaggtttg tctttttttc ggaagggtgg 151 agtatatccc tctctctctc TATAAATAcc ctcctccatg gattcgttac 201 CACATTCTCC TCTCTCTCTC TCCCTCTCTC ATCCATTTCA ATTCTCTCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00188 Mean Expected Number 0.001 -strand -89 : -98 TCAACGTtTC AC RSP00331 Mean Expected Number 0.005 -strand -6 : -14 GAATCCATG AC RSP00864 Mean Expected Number 0.006 -strand +51 : +43 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +21 : +13 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +19 : +11 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand -30 : -38 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand -32 : -40 AGAGAGAGA AC RSP00865 Mean Expected Number 0.003 -strand +23 : +15 GGAGAGAGA AC RSP01296 Mean Expected Number 0.003 +strand -31 : -23 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -31 : -22 CTATAAATAC AC RSP01480 Mean Expected Number 0.007 -strand -168 : -175 TATTTTAT Totally 11 motifs of 7 different REs have been found Description of REs found 182. Group TF: ABI5 /AC: RSP00188//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.2 /TF: ABI5 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1348. Group TF: AT-1SNBP /AC: RSP01480//OS: Glycine max /GENE: GS15/RE: AT-cm /TF: AT-1SNBP ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1297_C09.8|1462959..1465969 |SUPPORT| 6 exon(s)|Contig: NT_1071761.txt | -200:+51 from mRNA start|,5"-UTR: +99 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.20 T - 0.29 C - 0.34 1 gttttggccc gtttccttcc gttttcatgc tggtctcgag tgagagtcgg 51 tcggtcagaa ttcacactct gaaacacacg ccggtcgccg tcgtcaacgt 101 tggtcttggg cacctcgcgt ttcacacttt tcttctgtac catttcgccg 151 agctttaccc cgcggctcgt aTATAAATCc tctcgatctg acgcggattc 201 TGCTCATTCC AAATCGAATC CACCAACATC CCCCCCCCCC CCGGCATTGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.005 -strand -25 : -31 TTATATA AC RSP00253 Mean Expected Number 0.003 -strand -2 : -9 AATCCGCG AC RSP00695 Mean Expected Number 0.005 +strand -29 : -23 TATAAAT Totally 3 motifs of 3 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1003_F05.8|37105..39033 |SUPPORT| 1 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +705 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.18 T - 0.25 C - 0.22 1 caaaaggatg tacatagcca aacagtagct agacaaaggc aggtatgttt 51 ttcgtagtta gcaataataa tactccaaga ttagaagaga tatcgagata 101 gttataatca caaaagcttc tagaatggcg caaaaaagaa aaaaagagct 151 ggaccgcttt gatggcTATA AATCactctc tatgctgtat ccaatctccc 201 ACATCACCCA CACTATCAAA GCTTTTTGGC TGCCACTCGC ACCGCTCTCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00915 Mean Expected Number 0.005 -strand +8 : -2 GGTGATGTGG Totally 1 motifs of 1 different REs have been found Description of REs found 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1267_F10.32|complement(350594..351646) |SUPPORT| 2 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +73 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.19 T - 0.32 C - 0.14 1 atattaatgc tgtagtatat tttgtaggta actattatat aaattgacta 51 ttaaatatat tgactatatg taaattggag tagctaatag ttgagctgta 101 cCCAATtgac tatatgtaaa tatattgact attgaacttg ctcttatgca 151 tatcgcctcT ATAAATAata acgacccagc acgaaacgcg ggtataagat 201 ATGAGCAGTG TGCAGATCGT TTGAGCAGCT AGCAACAAAT TACAAGAGGG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.006 +strand -42 : -34 CTATAAATA Totally 1 motifs of 1 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1006_D05.18|433501..435343 |SUPPORT| 2 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +64 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.13 T - 0.27 C - 0.26 1 gaaagaaaga aataaagcat atacttttaa gcaaaaacaa atgtaaagag 51 catgtcacct tgtcgattct ctatggtgat agggtccagg gcaatgccat 101 gtcatgctat cttatccctg tgctttgcac acagcttttt caccaaatcc 151 ctgcaagaat cctccTATAA ATAcccaccc aattgatcca tcaatttccc 201 ATCACAAAAC ACATAAAACT ATATCATCAT CTTCCATAGC TGTACACATC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00158 Mean Expected Number 0.008 -strand -164 : -174 TtTTTGCTTAA AC RSP00460 Mean Expected Number 0.004 +strand -105 : -96 GcCATGTCAT AC RSP00860 Mean Expected Number 0.002 +strand -197 : -189 AGAAAGAAA AC RSP01053 Mean Expected Number 0.003 -strand -85 : -93 GATAAGATA AC RSP01296 Mean Expected Number 0.006 +strand -36 : -28 CTATAAATA AC RSP01301 Mean Expected Number 0.002 +strand -36 : -27 CTATAAATAC Totally 6 motifs of 6 different REs have been found Description of REs found 153. Group RE: D3 /AC: RSP00158//OS: Glycine max /GENE: GmAux28/RE: D3 /TF: unknown 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 973. Group TF: HvMCB1 /AC: RSP01053//OS: Hordeum vulgare /GENE: ITR1/RE: GATA-core /TF: HvMCB1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0090H18.21|2321955..2322722 |SUPPORT| 1 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.21 T - 0.27 C - 0.17 1 tcgaagatct agaatatatc gtatctgcta ctatatttat gttttatgag 51 agatgaagag ggtacacatg acaggtggga ggtagaattg aatggaggta 101 ttaactaacc aagtggctaa ttaaactagt taattaATTG Caagctaatt 151 aagctagctg ataaccatat aTATAAACCc cattgcacct tggcaaccaa 201 GAAGGGCGAG AAGCCAAGAA ATCATCTCTC CATCCATTGC TCGCAGATGG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00122 Mean Expected Number 0.010 -strand -120 : -126 CTCCCAC AC RSP00304 Mean Expected Number 0.006 +strand -132 : -125 TGACAGGT AC RSP00595 Mean Expected Number 0.003 -strand -47 : -55 GCTTAATTA Totally 3 motifs of 3 different REs have been found Description of REs found 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1113_G05.29|complement(2570819..2571606) |SUPPORT| 1 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +118 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.20 T - 0.25 C - 0.32 1 tcgctgacca gtcaaaccac ctcctccact tgtcacttcc actcatcacc 51 tcgaacctcg agccgtgggc cccacatgtc attggaacag cgtgtgtctc 101 ctcttgtcgc atttggaata gtcgtcgttg gtttcttgcc gccttgaccc 151 caaccaccag cgtcgtaTAT AAATCccccc tgcacaggaa agctttcgtc 201 ACGAAACAAC CTTGCGTTGA GCTTAGCTTT AGCTGATCGA ATCGAGAAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.009 -strand -29 : -35 TTATATA AC RSP00378 Mean Expected Number 0.009 -strand -185 : -191 TTTGACT AC RSP00460 Mean Expected Number 0.004 +strand -128 : -119 cACATGTCAT AC RSP00471 Mean Expected Number 0.003 -strand -124 : -134 aTGTGGGGCCC AC RSP00695 Mean Expected Number 0.009 +strand -33 : -27 TATAAAT AC RSP01692 Mean Expected Number 0.002 -strand +41 : +34 TTCGATCA AC RSP01751 Mean Expected Number 0.002 +strand -176 : -168 TCCACTTGT AC RSP01755 Mean Expected Number 0.009 +strand -50 : -43 CAACCACC Totally 8 motifs of 8 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 363. Group TF: WRKY1 /AC: RSP00378//OS: Petroselinum crispum /GENE: WRKY1/RE: WB /TF: WRKY1 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1509. Group RE: CARE J /AC: RSP01692//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE J /TF: unknown 1557. Group TF: AREB2/ABF4 /AC: RSP01751//OS: Arabidopsis thaliana /GENE: COX5b-1/RE: distalB-like /TF: AREB2/ABF4 1560. Group TF: C1 /AC: RSP01755//OS: Glycine max /GENE: a2/RE: C1BS1 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0018M09.22|complement(4732879..4733567) |SUPPORT| 1 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +110 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.18 T - 0.16 C - 0.45 1 ttccccattt taccccctcc actcgccctt caatctccca ctgccacctc 51 ggccccacca ccaacttacc caggaaacac ccgtccgatt cacatccaac 101 gatccgcaac ccaggggcaa atccgccatt cgttccccac ctcaaaccct 151 agcctcgccg catcccgacT ATAAAACcct cccctctccg cgaaccctaa 201 CACCATCCGG CGGCGGCGCA GCAGCAGCAG AGGTGAGCTC GGCGGCGGCG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00263 Mean Expected Number 0.003 +strand -108 : -100 CATCCAACG AC RSP00615 Mean Expected Number 0.008 -strand +37 : +32 CTCACC AC RSP01037 Mean Expected Number 0.000 +strand -199 : -184 TCCCCATTTTACCCCc AC RSP01304 Mean Expected Number 0.003 +strand -10 : -1 cGAACCCTAA Totally 4 motifs of 4 different REs have been found Description of REs found 255. Group RE: Non /AC: RSP00263//OS: Triticum aestivum /GENE: H3/RE: Non /TF: unknown ||Identical REs AC: RSP01563 591. Group RE: C-rich GG1 /AC: RSP00615//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: C-rich GG1 /TF: unknown 961. Group RE: FP56 /AC: RSP01037//OS: Petroselinum crispum /GENE: 4CL1/RE: FP56 /TF: unknown 1197. Group RE: Telo box /AC: RSP01304//OS: Lycopersicon esculentum /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1756_H07.27|complement(4896119..4899272) |SUPPORT| 2 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +51 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.25 T - 0.16 C - 0.40 1 ggcgaacaaa ccaagcggac gcggccgccg ccggagctga gcgagcccat 51 cgttctccgg cgatggcagg caaaccatcg gtacatgccg cgctttccgc 101 gagacgcaaa agcttcccag ctcgccgccc gcgcgcgtcc catcattctc 151 gccaccccca atcgcccTAT AAATGgccgc gccgccatcg ctggtagtcc 201 AGCACCTCGT CGACTTCTTC CAGCTTCCAT AGCTAGCTAG CTCGGCTCGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00003 Mean Expected Number 0.006 -strand -25 : -34 CCATTTATAG AC RSP00004 Mean Expected Number 0.007 -strand -28 : -33 TTTATA AC RSP00040 Mean Expected Number 0.008 +strand -196 : -190 AACAAAC AC RSP00147 Mean Expected Number 0.007 +strand -33 : -28 TATAAA AC RSP00503 Mean Expected Number 0.002 +strand +33 : +40 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand +40 : +33 CTAGCTAG AC RSP00695 Mean Expected Number 0.001 +strand -33 : -27 TATAAAT AC RSP00987 Mean Expected Number 0.009 +strand +21 : +30 CAGCTtCCAT AC RSP01710 Mean Expected Number 0.002 -strand -25 : -34 CCATTTATAG Totally 9 motifs of 8 different REs have been found Description of REs found 3. Group TF: AGL3; MADS-box TF /AC: RSP00003//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: CArG1 (AGL3) /TF: AGL3; MADS-box TF 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 39. Group RE: AACA box (D) /AC: RSP00040//OS: Oryza sativa /GENE: GluB-1/RE: AACA box (D) /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 908. Group RE: H-box-like motif /AC: RSP00987//OS: Antirrhinum majus /GENE: CHS/RE: H-box-like motif /TF: unknown 1518. Group TF: RIN /AC: RSP01710//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Intermediate /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1654_A02.12|complement(5408899..5411353) |SUPPORT| 1 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +94 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.21 T - 0.37 C - 0.14 1 ttaagaaatt tttttttata gagttagtca aacttaaagt agtttgactt 51 gactaaagtt aaaacgtgta ttgtaatcta aaatggaggg agtaaaataa 101 atgagtggat atttagtttc ccagcttgtt ggctactctc tcaaggtgtg 151 atttcaggct ttccgcaTAT AAATAgggtg gtatgcatgt agtacattgt 201 ATTTGTGCAT CAGCTGGCCT TTTGTGACTT TTGTCCATCA ATCATACAGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00559 Mean Expected Number 0.007 +strand -54 : -44 TGTgATTTCAG AC RSP00713 Mean Expected Number 0.008 -strand +16 : +10 CAGCTGA AC RSP00934 Mean Expected Number 0.003 +strand -92 : -83 ATATTTAGTT Totally 3 motifs of 3 different REs have been found Description of REs found 535. Group RE: 2'/Box II J1 /AC: RSP00559//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: 2'/Box II J1 /TF: unknown 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 863. Group RE: AT-2b /AC: RSP00934//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2b /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1654_A02.26|5459656..5461945 |SUPPORT| 2 exon(s)|Contig: NT_1071781.txt | -200:+51 from mRNA start|,5"-UTR: +259 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.18 T - 0.25 C - 0.22 1 actctgaatt aatctaccag gagatgagca cacacaggac ctagcttttc 51 cctgcatgat gattattcaa agaaaaattc catgattcca cattactatc 101 acaccaggaa tagttcaact gacaagctgc gcagctggac tgaaaccttc 151 agctcatgtt caTATAAACC attctggtaa gtacaagcta atgagagaat 201 ACATTGTCCA TTAACACTAG AGAGAAGCTA GCTAGTGAGA TAACACAGAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand +28 : +35 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +35 : +28 CTAGCTAG AC RSP00698 Mean Expected Number 0.003 +strand -196 : -186 TGAATTAATCt Totally 3 motifs of 2 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0461D06.18|complement(75923..82135) |SUPPORT| 9 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +406 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.22 T - 0.31 C - 0.18 1 ccagaattag ccctagggta caatgtgaga aagagagaat taagaagttt 51 ggtttctgcg tgtttacaat gtgagaaaga tgcaggagaa gagattttac 101 tattccggaa gctggtagga gaatttgtct ttgcgtttac agccgctcct 151 tcaagaccca gtacccAATA AATCcactcc ttaaatgact ttctttaggg 201 ATTTCTACAT AGGATTTGAT GTCCTAAGAT ATCCTGTTCT CCAATAGGTT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00861 Mean Expected Number 0.002 +strand -173 : -165 AGAAAGAGA AC RSP01192 Mean Expected Number 0.002 +strand -188 : -179 CTAGGGTaCA Totally 2 motifs of 2 different REs have been found Description of REs found 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 1103. Group RE: D-box /Group TF: D factor /AC: RSP01192//OS: Nicotiana tabacum /GENE: Adh2/RE: D-box /TF: D factor ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0003H22.2|complement(140044..143155) |SUPPORT| 6 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +309 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.29 T - 0.27 C - 0.27 1 tcgaggaaca taaatagaaa tggcgcgaaa tctgtctgcc gtagctttct 51 ttgggcgggt cggtggtggc agtggcagca atggcagact gccaggcggg 101 tcacgttggt tgacccctct tctctctctc tctctctctc tttctctctc 151 ctactcgcgc gtcgtcgccC ATAAATCtgg cgggaaccaa gaggcctcgc 201 GCCATTATAG GCGCGTGCGC GTCTCTCGGT TCTGTGAATT GTGAGAGATT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00005 Mean Expected Number 0.004 -strand -184 : -193 CTATTTATGT AC RSP00653 Mean Expected Number 0.005 +strand -59 : -49 TTCTCTCTCCT AC RSP00861 Mean Expected Number 0.002 -strand -56 : -64 AGAAAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -60 : -68 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -62 : -70 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -64 : -72 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -66 : -74 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -68 : -76 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -70 : -78 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -72 : -80 AGAGAGAGA AC RSP00865 Mean Expected Number 0.002 -strand -50 : -58 GGAGAGAGA AC RSP01283 Mean Expected Number 0.000 -strand -61 : -77 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 -strand -63 : -79 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 -strand -65 : -81 GAGAGAGAGAGAGAGAA Totally 14 motifs of 6 different REs have been found Description of REs found 5. Group TF: AGL3; MADS-box TF /AC: RSP00005//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: CArG3 (AGL3) /TF: AGL3; MADS-box TF 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0003H22.6|160154..160767 |SUPPORT| 1 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +80 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.13 T - 0.20 C - 0.32 1 atattctaat tgaaacagtt tgtattacag atcacacatc ttccgtgtac 51 caaattcgct aatcacccgg atcgcgtgtg cccgtgcgcg gaaaagcaac 101 accagcatgc acacacacac accaaaaacg caaatccaag catcgcacgc 151 tacatcagca acaacggcac taTATAAACC catcttaacg acacctgatt 201 AGCAGCTCCA GTACACTAAT TAACCCAAAC TCCCTCCACA CACATTAACC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00195 Mean Expected Number 0.002 +strand -159 : -149 TCCGTGTACCA AC RSP00272 Mean Expected Number 0.001 +strand -138 : -128 TCACcCGGATC AC RSP00523 Mean Expected Number 0.002 -strand -122 : -128 ACACGCG AC RSP00597 Mean Expected Number 0.006 -strand +49 : +38 GTTAATgTGTGT AC RSP00597 Mean Expected Number 0.006 -strand +24 : +13 GTTAATTaGTGT AC RSP00697 Mean Expected Number 0.006 +strand -183 : -178 GTTTGT AC RSP00701 Mean Expected Number 0.003 +strand -135 : -128 CCCGGATC Totally 7 motifs of 6 different REs have been found Description of REs found 188. Group RE: Box II /AC: RSP00195//OS: Oryza sativa /GENE: Gt2/RE: Box II /TF: unknown 264. Group RE: Type II element /AC: RSP00272//OS: Nicotiana tabacum /GENE: artifical construction/RE: Type II element /TF: unknown 499. Group TF: DPBF-1; DPBF-2 /AC: RSP00523//OS: Daucus carota /GENE: Dc3/RE: E3-core /TF: DPBF-1; DPBF-2 573. Group RE: GT-1/16 JJ1 /AC: RSP00597//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: GT-1/16 JJ1 /TF: unknown 663. Group RE: Box II /AC: RSP00697//OS: Brassica oleracea /GENE: SLG13/RE: Box II /TF: unknown ||Identical REs AC: RSP00762 RSP00767 RSP00772 RSP00777 667. Group RE: Oct (d) /AC: RSP00701//OS: Triticum aestivum /GENE: H3/RE: Oct (d) /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0047A17.32|complement(302507..309098) |SUPPORT|16 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +955 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.18 T - 0.23 C - 0.34 1 gcggacagca cgcgcgacct ctcactgcta cgtgggccct tatccaagcc 51 acgtcaccct gatctatcta aacccacctt ttttttttcc tctgaagtaa 101 ttaaccacgg taaataaATT GGtcgaaacg ggtaattaac gcagtgtgtg 151 ggagggagga gtgcccaaTA TAAAACcaag cctcctccct acccatctcc 201 TCCGTTCCGC GCATCGCTAC ACCCCAAAAA CCTCTCACGC GCTCTCTCCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00113 Mean Expected Number 0.002 -strand -145 : -153 TGACGTGGC AC RSP00122 Mean Expected Number 0.003 -strand -47 : -53 CTCCCAC AC RSP00189 Mean Expected Number 0.002 -strand -165 : -174 cCCACGTAGC AC RSP00214 Mean Expected Number 0.008 -strand -145 : -152 TGACGTGG AC RSP00215 Mean Expected Number 0.008 +strand -152 : -145 CCACGTCA AC RSP00248 Mean Expected Number 0.009 +strand -153 : -144 GCCACGTCAc AC RSP00858 Mean Expected Number 0.001 +strand -70 : -63 GGTAATTA AC RSP00948 Mean Expected Number 0.006 +strand -92 : -86 GGTAAAT AC RSP01106 Mean Expected Number 0.001 +strand -155 : -145 AaGCCACGTCA AC RSP01259 Mean Expected Number 0.002 +strand -173 : -166 CTACGTGG AC RSP01280 Mean Expected Number 0.003 -strand -143 : -153 GGTGACGTGGC AC RSP01729 Mean Expected Number 0.001 -strand -143 : -154 GGTGACGTGGCT Totally 12 motifs of 12 different REs have been found Description of REs found 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 794. Group TF: DF1 /AC: RSP00858//OS: Pisum sativum /GENE: pra2/RE: GT2 /TF: DF1 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 1024. Group RE: rHex /AC: RSP01106//OS: Spinacia oleracea /GENE: rps22/RE: rHex /TF: unknown 1161. Group TF: GBF1 /AC: RSP01259//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS6 /TF: GBF1 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1537. Group TF: STF1/HY5 /AC: RSP01729//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0476H10.41|707230..708245 |SUPPORT| 2 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +489 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.19 T - 0.24 C - 0.29 1 caaaatgtgt gtggtttttg caacttgaac gataaaacat aaaatatgta 51 gttttatgaa atttactcaa aaaaaattgt cgcactattt tatggcatgc 101 accgaaatgc ctctcccggt gagcgtgagc tcgctaacgc taggccgcta 151 ccggaacaag cggcgccTAT AAATAaagcc ccaccccacc actgcgccgc 201 ACCAAGCACA CAAATCACAG CTGCTGCTGC TGCTGCTCTG CTCCCCTCCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00934 Mean Expected Number 0.006 +strand -157 : -148 ATATgTAGTT AC RSP01296 Mean Expected Number 0.002 +strand -34 : -26 CTATAAATA AC RSP01480 Mean Expected Number 0.003 +strand -115 : -108 TATTTTAT AC RSP01480 Mean Expected Number 0.008 -strand -155 : -162 TATTTTAT Totally 4 motifs of 3 different REs have been found Description of REs found 863. Group RE: AT-2b /AC: RSP00934//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2b /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1348. Group TF: AT-1SNBP /AC: RSP01480//OS: Glycine max /GENE: GS15/RE: AT-cm /TF: AT-1SNBP ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0040I22.20|1853215..1855557 |SUPPORT| 5 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +80 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.20 T - 0.25 C - 0.32 1 accatattag ccgctaagcc cactaaattc agtcattcac acattcaccc 51 ctcctacatt tatttctcat atcacacccc tgaggaaggt cgccattgcg 101 aacagactgc aattcACAAT ctcctcaagg gtattattgc acaagtaccg 151 aatagattag cactgtgTAT AAAGCtctac ggccgccgcg aactgccggg 201 CGCTAGGGTT TCGGGTTCCT CGACCTCTCG CCGCCGTCGT CCCGCGCGCT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.005 -strand -154 : -164 TGAATgTGTGA AC RSP01604 Mean Expected Number 0.002 +strand -39 : -32 ACTGTGTA Totally 2 motifs of 2 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 1425. Group TF: SPF1 /AC: RSP01604//OS: Ipomoea batatas /GENE: Sporamin; beta-amylase/RE: SP8a /TF: SPF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1004_H01.23|2019641..2024190 |SUPPORT| 5 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +96 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.30 C - 0.21 1 cagtgcctga tttcatacta gtagtaaaat aaacctggag ttcattatac 51 tgatacccct tttaccatgt gcccaacacc cgtgataagt ctggaatgca 101 aaagattcta caccaaattc gtacagtagt actagtaatc gtttattttt 151 cgtacaaaat catggtgaAA TAAATCgaat tcaaggacaa acgtcagctg 201 AAGGATTCAA ATTCGTTTGC GAGTCTCTTC GTTTTTACGT GGCGCGCCAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00043 Mean Expected Number 0.002 +strand +36 : +43 TACGTGGC AC RSP00051 Mean Expected Number 0.003 -strand +43 : +34 GCCACGTAaA AC RSP00052 Mean Expected Number 0.001 +strand +35 : +45 tTACGTGGCGC AC RSP00065 Mean Expected Number 0.000 +strand +37 : +45 ACGTGGCGC AC RSP00075 Mean Expected Number 0.002 +strand +35 : +44 tTACGTGGCG AC RSP00091 Mean Expected Number 0.001 +strand -1 : +11 GAAGGaTTCAAA AC RSP00247 Mean Expected Number 0.004 -strand +43 : +34 GCCACGTAAa AC RSP00521 Mean Expected Number 0.008 +strand -125 : -119 ACACCCG AC RSP00713 Mean Expected Number 0.010 -strand -1 : -7 CAGCTGA AC RSP00894 Mean Expected Number 0.008 +strand -23 : -16 AATTCAAG AC RSP00961 Mean Expected Number 0.005 +strand -104 : -97 TGCAAAAG AC RSP01031 Mean Expected Number 0.007 -strand -92 : -99 AGAATCTT AC RSP01034 Mean Expected Number 0.006 +strand +37 : +43 ACGTGGC Totally 13 motifs of 13 different REs have been found Description of REs found 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 50. Group RE: A3 /AC: RSP00051//OS: Hordeum vulgare /GENE: HVA22/RE: A3 /TF: unknown 51. Group RE: ABRE /AC: RSP00052//OS: Oryza sativa; /GENE: Rab-16A/RE: ABRE /TF: unknown 64. Group TF: EmBP-1 /AC: RSP00065//OS: Triticum aestivum /GENE: Em/RE: Em1a /TF: EmBP-1 74. Group TF: TAF-1 /AC: RSP00075//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: Iwt /TF: TAF-1 89. Group RE: ARE 76/65 /AC: RSP00091//OS: Chlamydomonas reinhardtii /GENE: Nia1/RE: ARE 76/65 /TF: unknown 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 497. Group TF: DPBF-1; DPBF-2 /AC: RSP00521//OS: Daucus carota /GENE: Dc3/RE: E1-core /TF: DPBF-1; DPBF-2 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 825. Group TF: Dof family /AC: RSP00894//OS: Solanum melongena /GENE: SmCP/RE: ERE 2 /TF: Dof family 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 956. Group TF: AEF /AC: RSP01031//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 2 /TF: AEF 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0025F02.31|2894012..2895748 |SUPPORT| 1 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +103 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.21 T - 0.27 C - 0.19 1 ttgtgtcagc aatagagagt gttttcccaa gataatggca tcgtatattt 51 tcacgtggag atagactttg atcgtttcag aaaacgatat ctacctttga 101 cgttagacga gaagcctgaa taaattccat gcactaaatt aaatgagtag 151 gcatcggctc tgctgatcTA TAAATAtata cgagctgtgt ccgcagcaac 201 AAGAGCACGA GCTTACCTAG CTAGGTCCAG AGAAAAAACT GATACAACGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand +17 : +24 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +24 : +17 CTAGCTAG AC RSP00640 Mean Expected Number 0.002 +strand -150 : -143 TCACGTGG AC RSP01296 Mean Expected Number 0.003 +strand -33 : -25 CTATAAATA Totally 4 motifs of 3 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 616. Group RE: G-box /Group TF: GBF /AC: RSP00640//OS: Zea mays /GENE: GRF1/RE: G-box /TF: GBF ||Identical REs AC: RSP00641 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0025F02.46|2943939..2945595 |SUPPORT| 1 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +42 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.11 T - 0.30 C - 0.22 1 aacttcggct aagtttagtt acaaactatt tctttaaact tccaattttt 51 ccatcacatc aaaacttttc tacacataaa ctttcaactt tttcatcaca 101 tcgttCCAAT ttcaactaaa cttttaattt taacgttaac taaacccacc 151 cttcaactcg atcTATAAAT Acatgctgcg ggcgcagcga caagatcacc 201 AGGTAGAACC AGAGAAAAAG AACATTAACG ATAAGTAAAG TAATGGAGAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.010 +strand -38 : -30 CTATAAATA AC RSP01301 Mean Expected Number 0.002 +strand -38 : -29 CTATAAATAC AC RSP01345 Mean Expected Number 0.001 +strand -59 : -49 AAACCCACCCT AC RSP01641 Mean Expected Number 0.004 -strand -6 : -15 TCTTGTCgCT Totally 4 motifs of 4 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1228. Group RE: IMH2 /AC: RSP01345//OS: Cucumis sativus /GENE: ms/RE: IMH2 /TF: unknown 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0008E01.37|complement(3014010..3017092) |SUPPORT| 2 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +66 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.18 T - 0.27 C - 0.22 1 agtttgttgt ctccgtctgg atatttctaa ccttgataag aataactaaa 51 ccctctagat tgattggacc gactagcgac gacgtcgaca aatttgataa 101 ataaattaag caaatttttt tgctccccca gtcccagatc gacgtcgatc 151 gtagtactag cgaaagTATA AATAacgcgt aatcctttgc acatagaagg 201 GGCATCCAAA CTAGCAACTT AATTAGGCAC CTAATTAACT CCGACGATCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00158 Mean Expected Number 0.007 -strand -85 : -95 aATTTGCTTAA AC RSP00231 Mean Expected Number 0.009 -strand -134 : -140 CCAATCA AC RSP00837 Mean Expected Number 0.004 +strand -65 : -56 AGATCGACGt AC RSP01724 Mean Expected Number 0.000 +strand -123 : -112 GACgACGTCGAC Totally 4 motifs of 4 different REs have been found Description of REs found 153. Group RE: D3 /AC: RSP00158//OS: Glycine max /GENE: GmAux28/RE: D3 /TF: unknown 224. Group RE: CCAAT box 1 /AC: RSP00231//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CCAAT box 1 /TF: unknown 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown 1532. Group TF: STF1/HY5 /AC: RSP01724//OS: Arabidopsis thaliana /GENE: NAC1 (At1g56010)/RE: C/A-box /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0046L23.18|3216923..3221257 |SUPPORT| 3 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.20 T - 0.31 C - 0.21 1 gctccaccct atcaatatca ctattggttt tgtgcatgaa ttaattacaa 51 tcttccattg gatgaaagtg agagaaagaa aaatcctatc gttgtgtctg 101 tttggaccac aagcgtatga cgattttttt ttgtaggaga actggaaaac 151 caagtgtgcc gtactcTATA AATAgtcttt gatcagtgtg gcgcatcgtt 201 TATCATCCAA AGATACAACG ACCGTGTCTT CTCGAGCTCT CTCCCTGACA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00235 Mean Expected Number 0.001 -strand -135 : -146 TTcATCCAATGG AC RSP00716 Mean Expected Number 0.002 -strand -169 : -177 CAAAACCAA AC RSP00860 Mean Expected Number 0.001 +strand -128 : -120 AGAAAGAAA AC RSP01000 Mean Expected Number 0.005 -strand -5 : -14 ATGCgCCACA AC RSP01296 Mean Expected Number 0.003 +strand -35 : -27 CTATAAATA AC RSP01708 Mean Expected Number 0.010 +strand -35 : -26 CTATAAATAG AC RSP01708 Mean Expected Number 0.010 -strand -26 : -35 CTATTTATAG Totally 7 motifs of 6 different REs have been found Description of REs found 228. Group TF: LFU; WUS /AC: RSP00235//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: LBS/WBS1 /TF: LFU; WUS 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0703B01.16|complement(3268601..3269228) |SUPPORT| 1 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +98 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.24 T - 0.22 C - 0.29 1 gtacgtcacc cgtggcgcgg tgacatggcc aagcttccgt gagagccaag 51 tagagtagta gagcgctcga gccgagcttg agccccatct ccttcccttg 101 tcatcttcca ggacgtcacc ttcacttcgc ttcgcctctg cttgcgtgcc 151 aagtctaaga cgagcctTAT AAATAggggg ccaatcctct caaactagct 201 TAATTACCAG CTAAAGCAAA CCAAGAGACG AGGTATATAT CTCGACGACG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00595 Mean Expected Number 0.001 +strand -3 : +6 GCTTAATTA AC RSP00683 Mean Expected Number 0.007 +strand -156 : -147 GCCAAGTaGA AC RSP00858 Mean Expected Number 0.004 -strand +8 : +1 GGTAATTA AC RSP00913 Mean Expected Number 0.003 +strand -182 : -173 GGTGACATGG AC RSP00913 Mean Expected Number 0.005 -strand -96 : -105 GATGACAaGG AC RSP01073 Mean Expected Number 0.001 -strand -57 : -65 CAAGCAGAG AC RSP01108 Mean Expected Number 0.009 -strand +6 : -1 TAATTAA AC RSP01280 Mean Expected Number 0.001 +strand -182 : -172 GGTGACaTGGC AC RSP01654 Mean Expected Number 0.010 -strand -81 : -90 GGTGACGTCC Totally 9 motifs of 8 different REs have been found Description of REs found 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 794. Group TF: DF1 /AC: RSP00858//OS: Pisum sativum /GENE: pra2/RE: GT2 /TF: DF1 844. Group TF: Opaque-2 /AC: RSP00913//OS: Zea mays /GENE: b-32/RE: B1 /TF: Opaque-2 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1026. Group RE: rAT-1 /AC: RSP01108//OS: Spinacia oleracea /GENE: rps22/RE: rAT-1 /TF: unknown 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0703B01.25|3306123..3308637 |SUPPORT| 5 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +32 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.26 T - 0.19 C - 0.24 1 tatgcacagg agatggaagc aaagcagacg gcgaaaatgc ggcacagcat 51 gaggcgctgg accaccgtat cctctcactg aaaacctcga gaacggaagg 101 tctcacacaa accaagatgg agatcgcttt aaatccacta gacatcacca 151 ttgcctttgc atctgcaTAT AAAGCagcag gtggccactg tgcaggctgc 201 ATAGCGAGAA GAAGCTAGGC TTTGTTGTCA ACATGGCAAG AGCTGTGCTT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00179 Mean Expected Number 0.009 +strand -73 : -67 TTTAAAT AC RSP00301 Mean Expected Number 0.008 -strand -40 : -46 TGCAAAG AC RSP01058 Mean Expected Number 0.004 -strand -61 : -68 TAGTGGAT Totally 3 motifs of 3 different REs have been found Description of REs found 173. Group RE: AT-rich motif /AC: RSP00179//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: AT-rich motif /TF: unknown 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 978. Group TF: GT-3a /AC: RSP01058//OS: Brassica napus /GENE: extA/RE: GT-3a Box III /TF: GT-3a ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0056I22.23|complement(3782796..3784248) |SUPPORT| 2 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +63 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.16 T - 0.28 C - 0.23 1 cacagtcaac ttgatacggc atgcaattct tccactcata aaaaaaatat 51 agaattaatt agatagatca cgatcaagtt gagtgtcaac gagctagagc 101 tctactgtca tcaactactc gatcgatcag gatcagcaaa acctagcttc 151 attgtgccTA TAAATAcgct tggtttgcat gccctgtctt ctcatcactt 201 ATCAGTCATC ACACATTGGC AGCTAATAGT AACAATTAAT CAGTAACGAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.005 +strand -43 : -35 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -43 : -34 CTATAAATAC Totally 2 motifs of 2 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0056I22.41-1|3826019..3826796 |SUPPORT| 2 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +103 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.18 T - 0.32 C - 0.25 1 gtttttggga aaaatttttg gggaattgaa cgggcccaga agttagtaga 51 tcttactatc ttagatcatt cgtctcatct gcccattgcg ccgtaacgta 101 cgtgtcgtct tctagctgca gccagtttca tgcttatcac cgcctatgac 151 tcagcttttc agcacTATAA ATAtgactct aacctcatac gtcacagatc 201 AGAGCACTAG CTAGCTAGCT AGCTTTTGCT CCTACATCTT CACTTCAGTA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.005 +strand -104 : -95 CGtACGTGTC AC RSP00070 Mean Expected Number 0.004 +strand -102 : -95 TACGTGTC AC RSP00072 Mean Expected Number 0.009 +strand -103 : -97 GTACGTG AC RSP00075 Mean Expected Number 0.003 +strand -103 : -94 GTACGTGtCG AC RSP00232 Mean Expected Number 0.006 +strand -12 : -3 ACGTCAcAGA AC RSP00337 Mean Expected Number 0.009 -strand -27 : -35 ATATTTATA AC RSP00503 Mean Expected Number 0.003 +strand +7 : +14 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 +strand +11 : +18 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 +strand +15 : +22 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +22 : +15 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +18 : +11 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +14 : +7 CTAGCTAG AC RSP00871 Mean Expected Number 0.008 -strand -46 : -55 GcTGAGTCAT AC RSP01296 Mean Expected Number 0.002 +strand -36 : -28 CTATAAATA Totally 14 motifs of 9 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 69. Group TF: TRAB1 /AC: RSP00070//OS: Oryza sativa /GENE: Osem/RE: ABRE motif A /TF: TRAB1 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 74. Group TF: TAF-1 /AC: RSP00075//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: Iwt /TF: TAF-1 225. Group RE: LS7 /Group TF: TGA2 & NPR1/NIM1 /AC: RSP00232//OS: Arabidopsis thaliana /GENE: PR-1/RE: LS7 /TF: TGA2 & NPR1/NIM1 323. Group TF: SEF1 /AC: RSP00337//OS: Glycine max /GENE: beta-conglicinin (7S globulin) alpha' and beta subunits genes/RE: SEF1 BS /TF: SEF1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 807. Group RE: GLM1 /AC: RSP00871//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM1 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBb0056I22.42|3829909..3830815 |SUPPORT| 2 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +108 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.19 T - 0.24 C - 0.31 1 tcaatggcta aatgccaagc atccatctcc ccaaccgcta acgttccatg 51 actccctgtc tgtgcacggg ccctacaccg ttgcaacacg cgtcaaactt 101 gctcgatctc ttgctcatct gcgtgcacct cgcgatctca taggactatg 151 agcaagcgtc gtcgccTATA AATAcgcttg gtatgcatgc attgcctctc 201 ATCAAACACT GCACTTCGCA GTGGTATTAG CAGCTACTAC AAAGAACAAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00143 Mean Expected Number 0.008 -strand -107 : -116 GACGCGTGTt AC RSP01044 Mean Expected Number 0.001 +strand -175 : -164 TCTCcCCAACCG AC RSP01236 Mean Expected Number 0.005 -strand -50 : -59 TCATAGTCcT AC RSP01296 Mean Expected Number 0.001 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -35 : -26 CTATAAATAC Totally 5 motifs of 5 different REs have been found Description of REs found 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 968. Group RE: box L /AC: RSP01044//OS: Petroselinum crispum /GENE: CCoAOMT/RE: box L /TF: unknown 1141. Group RE: 10 bp Z-BAC- /AC: RSP01236//OS: Phaseolus vulgaris /GENE: BAC/RE: 10 bp Z-BAC- /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0016G10.27|4182465..4185089 |SUPPORT| 3 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +130 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.25 C - 0.28 1 tcaaaattta ataataagtg ggctacgagt aacagcccgt acgcgcacgt 51 gtggtgtgtg tgcatgtgcg tataaggcat gcttaattta tgtacaaacc 101 tatttttata cctcgaggaa aaatgggaaa aaaaacacct gtcggccgga 151 agataaaaat tccaccTATA AACCcccctc ggccgttccc acctctcccc 201 TTCTTTTTCG CCACCCGATC CGGCAACAAC AACGTACGTA ACCTCCTCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00016 Mean Expected Number 0.008 -strand -135 : -141 CATGCAC AC RSP00049 Mean Expected Number 0.005 +strand -157 : -148 CGCACGTGTg AC RSP01152 Mean Expected Number 0.002 -strand -148 : -157 CACACGTGCg Totally 3 motifs of 3 different REs have been found Description of REs found 15. Group RE: RY /AC: RSP00016//OS: Glycine max /GENE: beta-conglycinin/RE: RY /TF: unknown 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 1067. Group TF: EmBP-1 (+VP1) /AC: RSP01152//OS: Zea mays /GENE: Em/RE: Em1b /TF: EmBP-1 (+VP1) ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1791_B03.42-1|complement(4752810..4758017) |SUPPORT|11 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +742 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.14 G - 0.27 T - 0.16 C - 0.42 1 ttcgggtagg aatccgcgtc cgcgcgcgga ccttctcgaa gaaagtcaaa 51 gcgcgccccg ctccacgtca cgtcggcccg ggtggggccc acgcccagat 101 ctaacccctg gtccgtccga tccccgcgaa gccgacggcc cggatccgac 151 ccgcggcctc acccccgccT ATAAATAccg cccgcgaggg cgtccgcccc 201 TCGCGCGTCA CAGTCTCGCA TCGCTTCGCT TCCCAGTTTC GGGTCTCTCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.003 -strand -26 : -31 TTTATA AC RSP00147 Mean Expected Number 0.003 +strand -31 : -26 TATAAA AC RSP00214 Mean Expected Number 0.007 -strand -131 : -138 TGACGTGG AC RSP00215 Mean Expected Number 0.007 +strand -138 : -131 CCACGTCA AC RSP00233 Mean Expected Number 0.006 +strand -139 : -130 TCcACGTCAC AC RSP00253 Mean Expected Number 0.005 +strand -190 : -183 AATCCGCG AC RSP00378 Mean Expected Number 0.002 -strand -151 : -157 TTTGACT AC RSP00471 Mean Expected Number 0.004 +strand -121 : -111 GgGTGGGGCCC AC RSP00695 Mean Expected Number 0.000 +strand -31 : -25 TATAAAT AC RSP01275 Mean Expected Number 0.004 +strand -139 : -130 TCCACGTCAc AC RSP01296 Mean Expected Number 0.000 +strand -32 : -24 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -32 : -23 CTATAAATAC AC RSP01505 Mean Expected Number 0.002 -strand -79 : -87 GATCGGACG Totally 13 motifs of 13 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 226. Group RE: LS5 /Group TF: TGA2 & NPR1/NIM1 /AC: RSP00233//OS: Arabidopsis thaliana /GENE: PR-1/RE: LS5 /TF: TGA2 & NPR1/NIM1 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 363. Group TF: WRKY1 /AC: RSP00378//OS: Petroselinum crispum /GENE: WRKY1/RE: WB /TF: WRKY1 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1791_B03.42-2|complement(4755509..4758016) |SUPPORT| 3 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +741 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.14 G - 0.27 T - 0.16 C - 0.42 1 tcgggtagga atccgcgtcc gcgcgcggac cttctcgaag aaagtcaaag 51 cgcgccccgc tccacgtcac gtcggcccgg gtggggccca cgcccagatc 101 taacccctgg tccgtccgat ccccgcgaag ccgacggccc ggatccgacc 151 cgcggcctca cccccgccTA TAAATAccgc ccgcgagggc gtccgcccct 201 CGCGCGTCAC AGTCTCGCAT CGCTTCGCTT CCCAGTTTCG GGTCTCTCGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.003 -strand -27 : -32 TTTATA AC RSP00147 Mean Expected Number 0.003 +strand -32 : -27 TATAAA AC RSP00214 Mean Expected Number 0.007 -strand -132 : -139 TGACGTGG AC RSP00215 Mean Expected Number 0.007 +strand -139 : -132 CCACGTCA AC RSP00233 Mean Expected Number 0.006 +strand -140 : -131 TCcACGTCAC AC RSP00253 Mean Expected Number 0.005 +strand -191 : -184 AATCCGCG AC RSP00378 Mean Expected Number 0.002 -strand -152 : -158 TTTGACT AC RSP00471 Mean Expected Number 0.004 +strand -122 : -112 GgGTGGGGCCC AC RSP00695 Mean Expected Number 0.000 +strand -32 : -26 TATAAAT AC RSP01275 Mean Expected Number 0.004 +strand -140 : -131 TCCACGTCAc AC RSP01296 Mean Expected Number 0.000 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -33 : -24 CTATAAATAC AC RSP01505 Mean Expected Number 0.002 -strand -80 : -88 GATCGGACG Totally 13 motifs of 13 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 226. Group RE: LS5 /Group TF: TGA2 & NPR1/NIM1 /AC: RSP00233//OS: Arabidopsis thaliana /GENE: PR-1/RE: LS5 /TF: TGA2 & NPR1/NIM1 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 363. Group TF: WRKY1 /AC: RSP00378//OS: Petroselinum crispum /GENE: WRKY1/RE: WB /TF: WRKY1 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1058_F07.19|complement(4946680..4947744) |SUPPORT| 2 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +49 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.21 C - 0.32 1 ttcggccacc atccaaccgg aacgtgcaga tgccggcgta cgtacgtgga 51 cgtcaacgca tttgaaccgg tcctcgtttg aacaatctcg cgcccaaagt 101 cagaccatgc atttgccggt cgttatcgAT TGTcctcaac tcctcatcca 151 tgcatcgcct gtcagctcTA TAAAGCcaca cgagccaccg gaagcttgac 201 ATCACAATTA AAGTCACAGC ATAGTAACCA ACCGAACCAA TCATCAGCCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00072 Mean Expected Number 0.007 +strand -159 : -153 GTACGTG AC RSP00349 Mean Expected Number 0.001 +strand -54 : -46 TCCATGCAT AC RSP00350 Mean Expected Number 0.002 +strand -56 : -46 CaTCCATGCAT AC RSP00628 Mean Expected Number 0.006 +strand -120 : -113 AACAATCT AC RSP01003 Mean Expected Number 0.006 +strand +4 : +13 ACAATTAAaG AC RSP01276 Mean Expected Number 0.001 +strand -159 : -152 GTACGTGG AC RSP01550 Mean Expected Number 0.000 +strand -158 : -147 TACGTGgACGTC AC RSP01639 Mean Expected Number 0.005 +strand -73 : -64 GATTGTCCTC AC RSP01734 Mean Expected Number 0.009 -strand -151 : -157 TCCACGT AC RSP01776 Mean Expected Number 0.002 +strand +4 : +14 ACAATTAAAGt Totally 10 motifs of 10 different REs have been found Description of REs found 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 334. Group TF: VP1 (VIVAPAROUS1) /AC: RSP00349//OS: Zea mays, Zea mays /GENE: C1/RE: Sph-core /TF: VP1 (VIVAPAROUS1) 335. Group RE: VP1 RE /AC: RSP00350//OS: Zea mays /GENE: C1/RE: VP1 RE /TF: unknown 604. Group TF: CCA1 /AC: RSP00628//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS1 /TF: CCA1 928. Group TF: DEF/GLO /AC: RSP01003//OS: Antirrhinum majus /GENE: DEFH125/RE: CArG1 /TF: DEF/GLO 1175. Group RE: Box III /AC: RSP01276//OS: Petroselinum crispum /GENE: CHS/RE: Box III /TF: unknown 1389. Group RE: ABRE3a/3b /AC: RSP01550//OS: Sorghum bicolor; Sorghum vulgare /GENE: Sbdhn2/RE: ABRE3a/3b /TF: unknown 1459. Group RE: ARE /AC: RSP01639//OS: Nicotiana tabacum /GENE: PR-Q; ACS2/RE: ARE /TF: unknown 1542. Group TF: CAMTA3 /AC: RSP01734//OS: Arabidopsis thaliana /GENE: CBF2/RE: CM4 /TF: CAMTA3 1575. Group TF: SIP1 /AC: RSP01776//OS: Lotus japonicus /GENE: AT-rich motif/RE: 39-bp element /TF: SIP1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1476_F05.33|5248878..5251911 |SUPPORT| 3 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +1602 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.25 T - 0.19 C - 0.37 1 aaaaaaggaa aactccgtgc acgcggtcca cagcccaccc cgggttcccc 51 ctgcccccac ggcggtggaa tcggcacgcg aggtgggccc cacatggcgg 101 cgcgggtcca gtgaaccacg cctttgcacg cgagacctcc tcccccgcgg 151 cctccaccac caccccacTA TAAATAcacg gcgaagggaa ggcctcccct 201 TCTCAGCCTC ATCTTTTGGT TGGTTTCGTT TTGGTATTCC CATACACTTT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00471 Mean Expected Number 0.008 -strand -106 : -116 aTGTGGGGCCC AC RSP00695 Mean Expected Number 0.002 +strand -32 : -26 TATAAAT AC RSP01296 Mean Expected Number 0.000 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.002 +strand -33 : -24 CTATAAATAC AC RSP01454 Mean Expected Number 0.006 -strand +24 : +18 ACCAACC Totally 5 motifs of 5 different REs have been found Description of REs found 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1325. Group RE: AC-II /Group TF: PtMYB4 /AC: RSP01454//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-II /TF: PtMYB4 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1372_D06.28|5894519..5896371 |SUPPORT| 1 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +71 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.19 T - 0.20 C - 0.36 1 tacgaccacg aacaggaggg ggacaaatca acaagcaaat cataggggtc 51 ccacatttca gaggtagcca aagattcact ggcaggtggg cccttcacac 101 tttgaaggaa tcaacaacga caccccccaa gtcatggatt ccttctcgct 151 ccctctccac gtcgccTATA AATCcgacgc ggccgctccc cactccaccc 201 ACAGCCCACA CTTCCATTGC TCCTCCCCTC TCCTCTACAG TCTGTGTTGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00079 Mean Expected Number 0.001 -strand -111 : -120 CCCACCTgCC AC RSP00189 Mean Expected Number 0.006 +strand -45 : -36 TCCACGTcGC AC RSP00303 Mean Expected Number 0.000 +strand -117 : -106 AGGTGGGCCCtT AC RSP00331 Mean Expected Number 0.005 -strand -60 : -68 GAATCCATG AC RSP00682 Mean Expected Number 0.005 -strand -36 : -45 GCgACGTGGA AC RSP00695 Mean Expected Number 0.008 +strand -34 : -28 TATAAAT AC RSP00986 Mean Expected Number 0.007 +strand -44 : -37 CCACGTCG AC RSP01301 Mean Expected Number 0.008 +strand -35 : -26 CTATAAATcC Totally 8 motifs of 8 different REs have been found Description of REs found 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 290. Group TF: PCF1; PCF2 /AC: RSP00303//OS: Oryza sativa /GENE: PCNA/RE: IIa /TF: PCF1; PCF2 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1234_B11.30|5983565..5986352 |SUPPORT| 7 exon(s)|Contig: NT_1071801.txt | -200:+51 from mRNA start|,5"-UTR: +636 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.26 T - 0.24 C - 0.30 1 ctagggtcag accgtcagag cgtttattct gcgggggacc ttactgggcc 51 tccctgtttg ggccctttca acgcgtaatg ggccggccca tttccgagct 101 actcagatca ggacttgtgt tacggcctcg ccacaaggat cggtgcacag 151 taagattccg cggtaataat AATAAATCtg tacggagtcg ctggcctcgc 201 CTCGCCTCGG CATCTTCTAC TGCTCGCCAT CGCACTCCAC CTCGGGTGAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00574 Mean Expected Number 0.003 -strand -170 : -177 CAGAATAA AC RSP01072 Mean Expected Number 0.003 -strand -122 : -131 ATTACGcGTT AC RSP01214 Mean Expected Number 0.007 +strand -148 : -139 CCTGTTTGGG Totally 3 motifs of 3 different REs have been found Description of REs found 550. Group RE: AT-rich K /AC: RSP00574//OS: Lycopersicon esculentum /GENE: rbcS1/RE: AT-rich K /TF: unknown 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1122. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01214//OS: Brassica oleracea /GENE: BoCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1548_F12.8|complement(154746..161381) |SUPPORT|11 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +47 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.21 T - 0.22 C - 0.31 1 ggatgtcata tcttaaattt tacaaaatta taatggcata gttccaattt 51 tcccaacaaa gaatctatgg atgctacgac actgacagtt ggggcccaat 101 ctctgctcac acatcgtccc ctctccccat cccaaaccgc agctctgtct 151 tccccaaacg acgcggaccg TATAAAACtc cgccgcgacg ccgagcacgc 201 GCGCCGGCTC TAGAAGCTTC TAGAAGGCGC AGCTGCAGCG CTGGCTAATG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00416 Mean Expected Number 0.007 -strand -128 : -134 CATCCAT AC RSP00887 Mean Expected Number 0.001 +strand -142 : -134 AAGAATCTA Totally 2 motifs of 2 different REs have been found Description of REs found 398. Group RE: Box-1 /AC: RSP00416//OS: Hordeum vulgare /GENE: EPB-1/RE: Box-1 /TF: unknown 819. Group TF: CCA1 /AC: RSP00887//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: CCA1 motif (1) /TF: CCA1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1548_F12.17|202347..203609 |SUPPORT| 3 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +148 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.16 T - 0.20 C - 0.39 1 caagagatca aagcgaagct agactgaatc actggacgga cagggagaca 51 ggttgcccgc ctctgtgcgc ccctgaaccc cgacaccctg cccccccccc 101 cccccctcgc accgattctt cctcatctcc tctcgctgtc ccaccaacac 151 cactgcacgt ctctgcataT ATAAACCtca tctcgttccc tacttgcaac 201 TAAAGTCATC GCCATCATCG ATCGATCGAT CACAACTACT AGAAATCCAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.007 -strand -27 : -33 TTATATA AC RSP00320 Mean Expected Number 0.002 +strand +13 : +23 cATCATCGATC Totally 2 motifs of 2 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1520_C09.26|complement(418056..419888) |SUPPORT| 5 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +122 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.24 T - 0.20 C - 0.35 1 atcctgaaga atggacgaac agtgagtcga caaggcgacg gcactccgtt 51 tcgcgcggtc gcagctgcgc ctcccccacc cctcacctgc tgaccaacct 101 acgctagcta tcttcctctt gtcgtcctcc tcctccgtcg catggcggcg 151 cgcggtttct gcaggTATAA ATAgcggccg tgtccagaca cgctagtctc 201 ACACCAACAT ACGGAGTTCG AGTGACATAC GAGCAGCAGC CAACACAAGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00114 Mean Expected Number 0.006 +strand -83 : -74 CTTGTCGTCc AC RSP00695 Mean Expected Number 0.004 +strand -35 : -29 TATAAAT Totally 2 motifs of 2 different REs have been found Description of REs found 112. Group RE: B2 /AC: RSP00114//OS: Glycine max /GENE: GmAux28/RE: B2 /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0016F11.25|618114..620403 |SUPPORT| 4 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +150 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.21 T - 0.24 C - 0.30 1 ctaaccatgt ttctatgccg gtgtagtgca gactggagca acggcgggcg 51 atcgcgccgc tgaattaatc ggattactaa ttgacagccc aatgattttg 101 cagctgcgcc tccctcacca acccacgacc cgctgaatat gttagccact 151 ccatggctga tgccgcacTA TAAATAagcc acacgccctc catgtatgcc 201 TCACTCGAGC TCGAACAATC TATATATTGT CAGAGACGCA CACTTTACTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00628 Mean Expected Number 0.005 +strand +14 : +21 AACAATCT AC RSP00698 Mean Expected Number 0.001 +strand -140 : -130 TGAATTAATCG AC RSP00763 Mean Expected Number 0.000 +strand -140 : -130 TGAATTAATCG AC RSP00950 Mean Expected Number 0.006 +strand -87 : -77 CTCACCAACCC AC RSP01016 Mean Expected Number 0.003 -strand -187 : -194 AGAAACAT AC RSP01083 Mean Expected Number 0.001 +strand -88 : -77 cCTCACCAACCC AC RSP01237 Mean Expected Number 0.002 +strand +18 : +27 aTCTATATAT AC RSP01296 Mean Expected Number 0.001 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.009 +strand -33 : -24 CTATAAATAa AC RSP01511 Mean Expected Number 0.004 -strand -35 : -42 GCGGCATC Totally 10 motifs of 10 different REs have been found Description of REs found 604. Group TF: CCA1 /AC: RSP00628//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS1 /TF: CCA1 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 724. Group RE: Box III /AC: RSP00763//OS: Brassica oleracea /GENE: SLG2/RE: Box III /TF: unknown ||Identical REs AC: RSP00768 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 941. Group TF: AEF /AC: RSP01016//OS: Arabidopsis thaliana /GENE: GapA/RE: AE box 1 /TF: AEF 1001. Group TF: DcMYB1 /AC: RSP01083//OS: Daucus carota /GENE: DcPAL1/RE: box-L5 /TF: DcMYB1 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1365. Group RE: OLS /AC: RSP01511//OS: Triticum aestivum /GENE: H1 (TH315)/RE: OLS /TF: unknown ||Identical REs AC: RSP01512 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0016F11.33|648011..650401 |SUPPORT| 3 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +113 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.19 T - 0.22 C - 0.39 1 ggagcctaga aagggagtcg catgcgttta ttatgttctt aacaaaaccg 51 tcgtccgagt cagccaatct cccctctgac gccgtgagcc ttagccctta 101 agctttgctt gccacagccc acagccacca cctcctcgtt ctctccgtct 151 cgtcgtctcc cctccctTAT AAAACacatc caacccatgc agccgccacc 201 GTACCCCGCA CTCCCGCCGC CGCCGTCGTC TACGTGAGCG ATCACGTCAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00092 Mean Expected Number 0.006 +strand -161 : -155 TAACAAA AC RSP00758 Mean Expected Number 0.004 -strand -165 : -171 ACATAAT AC RSP00916 Mean Expected Number 0.008 -strand +51 : +42 GATGACGTGA AC RSP00917 Mean Expected Number 0.008 -strand +51 : +42 GATGACGTGA AC RSP00997 Mean Expected Number 0.007 -strand +51 : +42 GATGACGTGA AC RSP01661 Mean Expected Number 0.000 -strand +51 : +40 gATGACGTGATC AC RSP01664 Mean Expected Number 0.000 -strand +51 : +40 GATGACGTgATC Totally 7 motifs of 7 different REs have been found Description of REs found 90. Group TF: GAmyb /AC: RSP00092//OS: Hordeum vulgare /GENE: Amy pHV19/RE: TAACAAA box /TF: GAmyb ||Identical REs AC: RSP00393 RSP01051 720. Group RE: submotif C /AC: RSP00758//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif C /TF: unknown 847. Group TF: Opaque-2 /AC: RSP00916//OS: Zea mays /GENE: b-32/RE: B4 /TF: Opaque-2 848. Group TF: Opaque-2 /AC: RSP00917//OS: Zea mays /GENE: b-32/RE: B5 /TF: Opaque-2 918. Group TF: Opaque-2 (O2) /AC: RSP00997//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-2 /TF: Opaque-2 (O2) 1479. Group TF: HY5 /AC: RSP01661//OS: Arabidopsis thaliana /GENE: CKX5/6 (At1g75450)/RE: C/G-box /TF: HY5 1482. Group TF: HY5 /AC: RSP01664//OS: Arabidopsis thaliana /GENE: ARR9 (At3g57040)/RE: C-box (2) /TF: HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OSJNBa0053L11.39|complement(743441..747640) |SUPPORT| 9 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +97 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.18 T - 0.27 C - 0.28 1 ttagatggac ccgcatgcgg actcctattt taagctcatg attttctaaa 51 aaataaaata tccaatcaaa atatcaacca gcgtcgctgg gttggacgac 101 aggagtaaaa gctagctatc gtcttttgat ccggccctga TCAATggatt 151 tccactctct cagctcggcc taTATAAAGC taacgagtac actccactcc 201 CACAGCCATC TCCTCTCTAC TGTCAATCTC AAGTGCGTGC CCGGTATCAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01210 Mean Expected Number 0.006 +strand -176 : -167 CTATTTTAAG AC RSP01480 Mean Expected Number 0.008 -strand -141 : -148 TATTTTAT Totally 2 motifs of 2 different REs have been found Description of REs found 1120. Group RE: EM2 /Group TF: MADS box TFs /AC: RSP01210//OS: Lepidium africanum /GENE: LaCRC/RE: EM2 /TF: MADS box TFs 1348. Group TF: AT-1SNBP /AC: RSP01480//OS: Glycine max /GENE: GS15/RE: AT-cm /TF: AT-1SNBP ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1136_C12.20-2|946121..948081 |SUPPORT| 5 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +42 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.22 T - 0.20 C - 0.23 1 ctaacaagca ctaatggagt attaaaaaag atctgagcat ggatgaggtc 51 aaagtccacc aataggatct gagcagtagc agtcattggt gggccagcac 101 ctcccatgca ttcctatcca cctcagctcc ctgACAATag acgcaagtat 151 ccagttcacT ATAAATGaag gcctccggct acgatctgca ggagaaaaaa 201 CAGTCAGAAG CTAAGGAAGA AAAAGTATAG ACACAGTGAT ACAATGGCCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00210 Mean Expected Number 0.000 +strand -84 : -73 tCCACCTCAGCT AC RSP00847 Mean Expected Number 0.006 +strand -83 : -74 CCACCTCAgC Totally 2 motifs of 2 different REs have been found Description of REs found 203. Group TF: MAT2 (ROM2) /AC: RSP00210//OS: French Phaseolus vulgaris /GENE: DLEC2/RE: DLEC2,B /TF: MAT2 (ROM2) 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1202_E07.33|complement(1081269..1082376) |SUPPORT| 2 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +109 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.13 T - 0.28 C - 0.35 1 aattgattag tttaagctgc aggttaatta gcaagtgagt cgtagtaagg 51 cagaggacgt tggccttctt attcaacgca gcattaacac gtttgctccc 101 ctcgaaccag acaccctacc ctacctgtcc tcctctcttc ttcctcctct 151 cctctccttc ctcctctTAT AAATCcacct cctccatctc aagttgcacc 201 GCTACTAGCA GCTAACCTAC CTACACTACA CTACACCACA CACTACACTT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00014 Mean Expected Number 0.004 +strand +11 : +21 gCTAACCTACC AC RSP00947 Mean Expected Number 0.005 +strand -179 : -173 GGTTAAT Totally 2 motifs of 2 different REs have been found Description of REs found 13. Group RE: MRE-core /AC: RSP00014//OS: Arabidopsis thaliana /GENE: CHS/RE: MRE-core /TF: unknown 876. Group TF: GT-2 /AC: RSP00947//OS: Oryza sativa /GENE: PHYA/RE: GT1-bx /TF: GT-2 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: OJ1136_C04.8|1216638..1222665 |SUPPORT| 7 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +261 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.21 T - 0.26 C - 0.25 1 agtacaattg aattggccgc tgcgttgtgt ggccgtaaca gaaaaaaaga 51 agaaaaaaaa agagagagcg acgccaccac ctgcccttgg ctatccgttc 101 ttctttctct ctccctcaac taaaacaagc taggaagaaa aagggagaaa 151 aaaagagggg ggaaatcCAT AAATCgccgc ttcttcttct tcatcttcct 201 TGTTGCTCCT CTTCGTCTTC CTCCGGCCTC CTATTGTAAT TGCTGCTTTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00355 Mean Expected Number 0.006 +strand -165 : -158 TAACAGAA AC RSP00445 Mean Expected Number 0.007 +strand -145 : -136 AAAAAAGAGA AC RSP00445 Mean Expected Number 0.007 +strand -52 : -43 AAAAAAGAGg AC RSP00653 Mean Expected Number 0.003 +strand -96 : -86 TTCTCTCTCCc AC RSP00865 Mean Expected Number 0.001 -strand -87 : -95 GGAGAGAGA Totally 5 motifs of 4 different REs have been found Description of REs found 340. Group RE: GARE2 /AC: RSP00355//OS: Oryza sativa /GENE: Rep-1/RE: GARE2 /TF: unknown 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 2 ( 8 contigs)|GENE: P0452F04.40|1449299..1450733 |SUPPORT| 1 exon(s)|Contig: NT_1071821.txt | -200:+51 from mRNA start|,5"-UTR: +80 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.24 T - 0.27 C - 0.14 1 ggagggtaca tctgcatgta aaattccctt gcatatttgc agtgatatac 51 aacaataaca tttgtatatt ttgagtctat tgtagaagtt ttcagagaga 101 attaagttag ccctaatact taatagatga gtagataatg aaccgagcaa 151 cagagcgagc taggtTATAA ATTgaagtgg ttaagccagt actccagttt 201 AATATGCGCG GACGCAGAAG TTCAGAAGAA GAAGAAGAAG CAGAGTGGCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00566 Mean Expected Number 0.007 +strand -174 : -165 CCTTGcATAT AC RSP00792 Mean Expected Number 0.005 +strand -58 : -49 CCgAGCAACA AC RSP01091 Mean Expected Number 0.003 -strand -121 : -131 ATAGAcTCAAA Totally 3 motifs of 3 different REs have been found Description of REs found 542. Group RE: TATA P /AC: RSP00566//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: TATA P /TF: unknown 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 1009. Group RE: box 1 /AC: RSP01091//OS: Pisum sativum /GENE: GS2/RE: box 1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0681F10.5|complement(144106..146040) |SUPPORT| 5 exon(s)|Contig: NT_0798722.txt | -200:+51 from mRNA start|,5"-UTR: +50 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.15 T - 0.24 C - 0.30 1 gaaatcgttg caatgctgtc tcaatttctc tcattaaaag aaaacaaaat 51 cgttgcaatg ccgtctcaat ttctctcaga aaaagggaaa aaagaaaaga 101 aaagaaaaaa gaaaattaca tttccagccc aacaccacga tctcccatct 151 ccttcctctc tcccgcTATA AAACgacggc atgtcgcgcc gtctcccgcc 201 TATCGCCGAT CGAAGCTTAC GAGCTATCTG CTCTTCTCTC TCTCTCCGCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.008 +strand -113 : -104 AAAAAAGAaA AC RSP00445 Mean Expected Number 0.008 +strand -96 : -87 AAAAAAGAaA AC RSP00863 Mean Expected Number 0.002 -strand -40 : -48 AGAGAGGAA AC RSP00864 Mean Expected Number 0.002 -strand +45 : +37 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +43 : +35 AGAGAGAGA AC RSP00865 Mean Expected Number 0.002 -strand +47 : +39 GGAGAGAGA AC RSP00989 Mean Expected Number 0.002 +strand -9 : -1 TCTCCCGCC Totally 7 motifs of 5 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 910. Group TF: E2F/DP /AC: RSP00989//OS: Zea mays /GENE: RBR3/RE: E2F/DP IV /TF: E2F/DP ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0680A03.13|complement(429487..433342) |SUPPORT| 4 exon(s)|Contig: NT_0798722.txt | -200:+51 from mRNA start|,5"-UTR: +63 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.27 T - 0.21 C - 0.35 1 gcaaggcaaa agcggggcgc ccccgttgcc gcggcgcgcg gcggcagggg 51 ggacatcccg cccgcggctg ggtcccccgc taccccgaca ccatgttcct 101 cctctgtctc tcgcgcgcgc cccactacta ctacacctcg tgcgtgtcag 151 cgccccacac ctgtatatat ataTATATAT Cgtcttgcat tgctctcgat 201 CGTGGATTGC AGAAGATGAT GCTGCAGTGA TCCCGTCCAC TAGCTGGTGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00471 Mean Expected Number 0.006 -strand -41 : -51 GTGTGGGGCgC AC RSP01237 Mean Expected Number 0.000 +strand -40 : -31 CTgTATATAT AC RSP01640 Mean Expected Number 0.004 +strand -99 : -90 CTcTGTCTCT Totally 3 motifs of 3 different REs have been found Description of REs found 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0680A03.22|complement(476097..477469) |SUPPORT| 1 exon(s)|Contig: NT_0798722.txt | -200:+51 from mRNA start|,5"-UTR: +171 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.17 T - 0.35 C - 0.24 1 tcgcaaagta atacccgatt ggacacattc tattacgaat ctggaccagt 51 attaggagaa agtattattt tgttaaccat tattaaaaaa aatcagtctc 101 ccaaagctgc cacctttgct ggttttcttg gtttgttcag tttgttgctt 151 gtgtgtcccc cagttgcaTA TAAACAtggg catgtcacac ctcacaaccc 201 CCCTTTGCTT TGGCCATTTT CTCAAGCACC TAATTTGCTT GGATCCTTCT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00735 Mean Expected Number 0.005 +strand -113 : -106 AAAAATCA AC RSP00792 Mean Expected Number 0.008 -strand -49 : -58 aCAAGCAACA AC RSP00872 Mean Expected Number 0.008 -strand -10 : -19 gGTGTGACAT Totally 3 motifs of 3 different REs have been found Description of REs found 698. Group TF: DET1; CCA1 /AC: RSP00735//OS: Arabidopsis thaliana /GENE: CAB2/RE: CCA1 BS /TF: DET1; CCA1 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0644B06.17|complement(309586..311093) |SUPPORT| 1 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +161 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.13 T - 0.29 C - 0.23 1 ggtagcagta ctgccgccat tgtgccaaaa accagctaat taaccatcgg 51 ttttcactaa tcaagcacaa tcatgctact aattaccctt ttcaacctat 101 aaatttatca cggtcagaTC AATttttcta attactttaa agataatata 151 atagtagtaa tcaacccTAT AAATAcacaa ggggtgcaac gaccatgcat 201 GTATAGCAAA AACACATTTC CAACATTCGG TCTTCACTAC TAGCTAGTAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.002 +strand -7 : +1 CATGCATG AC RSP00108 Mean Expected Number 0.002 -strand +1 : -7 CATGCATG AC RSP00350 Mean Expected Number 0.001 +strand -11 : -1 CGaCCATGCAT AC RSP00503 Mean Expected Number 0.002 +strand +40 : +47 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand +47 : +40 CTAGCTAG AC RSP00868 Mean Expected Number 0.009 -strand -48 : -59 TATTATATTATc AC RSP01296 Mean Expected Number 0.007 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.002 +strand -34 : -25 CTATAAATAC AC RSP01470 Mean Expected Number 0.007 +strand -8 : +2 cCATGCATGT Totally 9 motifs of 7 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 335. Group RE: VP1 RE /AC: RSP00350//OS: Zea mays /GENE: C1/RE: VP1 RE /TF: unknown 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0644B06.28|complement(357160..360491) |SUPPORT| 8 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +683 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.22 T - 0.34 C - 0.12 1 ttttttgaga actttgttaa cttttgtaga ggtctgatat atactctgat 51 agtgaaaaga gtgaagtatt atttaatgta cttttaattt aatgatgtcc 101 cagcagctta atttgagagt ttggcagaag tacgcatgaA TTGTatgtgt 151 caagtgatcg atggtTATAA ATAcggacac cgtgatggag tgatcgatct 201 AAAAATGCAG AGTATAAGTA CTACTCCTGT GGTAGTACAG TACAACACAG 251 T Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0644B06.51-2|439678..441734 |SUPPORT| 6 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +103 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.18 T - 0.33 C - 0.27 1 atcagaattc agagatcaac atcttttttt cttcaggacg aaaaaggcgt 51 acctgaaacg attctttggt caccccctgc gcctgcccgt ccagcatttt 101 gtgtcttgtc atcctcgcca cctcattctt tctttctttc atctccttcc 151 tctatcgatc gaaacccTAT AAATCtacct gaaactgact ttgttgttgt 201 ATCAAGGAGA CAGCTTAGCT TAGCTGTTGT TGTTGCAGTC CAGTCAGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.004 +strand -84 : -77 GCCACCTC AC RSP00444 Mean Expected Number 0.000 -strand -59 : -72 AtGAAAGAAAGAAA AC RSP00444 Mean Expected Number 0.000 -strand -63 : -76 AAGAAAGAAAGAAt AC RSP00860 Mean Expected Number 0.008 -strand -64 : -72 AGAAAGAAA Totally 4 motifs of 3 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 424. Group TF: Dof1 /AC: RSP00444//OS: Zea mays /GENE: cyPPDK1/RE: box d /TF: Dof1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0514G12.30|505635..508355 |SUPPORT| 6 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +34 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.22 T - 0.31 C - 0.14 1 gataatgact gttgaataaa tgtgtgatca tgcatgatat agtgcagtac 51 cctttttttt gtgtatgttt tggaggtggg ggctaaaaca gtcagtgtgt 101 atatcctgta tctgtcacac ctcttttttt ttaagaaaaa gaaaaaaaag 151 tgccatcaag taaaatgtcT ATAAATAgtc cattacaaga acaatgctgc 201 GGCGATATAG GTGGAAGAGG TACTGATCAT CTGAAACACC ATAATGTGGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.002 +strand -172 : -165 CATGCATG AC RSP00108 Mean Expected Number 0.002 -strand -165 : -172 CATGCATG AC RSP00445 Mean Expected Number 0.007 -strand -72 : -81 AAAAAAGAGg AC RSP00778 Mean Expected Number 0.005 +strand -188 : -179 TGAATAAATG AC RSP01296 Mean Expected Number 0.004 +strand -32 : -24 CTATAAATA AC RSP01470 Mean Expected Number 0.008 +strand -173 : -164 TCATGCATGa AC RSP01470 Mean Expected Number 0.009 -strand -164 : -173 TCATGCATGa Totally 7 motifs of 5 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 733. Group RE: Box III /AC: RSP00778//OS: Arabidopsis thaliana /GENE: AtS1/RE: Box III /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0514G12.31|509082..512953 |SUPPORT| 6 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.16 T - 0.24 C - 0.28 1 cttccatact gaagatattc cgatgtcatc agctaatact tgcccacccc 51 cctcaactcc aactcttgtg tttactcttc gtcacgtgtt gcgaaaacga 101 aacgaaatcg aaatcatcct tgcagatgcc atgagcacca tcaccatgca 151 tggcatatgg ctcccTATAA AACcatgaca ttaccaaaaa caaattgctc 201 AAACTAGGCC ACCGGATCAA ACTTTAGTTG AGAGCAAAGG AAAGGCCTCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -56 : -49 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -49 : -56 CATGCATG AC RSP00447 Mean Expected Number 0.009 +strand +33 : +42 AGCAAAGgAA AC RSP00524 Mean Expected Number 0.009 -strand -112 : -118 ACACGTG AC RSP00978 Mean Expected Number 0.002 +strand -120 : -111 gTCACGTGTT AC RSP01076 Mean Expected Number 0.003 +strand -56 : -47 CATGCaTGGC Totally 6 motifs of 5 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 500. Group TF: DPBF-1; DPBF-2 /AC: RSP00524//OS: Daucus carota /GENE: Dc3/RE: E4-core /TF: DPBF-1; DPBF-2 900. Group RE: G-box /AC: RSP00978//OS: Glycine max /GENE: vspA/RE: G-box /TF: unknown 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0029D06.25|658612..660801 |SUPPORT| 3 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +408 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.24 T - 0.29 C - 0.21 1 gaaaaaaaag aaaagaaaaa caataaaaca agaggcaatc tgcttctctc 51 actgtctcta tgcactagag gtagaggagc aattaagcct cgtgttgtga 101 ttggttggct ggttggttag ttggcgcttt tatcgtggtg cctgttggca 151 tgcctgaacc tgaagagTAT AAATTgactc ctggtagttt tgccattggt 201 AGATACAGCC CTTGACTCTG CTGCCTCTTC AGTTCAGGTA CTGCCCTCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00377 Mean Expected Number 0.006 -strand -95 : -104 AACCAATCaC AC RSP00445 Mean Expected Number 0.005 +strand -197 : -188 AAAAAAGAaA AC RSP00960 Mean Expected Number 0.007 -strand -78 : -85 CAACTAAC Totally 3 motifs of 3 different REs have been found Description of REs found 362. Group RE: LS5 /AC: RSP00377//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS5 /TF: unknown 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 885. Group TF: HvGAMYB /AC: RSP00960//OS: Hordeum vulgare /GENE: ITR1/RE: MYB BS /TF: HvGAMYB ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: OSJNBa0019F11.33|complement(895816..896662) |SUPPORT| 1 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +26 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.27 T - 0.22 C - 0.20 1 ttcttgcatg cagctgcagc tgcagaaaca gctcgtgatt agcagattgc 51 atttagtggg tgggctgtca aatcgatcac agtcacagaa accacatgtg 101 agcagaacaa gttcttaaca taggagagat gacataGCAA Tggaaatggc 151 gaattcgtga tgcacataTA TAAAGCtagc aacaggtata ggcgatgtgt 201 GTGCTTGACA GTGTACAGTG CAGACCATGG GTGGCGACGG CAAGCACACC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00642 Mean Expected Number 0.003 -strand -146 : -153 TAAATGCA AC RSP01076 Mean Expected Number 0.005 +strand +26 : +35 CATGgGTGGC AC RSP01237 Mean Expected Number 0.005 -strand -26 : -35 CTtTATATAT AC RSP01469 Mean Expected Number 0.010 -strand -100 : -109 TCACATGTGg Totally 4 motifs of 4 different REs have been found Description of REs found 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: OSJNBa0062J13.25|complement(966030..968833) |SUPPORT| 2 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +26 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.29 T - 0.22 C - 0.20 1 agctcgtgat tagcagattg cattagtggg tggactgtca attcgatcac 51 agtcacagaa acgacatgtg agcagaacaa gttcttcctc ctgcagagat 101 cgaacATTGG agagatgaca tagcggtgac aatggcgatt tggcgattgc 151 atcaacgtgt tgcacataTA TAAAGCtagc gacaagtata ggcgatgcgt 201 GTGCTTGACA GTGTACAGTG CAGACCATGG GTGGCGACGG CAAGCGCACC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00188 Mean Expected Number 0.003 +strand -49 : -40 TCAACGTGTt AC RSP01076 Mean Expected Number 0.006 +strand +26 : +35 CATGgGTGGC AC RSP01237 Mean Expected Number 0.004 -strand -26 : -35 CTtTATATAT AC RSP01692 Mean Expected Number 0.003 +strand -159 : -152 TTCGATCA Totally 4 motifs of 4 different REs have been found Description of REs found 182. Group TF: ABI5 /AC: RSP00188//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.2 /TF: ABI5 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1509. Group RE: CARE J /AC: RSP01692//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE J /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: OSJNBa0062J13.48|1042503..1043508 |SUPPORT| 1 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +118 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.14 T - 0.34 C - 0.19 1 gatgaatata gacaatgata gaatgattta tatcgtgaaa cagatgaagt 51 actatataga agtactccta tcaattatct ctcatttgaa tttcttatgc 101 tgtcttctat ctcaagctac ccttgcatcc gtcctcatcg gcacgaaagt 151 atattcttTA TAAACCttaa tctctactta aaccatttgg aaatgcttcg 201 ATATGATGGA GAGAGTAGCT TTCTTCAATT AATTAAACAA GTCGATCACA 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0425F02.32|1346195..1348560 |SUPPORT| 8 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +456 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.39 G - 0.18 T - 0.21 C - 0.22 1 atttaccata gcattacatt aattgcatat gttttacaaa acaaacaata 51 ttacagtata tgtaacagtt ggacccctac ctagcctagt ccctttcagt 101 caagacaact actggacagt aaaacacttg cacacagaga gagagagaga 151 gagagagaac gacttgcaga taTATAAATA ctcatggagc cacccaccct 201 CATTAACAAA GAATCCGTCC AGCCTTGAGA AGCAGAGAAG AGGAGAGAAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00488 Mean Expected Number 0.004 +strand -124 : -115 CTACcTAGCC AC RSP00864 Mean Expected Number 0.002 +strand -65 : -57 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -63 : -55 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -61 : -53 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -59 : -51 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -57 : -49 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -55 : -47 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -53 : -45 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -51 : -43 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 +strand -64 : -48 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -62 : -46 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -60 : -44 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -58 : -42 GAGAGAGAGAGAGAGAA AC RSP01757 Mean Expected Number 0.005 +strand -102 : -95 GTCAAGAC Totally 14 motifs of 4 different REs have been found Description of REs found 464. Group RE: UVLRE1 /AC: RSP00488//OS: Glycine max /GENE: chs1/RE: UVLRE1 /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1562. Group TF: B /AC: RSP01757//OS: Glycine max /GENE: a2/RE: BBS /TF: B ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0493C11.9|complement(1605232..1606369) |SUPPORT| 2 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.22 T - 0.19 C - 0.40 1 tttccccaat ccctcccaat cccccacctc cccgcggcga aaaggtccag 51 aagctcccag aatcggcatg cgcggatcgg cgcgccacgt gtacggccat 101 gattcatctc ccccggatcc cgatccgtgt gaggcttcct ccagCCAATc 151 gcggcgctcc gccctccggT ATAAACCgcg cgcctctcga atccgcacct 201 CGTCACGCAC ACAGCAGTTG AGCTCTTTTT CCACTACGCA CTAGTAGTAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00002 Mean Expected Number 0.001 -strand -109 : -117 ACACGTGGC AC RSP00065 Mean Expected Number 0.002 -strand -111 : -119 ACGTGGCGC AC RSP00175 Mean Expected Number 0.006 -strand -110 : -117 CACGTGGC AC RSP00204 Mean Expected Number 0.008 -strand -108 : -117 tACACGTGGC AC RSP00254 Mean Expected Number 0.003 -strand -156 : -162 CCTTTTC AC RSP00272 Mean Expected Number 0.002 -strand -69 : -79 TCACaCGGATC AC RSP00682 Mean Expected Number 0.005 +strand -117 : -108 GCCACGTGtA AC RSP00783 Mean Expected Number 0.000 -strand -108 : -117 TACACGTGGC AC RSP00836 Mean Expected Number 0.003 -strand -72 : -79 CACGGATC AC RSP00839 Mean Expected Number 0.006 +strand -130 : -123 CGCGGATC AC RSP01255 Mean Expected Number 0.005 -strand -109 : -116 ACACGTGG AC RSP01507 Mean Expected Number 0.003 +strand -79 : -72 GATCCGTG AC RSP01518 Mean Expected Number 0.000 +strand -79 : -52 GATCCGTG-- ** bp --CCAAT Totally 13 motifs of 13 different REs have been found Description of REs found 2. Group RE: ABRE-3 /AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /TF: unknown 64. Group TF: EmBP-1 /AC: RSP00065//OS: Triticum aestivum /GENE: Em/RE: Em1a /TF: EmBP-1 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 264. Group RE: Type II element /AC: RSP00272//OS: Nicotiana tabacum /GENE: artifical construction/RE: Type II element /TF: unknown 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 738. Group TF: G-box binding TF /AC: RSP00783//OS: Nicotiana tabacum /GENE: OLIGO-GUS/RE: G-box 7 /TF: G-box binding TF 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 784. Group RE: OCT /AC: RSP00839//OS: Arabidopsis thaliana /GENE: H4A748/RE: OCT /TF: unknown ||Identical REs AC: RSP00845 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 1369. Group RE: Type III element /AC: RSP01518//OS: Triticum aestivum /GENE: H2B (TH 153)/RE: Type III element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0493C11.22-2|1654454..1656120 |SUPPORT| 1 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +101 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.20 T - 0.22 C - 0.26 1 gtaaaaatca gcatcgtcgt tcgagcaaca agggaagaaa cacgcacata 51 cttctatgca accaaaggaa aaaaatgtac ggtcgtgatc tagggaacct 101 cccttaacca acggccgatg acacgattca ccatcgcaaa gccgaaagta 151 atacagcgaa atctcctTAT AAAGCagccg tgtttcgttt cggacaccac 201 ATGCATGCAC GCGCTTTTTG TTTATGGCTA CCATTTCCAA CGTTGTCACG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00103 Mean Expected Number 0.008 +strand -157 : -148 GCACATACtT AC RSP00108 Mean Expected Number 0.003 +strand -1 : +7 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand +7 : -1 CATGCATG AC RSP00350 Mean Expected Number 0.001 -strand +11 : +1 CGTgCATGCAT AC RSP01074 Mean Expected Number 0.001 +strand -2 : +8 ACATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand +8 : -2 GCATGCATGt Totally 6 motifs of 4 different REs have been found Description of REs found 101. Group RE: Z element /AC: RSP00103//OS: Agrobacterium tumefaciens /GENE: nos/RE: Z element /TF: unknown 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 335. Group RE: VP1 RE /AC: RSP00350//OS: Zea mays /GENE: C1/RE: VP1 RE /TF: unknown 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0679C08.28|1739295..1739920 |SUPPORT| 1 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +143 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.29 T - 0.22 C - 0.24 1 ggaggctcct ttttctattc ttttaataaa ttaatagata gatatatgtc 51 taggttaatt aatatcatgt gggaaatgct agaatgactt agagggagta 101 gaattcgtct ccgaattacg agtcggattc caacatgacg acgaagcggc 151 tgtgccactg ccgccgccTA TAAAGCcggg ggaggggggg gggggggggg 201 GGCACGCCAC TACGCCACGC GACCTCACCT AACCGCGCGC GCGCCCGCCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00044 Mean Expected Number 0.002 -strand +24 : +14 GGtCGCGTGGC AC RSP01021 Mean Expected Number 0.008 -strand -174 : -180 ATTAAAA AC RSP01108 Mean Expected Number 0.010 +strand -145 : -139 TAATTAA AC RSP01108 Mean Expected Number 0.009 -strand -140 : -146 TAATTAA Totally 4 motifs of 3 different REs have been found Description of REs found 43. Group TF: ASF1 /AC: RSP00044//OS: Triticum aestivum /GENE: H3/RE: hex3 /TF: ASF1 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 1026. Group RE: rAT-1 /AC: RSP01108//OS: Spinacia oleracea /GENE: rps22/RE: rAT-1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0535G04.1|complement(2114518..2115153) |SUPPORT| 1 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +177 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.25 T - 0.29 C - 0.18 1 ggtatttatt atctgaaaga atctggtgag ttttcatatg gatgcctacg 51 tggagacatg ttgtgtggcc aactggggtc caacctgcca atcatgcatt 101 gggccagcca tcaggctact tgttagtcga tcgatcgatc gccacgacaa 151 ttcaTATATA TCttatttac aaggagagag agaggaggaa tcaatcgata 201 ATTCGAGACA TATAGTGATC AATCATGCAT CTTCTGGTTG TTGGAAGCTA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00189 Mean Expected Number 0.004 -strand -147 : -156 TCCACGTAGg AC RSP00231 Mean Expected Number 0.010 +strand -113 : -107 CCAATCA AC RSP00280 Mean Expected Number 0.007 -strand -147 : -156 TCCACGTAGg AC RSP00653 Mean Expected Number 0.003 -strand -19 : -29 cTCTCTCTCCT AC RSP00864 Mean Expected Number 0.002 +strand -26 : -18 AGAGAGAGA AC RSP00865 Mean Expected Number 0.001 +strand -28 : -20 GGAGAGAGA AC RSP01192 Mean Expected Number 0.003 +strand -128 : -119 CTGGGGTCCA AC RSP01259 Mean Expected Number 0.003 +strand -155 : -148 CTACGTGG AC RSP01470 Mean Expected Number 0.009 +strand +23 : +32 TCATGCATcT AC RSP01642 Mean Expected Number 0.006 -strand -140 : -149 AcATGTCTCC Totally 10 motifs of 10 different REs have been found Description of REs found 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 224. Group RE: CCAAT box 1 /AC: RSP00231//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CCAAT box 1 /TF: unknown 271. Group TF: Opaque-1 /AC: RSP00280//OS: Zea mays /GENE: alpha-22kDa zein/RE: O2-box /TF: Opaque-1 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 1103. Group RE: D-box /Group TF: D factor /AC: RSP01192//OS: Nicotiana tabacum /GENE: Adh2/RE: D-box /TF: D factor 1161. Group TF: GBF1 /AC: RSP01259//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS6 /TF: GBF1 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) 1462. Group RE: ARE /AC: RSP01642//OS: Nicotiana tabacum /GENE: WIPK/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0535G04.15-1|complement(2161946..2163036) |SUPPORT| 3 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +165 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.19 T - 0.24 C - 0.39 1 tatcatcgtg aagcagatcg aggccggagg cggttgccgg caacggccac 51 acgcgcacac atggtttcgc cccaaaacca cgtcccccgc ccgccgctat 101 ctgcctccat cgtccactga ttccttcttc attccgctac atcgatctct 151 tgggtcttgg cttgcctgcc TATAAATTcg caggccccca tgcctctccc 201 CAATCCAATC CATCCATCTC CCTTGCTTGC CGCTACACTC GATCTACTCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00331 Mean Expected Number 0.004 -strand -133 : -141 GAAACCATG AC RSP00431 Mean Expected Number 0.007 +strand -175 : -164 GGaGGCGGTTGC AC RSP00695 Mean Expected Number 0.003 +strand -30 : -24 TATAAAT AC RSP00880 Mean Expected Number 0.007 +strand -160 : -151 CAACGGCcAC AC RSP01138 Mean Expected Number 0.000 -strand -117 : -128 GACGTGGTTTTG AC RSP01139 Mean Expected Number 0.001 -strand -118 : -126 ACGTGGTTT AC RSP01301 Mean Expected Number 0.003 +strand -31 : -22 CTATAAATtC Totally 7 motifs of 7 different REs have been found Description of REs found 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 411. Group TF: AtMYB77 /AC: RSP00431//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB77 BS /TF: AtMYB77 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 1056. Group RE: Region C /AC: RSP01138//OS: Zea mays /GENE: Adh1/RE: Region C /TF: unknown 1057. Group RE: Region B1 /AC: RSP01139//OS: Zea mays /GENE: Adh1/RE: Region B1 /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0535G04.32-2|complement(2224250..2225328) |SUPPORT| 2 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +1118 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.19 T - 0.26 C - 0.20 1 gagcagaaaa aacagagaat ttttctgaag agcatagaaa caaagcacta 51 atttttcata atttgacaaa aaaaaattac atcacttgct gacatctggg 101 tccctccagt tcagatgata gtacatcacc tgtatggagt atggaaaaat 151 gtggcctttc ttttcctggc cTATAAATGg tatccactac ttccaatcct 201 GCAAGCAACA AGAGAGGACA GGAGAAGAAA ACCTTGGCCC TTGAATAGTT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00857 Mean Expected Number 0.005 -strand -83 : -92 tCATCTGAAC AC RSP01058 Mean Expected Number 0.005 -strand -12 : -19 TAGTGGAT Totally 2 motifs of 2 different REs have been found Description of REs found 793. Group RE: NON /AC: RSP00857//OS: Zea mays /GENE: H4C7/RE: NON /TF: unknown 978. Group TF: GT-3a /AC: RSP01058//OS: Brassica napus /GENE: extA/RE: GT-3a Box III /TF: GT-3a ------------------------------------------------------------ > O.sativa (japonica), Chr 6 (17 contigs)|GENE: P0529C07.38|complement(2680543..2684285) |SUPPORT| 4 exon(s)|Contig: NT_1072302.txt | -200:+51 from mRNA start|,5"-UTR: +166 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.16 T - 0.37 C - 0.22 1 tctttttttt ttacattgct aaacttcttg gtatcttatt cataaccatt 51 tataggatat taattcctcg taaaattgtc tccctcgact tgccctgttg 101 tccacgttga ctcgagactt aATTGTaact gtgtactact acgagcttaa 151 tcagcacaac ccgTATAAAT Gattccgtga gctggttgat cgccttgatt 201 TATTTGCAGA TTAATTCCGA TCGAAATTAA AGTTGCATCG TCTCTGCAAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00280 Mean Expected Number 0.005 +strand -100 : -91 TCCACGTtGA AC RSP01604 Mean Expected Number 0.004 +strand -73 : -66 ACTGTGTA AC RSP01642 Mean Expected Number 0.006 +strand -127 : -118 AAtTGTCTCC Totally 3 motifs of 3 different REs have been found Description of REs found 271. Group TF: Opaque-1 /AC: RSP00280//OS: Zea mays /GENE: alpha-22kDa zein/RE: O2-box /TF: Opaque-1 1425. Group TF: SPF1 /AC: RSP01604//OS: Ipomoea batatas /GENE: Sporamin; beta-amylase/RE: SP8a /TF: SPF1 1462. Group RE: ARE /AC: RSP01642//OS: Nicotiana tabacum /GENE: WIPK/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: B1026C12.10|40953..42827 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +31 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.28 T - 0.27 C - 0.16 1 agaatctgtg ggattaaacc gtagtacttg ttaaataata agagacataa 51 ataacaaaaa aaaagaggga tcaacgaaac cgtgatggat tcggtggtac 101 gtgtgtactt ggtatggatt ccggttgggt gcgcgtcgAT TGAttcattt 151 gattggtagg tattaatgct aTATATATCg ccgccaccgc gtgcttcggt 201 TACATATGCA GCTGGAGTAG TAGCAGCTCC GATGGAGGCG ACGACGACTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00489 Mean Expected Number 0.001 -strand -39 : -48 TACCTACCAA AC RSP00651 Mean Expected Number 0.005 -strand -40 : -50 ACCTACCAAtC AC RSP00698 Mean Expected Number 0.002 -strand -54 : -64 TGAATcAATCG AC RSP01152 Mean Expected Number 0.004 -strand -96 : -105 CACACGTACC AC RSP01176 Mean Expected Number 0.002 -strand +28 : +18 AGCTGCTaCTA AC RSP01237 Mean Expected Number 0.003 +strand -32 : -23 CTaTATATAT AC RSP01640 Mean Expected Number 0.008 -strand -151 : -160 tTATGTCTCT Totally 7 motifs of 7 different REs have been found Description of REs found 465. Group RE: UVLRE2 /AC: RSP00489//OS: Glycine max /GENE: chs1/RE: UVLRE2 /TF: unknown 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 1067. Group TF: EmBP-1 (+VP1) /AC: RSP01152//OS: Zea mays /GENE: Em/RE: Em1b /TF: EmBP-1 (+VP1) 1087. Group TF: Zmhox1a /AC: RSP01176//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 3 /TF: Zmhox1a 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0617C02.113|complement(300466..301469) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +262 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.29 T - 0.22 C - 0.25 1 cgtgccgtgc cgggcctggg ccggctacag cactgccgtg ctcgggccgg 51 cccggcttgg cacggcccat ttggccaggt ataagtagag tcctaaaata 101 gtcgtaaaca ctggtcatgc agatgcagcc gtgcaggtga tgaggagcac 151 tagtacagta caggtaccAA TAAATCataa gtatagataa cgtagatcca 201 GTGACATTCA TTGATGAGGT TTGCGTTTCC AAGGCCATCT GCATCATCAG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00005 Mean Expected Number 0.008 +strand -108 : -99 CTAAAATAGT AC RSP00354 Mean Expected Number 0.004 +strand -13 : -6 TAACGTAG AC RSP00395 Mean Expected Number 0.006 +strand -13 : -4 TaACGTAGAT AC RSP01103 Mean Expected Number 0.003 -strand +22 : +15 AAACCTCA Totally 4 motifs of 4 different REs have been found Description of REs found 5. Group TF: AGL3; MADS-box TF /AC: RSP00005//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: CArG3 (AGL3) /TF: AGL3; MADS-box TF 339. Group RE: GARE1 /AC: RSP00354//OS: Oryza sativa /GENE: Rep-1/RE: GARE1 /TF: unknown 378. Group TF: Opaque-1 /AC: RSP00395//OS: Zea mays /GENE: gamma-27kDa zein/RE: O2-like-box /TF: Opaque-1 1021. Group RE: AC1 /AC: RSP01103//OS: Spinacia oleracea /GENE: rps22/RE: AC1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0617C02.132|381360..382076 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +7 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.28 C - 0.22 1 aagaaagcat gcatatcctc tgtttttaat gagctaccag catgtatatc 51 atctgtgtta taatgaggtg atctgcaccg gaaggagact ttaatcatcc 101 agaaggatat atacaactaa attaaatggt tggactcctc atgttgaaga 151 tatactagta cagtacTATA TATCgaaacc atccaacgag cagagcaggt 201 AACAGCAATG GCCATCATCT CCATTGCCGG CCATCTCCTT GCTCTCATCC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00011 Mean Expected Number 0.004 +strand -190 : -181 GCATATCCTC AC RSP00263 Mean Expected Number 0.001 +strand -21 : -13 CATCCAACG AC RSP00501 Mean Expected Number 0.007 +strand -14 : -8 CGAGCAG Totally 3 motifs of 3 different REs have been found Description of REs found 11. Group RE: C2b-BS /AC: RSP00011//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: C2b-BS /TF: unknown 255. Group RE: Non /AC: RSP00263//OS: Triticum aestivum /GENE: H3/RE: Non /TF: unknown ||Identical REs AC: RSP01563 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1123_C12.109|600622..601539 |SUPPORT| 3 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +106 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.16 T - 0.27 C - 0.25 1 ttgtagaggc ttaggctgct ggaataaaat aaaaagaaaa tcagaagatg 51 atgggccggg cctacccaga cagagttaaa gcccaaatcc atcgccacct 101 cttgtctctc aagagaaacg gctccaagtt cttttccttt ttctacttac 151 tattattatt atataatata TATAAATAat cctcacctac ccgacaatct 201 CTCTCCCACC CCACCCCTTT CTCGTTTCGT TGGAAGAAGA AGAAGAAGAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.003 +strand -107 : -100 GCCACCTC AC RSP00157 Mean Expected Number 0.003 +strand -35 : -24 ATaTATATAAAT AC RSP00157 Mean Expected Number 0.003 -strand -24 : -35 ATTTATATAtAT AC RSP00163 Mean Expected Number 0.002 +strand -103 : -93 CCTcTTGTCTC AC RSP00286 Mean Expected Number 0.003 +strand -20 : -10 cCTCACCTACC AC RSP00802 Mean Expected Number 0.000 -strand -24 : -43 ATtTATATATATTATATAAT AC RSP00865 Mean Expected Number 0.001 -strand +6 : -3 GGAGAGAGA AC RSP00868 Mean Expected Number 0.003 +strand -44 : -33 TATTATATaATA AC RSP00868 Mean Expected Number 0.003 -strand -33 : -44 TATTATATaATA AC RSP00950 Mean Expected Number 0.004 +strand -19 : -9 CTCACCtACCC AC RSP01641 Mean Expected Number 0.004 +strand -101 : -92 TCTTGTCTCT Totally 11 motifs of 9 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 158. Group TF: ARF1 /AC: RSP00163//OS: Glycine max /GENE: Synthetic OLIGO/RE: DR5 /TF: ARF1 277. Group RE: Box L /AC: RSP00286//OS: Petroselinum crispum /GENE: PAL-1/RE: Box L /TF: unknown ||Identical REs AC: RSP01754 755. Group TF: BABF /AC: RSP00802//OS: Solanum tuberosum /GENE: patatin 21/RE: Box A-1 /TF: BABF 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1138_B05.116|841903..842698 |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +84 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.29 T - 0.14 C - 0.30 1 aataaccctg gccgtcggag gtgaccgtgc gcggcgggaa ggaagtgaag 51 gcgcgaggta gaagacaacg cgacgtcgac ggatcgagac ctccttccat 101 ccacgtgcgc gctcctcttc ctccgccgcg tccacatcct ctcccacccc 151 cacttcgccT ATAAATCaag ctaagcttca cgagctccaa gagagaaaga 201 GAACGAGAGA CGAGAGACAT CGCCGGCGAA AGGAGAGGAG AGCAGAGAGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00654 Mean Expected Number 0.008 +strand -54 : -45 CcCCCACTTC AC RSP00695 Mean Expected Number 0.003 +strand -41 : -35 TATAAAT AC RSP00861 Mean Expected Number 0.002 +strand -7 : +2 AGAAAGAGA AC RSP01497 Mean Expected Number 0.008 +strand -190 : -181 GCCGTCGGAg AC RSP01640 Mean Expected Number 0.007 -strand +22 : +13 CgATGTCTCT AC RSP01734 Mean Expected Number 0.010 +strand -101 : -95 TCCACGT Totally 6 motifs of 6 different REs have been found Description of REs found 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown 1542. Group TF: CAMTA3 /AC: RSP01734//OS: Arabidopsis thaliana /GENE: CBF2/RE: CM4 /TF: CAMTA3 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0022B05.122|complement(1073938..1074575) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +76 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.15 T - 0.25 C - 0.26 1 tatcaactgc atggtcagaa aaggcgggtg ttcaactgag ccatgaatca 51 ttgagtcatg gctcgaagct ttgttcttca cgagttggaa tccaaagtcc 101 ataacctttg cctctacagt ctgcacatat ctttatcaga atgaacaagc 151 agacaagtct tgagaactct aTATAAACAg aaccccatat ctcatcttcc 201 ATCACCAACA ATCTCTCATC AAACCATTTG CAACACAATA CCAAACCAAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00521 Mean Expected Number 0.002 -strand -170 : -176 ACACCCG AC RSP00778 Mean Expected Number 0.004 -strand -143 : -152 TGACTCAATG Totally 2 motifs of 2 different REs have been found Description of REs found 497. Group TF: DPBF-1; DPBF-2 /AC: RSP00521//OS: Daucus carota /GENE: Dc3/RE: E1-core /TF: DPBF-1; DPBF-2 733. Group RE: Box III /AC: RSP00778//OS: Arabidopsis thaliana /GENE: AtS1/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.103|1274342..1277977 |SUPPORT| 3 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.16 T - 0.17 C - 0.43 1 acgcacatct ccctggtcaa cacggatccc ccgtcgcggt caacggacgc 51 gtctcgagag tccaccaccg agtccaacat actaatcccc agatccgacg 101 gcccggatcc ctcctccccT CAATccgagc cgtccatccc cctcttaacc 151 ccccccacga aagaaaaaaa aTATAAATCg aatttaagtc gaaaccccac 201 GCGTCCGCCG CTCCCACCAC CCTCGTCTCT CCCCTCCACT TCGCGAGACC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00044 Mean Expected Number 0.009 -strand +6 : -5 GGACGCGTGGg AC RSP00143 Mean Expected Number 0.003 +strand -155 : -146 GACGCGTcTC AC RSP00683 Mean Expected Number 0.009 -strand +44 : +35 GCgAAGTGGA AC RSP00695 Mean Expected Number 0.004 +strand -29 : -23 TATAAAT AC RSP00701 Mean Expected Number 0.009 +strand -99 : -92 CCCGGATC AC RSP00836 Mean Expected Number 0.005 +strand -180 : -173 CACGGATC AC RSP00933 Mean Expected Number 0.000 -strand -24 : -36 TTTATAtTTTTTT AC RSP01497 Mean Expected Number 0.000 -strand -99 : -108 GCCGTCGGAT AC RSP01507 Mean Expected Number 0.005 -strand -173 : -180 GATCCGTG Totally 9 motifs of 9 different REs have been found Description of REs found 43. Group TF: ASF1 /AC: RSP00044//OS: Triticum aestivum /GENE: H3/RE: hex3 /TF: ASF1 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 667. Group RE: Oct (d) /AC: RSP00701//OS: Triticum aestivum /GENE: H3/RE: Oct (d) /TF: unknown 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.110|1311971..1312726 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.27 C - 0.20 1 caattaataa aaagaaatga gagtgaggcc aggagagttt tattttatcc 51 taattaatcc gctctcgccg agcagagcca agcatcatgg ctacttgcca 101 agttgccatg caaATTGTag gattaataat cgatttattt tgctgacatc 151 ttgggagctc atctggcTAT AAATAtatac cttgatcgat cgcgagtaat 201 ATCGCATCAG CATTCAACGA ACACACACAC AATCGGAATC GATTAAGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00501 Mean Expected Number 0.008 +strand -132 : -126 CGAGCAG AC RSP00681 Mean Expected Number 0.003 +strand -150 : -142 TAATTAATC AC RSP00792 Mean Expected Number 0.009 +strand -123 : -114 CCAAGCAtCA AC RSP01296 Mean Expected Number 0.004 +strand -34 : -26 CTATAAATA Totally 4 motifs of 4 different REs have been found Description of REs found 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.111|complement(1315130..1316064) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.16 T - 0.36 C - 0.27 1 tttcccatga gtgctttgtt catgactttc tggtcttatc acctcttcag 51 ctcttctccc atttctttct cttaataatt agggaccagt ccgccgtatc 101 aacgtttacc gtttcttctt tgccatgtgc ttaattaagt ccatggctcg 151 atcgagagcc agcccgtcTA TAAATActgc cgaaattgca tgtattaatc 201 ATCACCTCTA CTAGCTAGCT ATAGCTCTAG TTCTACTCTA ATTGCGCAGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00212 Mean Expected Number 0.003 +strand -128 : -120 TAATAATTA AC RSP00503 Mean Expected Number 0.003 +strand +11 : +18 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +18 : +11 CTAGCTAG AC RSP00595 Mean Expected Number 0.002 +strand -72 : -64 GCTTAATTA AC RSP01296 Mean Expected Number 0.001 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -33 : -24 CTATAAATAC Totally 6 motifs of 5 different REs have been found Description of REs found 205. Group TF: ATHB-2 /AC: RSP00212//OS: Arabidopsis thaliana /GENE: ATHB-2/RE: ATHB-2 BE /TF: ATHB-2 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.123|1345124..1345879 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.27 C - 0.20 1 caattaataa aaagaaatga gagtgaggcc aggagagttt tattttatcc 51 taattaatcc gctctcgccg agcagagcca agcatcatgg ctacttgcca 101 agttgccatg caaATTGTag gattaataat cgatttattt tgctgacatc 151 ttgggagctc atctggcTAT AAATAtatac cttgatcgat cgcgagtaat 201 ATCGCATCAG CATTCAACGA ACACACACAC AATCGGAATC GATTAAGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00501 Mean Expected Number 0.008 +strand -132 : -126 CGAGCAG AC RSP00681 Mean Expected Number 0.003 +strand -150 : -142 TAATTAATC AC RSP00792 Mean Expected Number 0.009 +strand -123 : -114 CCAAGCAtCA AC RSP01296 Mean Expected Number 0.004 +strand -34 : -26 CTATAAATA Totally 4 motifs of 4 different REs have been found Description of REs found 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.124|complement(1348283..1349217) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.16 T - 0.36 C - 0.27 1 tttcccatga gtgctttgtt catgactttc tggtcttatc acctcttcag 51 ctcttctccc atttctttct cttaataatt agggaccagt ccgccgtatc 101 aacgtttacc gtttcttctt tgccatgtgc ttaattaagt ccatggctcg 151 atcgagagcc agcccgtcTA TAAATActgc cgaaattgca tgtattaatc 201 ATCACCTCTA CTAGCTAGCT ATAGCTCTAG TTCTACTCTA ATTGCGCAGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00212 Mean Expected Number 0.003 +strand -128 : -120 TAATAATTA AC RSP00503 Mean Expected Number 0.003 +strand +11 : +18 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +18 : +11 CTAGCTAG AC RSP00595 Mean Expected Number 0.002 +strand -72 : -64 GCTTAATTA AC RSP01296 Mean Expected Number 0.001 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -33 : -24 CTATAAATAC Totally 6 motifs of 5 different REs have been found Description of REs found 205. Group TF: ATHB-2 /AC: RSP00212//OS: Arabidopsis thaliana /GENE: ATHB-2/RE: ATHB-2 BE /TF: ATHB-2 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.136|1378277..1379032 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.27 C - 0.20 1 caattaataa aaagaaatga gagtgaggcc aggagagttt tattttatcc 51 taattaatcc gctctcgccg agcagagcca agcatcatgg ctacttgcca 101 agttgccatg caaATTGTag gattaataat cgatttattt tgctgacatc 151 ttgggagctc atctggcTAT AAATAtatac cttgatcgat cgcgagtaat 201 ATCGCATCAG CATTCAACGA ACACACACAC AATCGGAATC GATTAAGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00501 Mean Expected Number 0.008 +strand -132 : -126 CGAGCAG AC RSP00681 Mean Expected Number 0.003 +strand -150 : -142 TAATTAATC AC RSP00792 Mean Expected Number 0.009 +strand -123 : -114 CCAAGCAtCA AC RSP01296 Mean Expected Number 0.004 +strand -34 : -26 CTATAAATA Totally 4 motifs of 4 different REs have been found Description of REs found 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0474G09.137|complement(1381436..1382370) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.16 T - 0.36 C - 0.27 1 tttcccatga gtgctttgtt catgactttc tggtcttatc acctcttcag 51 ctcttctccc atttctttct cttaataatt agggaccagt ccgccgtatc 101 aacgtttacc gtttcttctt tgccatgtgc ttaattaagt ccatggctcg 151 atcgagagcc agcccgtcTA TAAATActgc cgaaattgca tgtattaatc 201 ATCACCTCTA CTAGCTAGCT ATAGCTCTAG TTCTACTCTA ATTGCGCAGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00212 Mean Expected Number 0.003 +strand -128 : -120 TAATAATTA AC RSP00503 Mean Expected Number 0.003 +strand +11 : +18 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +18 : +11 CTAGCTAG AC RSP00595 Mean Expected Number 0.002 +strand -72 : -64 GCTTAATTA AC RSP01296 Mean Expected Number 0.001 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -33 : -24 CTATAAATAC Totally 6 motifs of 5 different REs have been found Description of REs found 205. Group TF: ATHB-2 /AC: RSP00212//OS: Arabidopsis thaliana /GENE: ATHB-2/RE: ATHB-2 BE /TF: ATHB-2 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: B1249D05.19|1420907..1421627 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +70 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.27 C - 0.20 1 gtaattagta gcatcgaata tcgtacgtac gtgctacttg aaaaagatgt 51 ggaaattaat tggaaagttc atttgggcca cgtgccaaat acaaacagtG 101 CAATtaatta gccatggtat tgcatgcaat cttcgagcta atagatgagc 151 tacttgtgat ataacgacTA TAAATAcctg atcagcgagc aacacatatc 201 GATCAGCTAG CACAGCACAA TCGCTTTAGC TACCTTGAGA AACTCTTCTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00072 Mean Expected Number 0.009 +strand -174 : -168 GTACGTG AC RSP00073 Mean Expected Number 0.002 +strand -124 : -115 GCCACGTGcC AC RSP00073 Mean Expected Number 0.002 -strand -115 : -124 GgCACGTGGC AC RSP00103 Mean Expected Number 0.005 -strand -167 : -176 GCACgTACGT AC RSP00153 Mean Expected Number 0.002 -strand -116 : -125 gCACGTGGCC AC RSP00175 Mean Expected Number 0.001 -strand -117 : -124 CACGTGGC AC RSP00183 Mean Expected Number 0.000 +strand -124 : -115 GCCACGTGCC AC RSP00204 Mean Expected Number 0.002 -strand -115 : -124 GgCACGTGGC AC RSP00332 Mean Expected Number 0.006 +strand -87 : -80 ATGGTATT AC RSP00509 Mean Expected Number 0.002 +strand -32 : -21 TATAAATACCtG AC RSP01034 Mean Expected Number 0.007 -strand -118 : -124 ACGTGGC AC RSP01296 Mean Expected Number 0.004 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -33 : -24 CTATAAATAC Totally 13 motifs of 12 different REs have been found Description of REs found 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 72. Group TF: TAF-1 /AC: RSP00073//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: PA /TF: TAF-1 ||Identical REs AC: RSP00274 101. Group RE: Z element /AC: RSP00103//OS: Agrobacterium tumefaciens /GENE: nos/RE: Z element /TF: unknown 149. Group RE: Box II /AC: RSP00153//OS: Petroselinum crispum /GENE: CHS/RE: Box II /TF: CPRF-1; CPRF-2; CPRF-3; ||Identical REs AC: RSP00154 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 177. Group TF: G-box binding TF /AC: RSP00183//OS: Nicotiana tabacum /GENE: OLIGO-GUS/RE: G-box 10 /TF: G-box binding TF 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 318. Group TF: S1F /AC: RSP00332//OS: Spinacia oleracea /GENE: RPL21/RE: S1 /TF: S1F 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: B1249D05.20|1425515..1426370 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.16 T - 0.36 C - 0.27 1 tttcccatga gtgctttgtt catgactttc tggtcttatc acctcttcag 51 ctcttctccc atttctttct cttaataatt agggaccagt ccgccgtatc 101 aacgtttacc gtttcttctt tgccatgtgc ttaattaagt ccatggctcg 151 atcgagagcc agcccgtcTA TAAATActgc cgaaattgca tgtattaatc 201 ATCACCTCTA CTAGCTAGCT ATAGCTCTAG TTCTACTCTA ATTGCGCAGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00212 Mean Expected Number 0.003 +strand -128 : -120 TAATAATTA AC RSP00503 Mean Expected Number 0.003 +strand +11 : +18 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +18 : +11 CTAGCTAG AC RSP00595 Mean Expected Number 0.002 +strand -72 : -64 GCTTAATTA AC RSP01296 Mean Expected Number 0.001 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -33 : -24 CTATAAATAC Totally 6 motifs of 5 different REs have been found Description of REs found 205. Group TF: ATHB-2 /AC: RSP00212//OS: Arabidopsis thaliana /GENE: ATHB-2/RE: ATHB-2 BE /TF: ATHB-2 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0507H12.1|<1832923..1837040 |SUPPORT| 8 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +60 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.17 T - 0.36 C - 0.22 1 attgttatta gttaacttat acagttttgg agtttccata ttgatattag 51 tgtactattc cacaaagatg ataattttgt tccttttccc acagatatcc 101 aaatccgtct tcattttcat atgaacggcg ttttttctgc cctttcgagt 151 atgccctcca gcctcctgct tggTATAAAC Ctgaacatat agcattggag 201 AAACCTGAAC TTCCCCTTGG AGTTTCTGAG CTCAGGAAAT ATCGTGGACC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00270 Mean Expected Number 0.004 +strand -181 : -171 TACAgTTTTGG AC RSP00405 Mean Expected Number 0.005 +strand -175 : -168 TTTGGAGT Totally 2 motifs of 2 different REs have been found Description of REs found 262. Group TF: OBP1 /AC: RSP00270//OS: Arabidopsis thaliana /GENE: GST6/RE: OBP1 BS /TF: OBP1 387. Group RE: adjb /AC: RSP00405//OS: Nicotiana tabacum /GENE: RNP2/RE: adjb /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1351_C05.121|2165048..2165864 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.16 T - 0.27 C - 0.24 1 aagctgcaga atggcttttc agctacaaga aggtgagcta accaactcct 51 ttgaaattaa taacaaatta aaaccagagc cagctgactg ctaataccct 101 tgctttggcc aacaaCCAAT gtcaagtttg tcaactagta atcaactaat 151 cttgatcaga tcctccTATA AATTgacgag aaacatgcag tattcaaatc 201 ATCAAGCAGC TCCTGGTTTT GCAGCTCTAG CTATTGCCTA GCAAGCTACT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00385 Mean Expected Number 0.008 -strand -144 : -151 ATTTCAAA AC RSP01600 Mean Expected Number 0.007 -strand -145 : -152 TTTCAAAG Totally 2 motifs of 2 different REs have been found Description of REs found 370. Group RE: ERE-core /AC: RSP00385//OS: Dianthus caryophillus /GENE: GST1/RE: ERE-core /TF: unknown ||Identical REs AC: RSP00893 1421. Group RE: Inr /AC: RSP01600//OS: Spinacia oleracea /GENE: RPS22/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1351_C05.123|2167860..2168717 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +61 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.17 T - 0.29 C - 0.24 1 taggttcaat attttgcatc atgcagagaa tggctttcag ctgcaaaaga 51 aggtaagcta accaactcgt tgaaacaaat taaccagcta gcatctgata 101 cccttgtttt ggccaacaaC CAATgtcaag ttgtcaccta atcaatcaat 151 ctctatgatc agctcctcTA TAAATTgctg cgaaagatgc acatctttgc 201 ATCACCAATT GAGCAGCTCT CGTTTTGCAG TTCTAGCTAG CTAGCCACTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand +33 : +40 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 +strand +37 : +44 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +44 : +37 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +40 : +33 CTAGCTAG AC RSP00597 Mean Expected Number 0.002 -strand -117 : -128 GTTAATTTGTtT AC RSP00961 Mean Expected Number 0.004 +strand -159 : -152 TGCAAAAG AC RSP00987 Mean Expected Number 0.009 +strand -116 : -107 CAGCTAgCAT AC RSP01032 Mean Expected Number 0.005 -strand -89 : -98 CCAAAACAAG AC RSP01208 Mean Expected Number 0.000 +strand -100 : -89 CCCTTGTTTTGG AC RSP01209 Mean Expected Number 0.004 +strand -98 : -89 CTTGTTTTGG AC RSP01651 Mean Expected Number 0.001 +strand +19 : +27 CTCGTTTTG Totally 11 motifs of 8 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 573. Group RE: GT-1/16 JJ1 /AC: RSP00597//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: GT-1/16 JJ1 /TF: unknown 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 908. Group RE: H-box-like motif /AC: RSP00987//OS: Antirrhinum majus /GENE: CHS/RE: H-box-like motif /TF: unknown 957. Group TF: FLC /AC: RSP01032//OS: Arabidopsis thaliana /GENE: SOC1/RE: CArG box /TF: FLC 1118. Group TF: LFY /AC: RSP01208//OS: Arabidopsis thaliana /GENE: AtCRC/RE: CL3 /TF: LFY 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs 1470. Group TF: TaVRT2 /AC: RSP01651//OS: Triticum aestivum /GENE: TaVRN1/RE: CArG motif /TF: TaVRT2 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1351_C05.125|2172474..2173220 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +123 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.16 T - 0.29 C - 0.21 1 tctaatcata ggtgagctaa ccgaggaaga acaatgcaac atattgggcc 51 acctctatta ccacctgatg atctcttctt cctaaccaat aattaacaaa 101 tccttgcaga tggtttggaa ggtcaacaac cagtgtcaag atctgaccat 151 gcaattagct ttgtgagcTA TAAATGtatc catacattgc tttgcatcaa 201 ACAACACTGA ATTTATTGCA GTAGTTAATT AGAACACTGA ATATATTAGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.002 +strand -153 : -146 GCCACCTC AC RSP00333 Mean Expected Number 0.002 +strand -21 : -13 CCATACATT AC RSP00447 Mean Expected Number 0.004 -strand -5 : -14 tGCAAAGCAA Totally 3 motifs of 3 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 319. Group TF: S2F /AC: RSP00333//OS: Spinacia oleracea /GENE: RPL21/RE: S2 /TF: S2F 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1714_H10.115|3187067..3189965 |SUPPORT| 4 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +30 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.15 T - 0.22 C - 0.33 1 tcatcgctaa ccaccaacac ctaatcgtca ttatccgaga ctgttagatc 51 cccgggccca cacgtcagtc tcaccccgcg aaataatcta atcctttaaa 101 cagaaagtca aaagcgaacg cgaagaaacc gaacagatcc ctttcttcct 151 cacgactcct ggattttTAT AAATTacacc cccgaaagat ttcttctctc 201 ACAATCCAGT CCTCGAACTC GAACCCAGCC ATGGCGACCA AGCAGAGCCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00095 Mean Expected Number 0.001 -strand -140 : -148 GTGGGCCCG AC RSP00110 Mean Expected Number 0.009 +strand -142 : -135 CACACGTC AC RSP00157 Mean Expected Number 0.001 +strand -38 : -27 ATTTtTATAAAT AC RSP00157 Mean Expected Number 0.001 -strand -27 : -38 ATTTATAaAAAT AC RSP01073 Mean Expected Number 0.001 +strand +39 : +47 CAAGCAGAG AC RSP01258 Mean Expected Number 0.008 -strand -134 : -141 TGACGTGT Totally 6 motifs of 5 different REs have been found Description of REs found 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 108. Group RE: ACGT motif /AC: RSP00110//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: ACGT motif /TF: unknown 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0050F10.4|complement(3634070..3644978) |SUPPORT|24 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.16 T - 0.18 C - 0.30 1 taccaacgga aaccaaaata tgtatcttaa tgagaaaaga ttaggtctct 51 ctagccatac gagcatatcc aacgtcttaa aaagcctaaa accctgaaaa 101 accccagtcc aaattcaaaa cctgagacag gcgaaactaa actcctaaga 151 cacTATAAAA Cgcacataaa cgaagccgtg aaaacgaaag cgataaggtt 201 CATTCGAAGC GTCGCCACCC TCTCGTCTCC CCCTCCCGCC TCCGCCTCGC 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0050F10.18|3687854..3689761 |SUPPORT| 4 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +60 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.30 T - 0.27 C - 0.25 1 cgttgaccag atggggaaaa gtccgaccgg ccctgcaaat gtggggccca 51 ctggtcaccg ccgaatcggt gtcgttttgc acggcgtgtg ccacgtcagc 101 gttcgagtga gccaagaaac cgacaagccg acaagctgga gtgatcgagg 151 gagagttttc tgctttTATA AATTcgagcg tgtgcgggtt tcgttttctc 201 ACTCGCTTGC TTAGCTCGAT TGCTTTGCTC TGATCTGGTT GATCGATCTC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00113 Mean Expected Number 0.001 -strand -103 : -111 TGACGTGGC AC RSP00120 Mean Expected Number 0.000 -strand -124 : -137 AAACGACACCGaTT AC RSP00208 Mean Expected Number 0.000 +strand -111 : -100 GCCACGTCAGCg AC RSP00214 Mean Expected Number 0.003 -strand -103 : -110 TGACGTGG AC RSP00215 Mean Expected Number 0.003 +strand -110 : -103 CCACGTCA AC RSP00247 Mean Expected Number 0.006 +strand -111 : -102 GCCACGTcAG AC RSP00248 Mean Expected Number 0.007 +strand -111 : -102 GCCACGTCAG AC RSP00440 Mean Expected Number 0.000 -strand -177 : -185 GGACTTTTC AC RSP00447 Mean Expected Number 0.008 -strand +29 : +20 AGCAAAGCAA AC RSP00471 Mean Expected Number 0.004 +strand -162 : -152 aTGTGGGGCCC AC RSP00695 Mean Expected Number 0.006 +strand -34 : -28 TATAAAT AC RSP01280 Mean Expected Number 0.001 -strand -101 : -111 GcTGACGTGGC AC RSP01499 Mean Expected Number 0.006 -strand -183 : -192 TTCCCCaTCT AC RSP01656 Mean Expected Number 0.000 -strand -101 : -112 gCTGACGTGGCA Totally 14 motifs of 14 different REs have been found Description of REs found 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 118. Group RE: Box B /AC: RSP00120//OS: Pisum sativum /GENE: AS1/RE: Box B /TF: unknown 201. Group TF: MAT2 (ROM2) /AC: RSP00208//OS: French Phaseolus vulgaris /GENE: DLEC2/RE: DLEC2,A /TF: MAT2 (ROM2) 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 420. Group RE: -NF-kB-box /AC: RSP00440//OS: Arabidopsis thaliana /GENE: PR-1/RE: -NF-kB-box /TF: unknown 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 1474. Group TF: HY5 /AC: RSP01656//OS: Arabidopsis thaliana /GENE: ARF19 (At1g19220)/RE: C/G-box /TF: HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0534H07.20|complement(4017585..4019077) |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +49 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.46 G - 0.13 T - 0.18 C - 0.23 1 aaaacaaaac cccaaacccc tagtcaacct tgcaaaacca aaaaccaaaa 51 gaacaagaac aaaaaaaata tataattatt attatacaaa atattaaaat 101 aataataaaa aatATTGGtc gacgcggttt acactaaggc gatgcgtgtc 151 cgacgcattc gtgattcgcc tataTATAAA CCaaattcgg acgcaaactt 201 AATCACAAAA ACACAAACGC GACAACGCAG CAGCAAAACC GCGAGACACA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00143 Mean Expected Number 0.001 +strand -60 : -51 GAtGCGTGTC AC RSP00212 Mean Expected Number 0.005 -strand -120 : -128 TAATAATTA AC RSP00459 Mean Expected Number 0.004 -strand -174 : -183 TTGACTAGGg AC RSP00576 Mean Expected Number 0.000 +strand -134 : -115 aATATaTAATTATTATTATA AC RSP00949 Mean Expected Number 0.005 +strand -180 : -173 TAGTCAAC Totally 5 motifs of 5 different REs have been found Description of REs found 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 205. Group TF: ATHB-2 /AC: RSP00212//OS: Arabidopsis thaliana /GENE: ATHB-2/RE: ATHB-2 BE /TF: ATHB-2 437. Group TF: O2 /AC: RSP00459//OS: coix /GENE: alpha-coixin/RE: O2u /TF: O2 552. Group RE: AT-rich FF1 /AC: RSP00576//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: AT-rich FF1 /TF: unknown 878. Group RE: TAGTCAAC motif /AC: RSP00949//OS: Petroselinum crispum /GENE: 4CL-1/RE: TAGTCAAC motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1014_E09.37|4293843..4295737 |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +232 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.16 T - 0.18 C - 0.47 1 ctacccctgc acaatgacat ccaccgaggg gcaagcccgt catttcagct 51 gcgcccacgg agtccacttc cccctcctcc cccacaacgg cgacaatacc 101 gtgagccacc cgccgggccc acctgtcaac gtcccctcca cccactacgc 151 cacgtcaccc ccctcccgcc ttTATAAAAC ctcgcgaaca aactcctcgt 201 CGTCCCCCCT CCTCCTCGTC GTCGTCGTCT CACCCAACGA ACTTTTCCGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.008 +strand -30 : -25 TTTATA AC RSP00004 Mean Expected Number 0.009 -strand -23 : -28 TTTATA AC RSP00095 Mean Expected Number 0.005 -strand -79 : -87 GTGGGCCCG AC RSP00113 Mean Expected Number 0.002 -strand -44 : -52 TGACGTGGC AC RSP00147 Mean Expected Number 0.009 +strand -28 : -23 TATAAA AC RSP00147 Mean Expected Number 0.008 -strand -25 : -30 TATAAA AC RSP00303 Mean Expected Number 0.003 -strand -77 : -88 AGGTGGGCCCGg AC RSP00304 Mean Expected Number 0.006 -strand -73 : -80 TGACAGGT AC RSP00713 Mean Expected Number 0.008 -strand -150 : -156 CAGCTGA AC RSP01106 Mean Expected Number 0.002 +strand -54 : -44 ACGCCACGTCA AC RSP01280 Mean Expected Number 0.007 -strand -42 : -52 GGTGACGTGGC AC RSP01729 Mean Expected Number 0.001 -strand -42 : -53 GGTGACGTGGCG Totally 12 motifs of 10 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 290. Group TF: PCF1; PCF2 /AC: RSP00303//OS: Oryza sativa /GENE: PCNA/RE: IIa /TF: PCF1; PCF2 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 1024. Group RE: rHex /AC: RSP01106//OS: Spinacia oleracea /GENE: rps22/RE: rHex /TF: unknown 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1537. Group TF: STF1/HY5 /AC: RSP01729//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0506C07.2|complement(4562673..4564453) |SUPPORT| 3 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.21 T - 0.20 C - 0.29 1 atctttacac gcgtggcata tagcatgttc ttgcaaattt gaacactcga 51 ggccgcgaaa gttccagaag aaacgcgttc cactgcaaca cgcggacgag 101 cgtgacgacg tcagcgtcct cggaacgcaa gggcactccg gtaatttctc 151 caccccttct cttggccTAT AAATTgccac ctgcgccgcg gcgaaagaac 201 GCAATCTCAT CGCAAGAAAA GAAAAAAAAT CCTATTCAAA TCGAAACCCC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00243 Mean Expected Number 0.005 -strand -65 : -72 GTGCCCTT AC RSP01075 Mean Expected Number 0.007 +strand -193 : -184 CaCGCGTGGC AC RSP01076 Mean Expected Number 0.005 +strand -193 : -184 CAcGCGTGGC Totally 3 motifs of 3 different REs have been found Description of REs found 236. Group TF: MNF1; MNB1a; MNB1b /AC: RSP00243//OS: Zea mays /GENE: PEPC/RE: MNF1 BS core /TF: MNF1; MNB1a; MNB1b 993. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01075//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE II /TF: CpbZIP1; CpbZIP2 (short) 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0084L07.3|4685455..4687755 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +43 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.15 T - 0.22 C - 0.29 1 ttttatttta cgtgcgctaa aaaaatggat ccaaaagaga ggtgatagaa 51 cgacgcagcc tagtatgaaa atcacacatg ttaagtccat tccaagaaaG 101 CAATgtgtat agagatgcag cctcaaaaag ccccctgact ctccacactc 151 ttttcaccct ccttacttct cTATAAATAa ataatagtac cacctcgcta 201 ACCAAACACA CACCAACCCA ACCCGAGCCC CCCAAGCGCA GCCATGGTGT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00950 Mean Expected Number 0.009 +strand +9 : +19 CaCACCAACCC AC RSP01296 Mean Expected Number 0.003 +strand -30 : -22 CTATAAATA AC RSP01469 Mean Expected Number 0.010 -strand -118 : -127 TaACATGTGT Totally 3 motifs of 3 different REs have been found Description of REs found 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0084L07.5|complement(4691202..4700742) |SUPPORT|22 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +87 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.15 G - 0.22 T - 0.20 C - 0.43 1 gccgctcatc cgcaatcagc gcgcccgcgc cgcccactca ctcacagccg 51 gatgggcccg atcatccggc gcgagagtgg gtcccacctg tcagtgagtg 101 ccaccaaaag cgggccgatc ctttccaaaa atccctcgtg ggaccctcgg 151 cttgacccgc cccggcTATA AATAgccccg cctctctcct ctccttgtct 201 CATCAACCCT CTCTCTCTCT CTCTCTCTGC CTCGGCGACC TCGCCTCCGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.005 -strand -29 : -34 TTTATA AC RSP00018 Mean Expected Number 0.002 -strand -69 : -75 ATTTTTG AC RSP00147 Mean Expected Number 0.005 +strand -34 : -29 TATAAA AC RSP00304 Mean Expected Number 0.006 -strand -108 : -115 TGACAGGT AC RSP00339 Mean Expected Number 0.008 -strand -69 : -75 ATTTTTG AC RSP00695 Mean Expected Number 0.001 +strand -34 : -28 TATAAAT AC RSP00864 Mean Expected Number 0.003 -strand +28 : +20 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand +26 : +18 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand +24 : +16 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand +22 : +14 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand +20 : +12 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand +18 : +10 AGAGAGAGA AC RSP01115 Mean Expected Number 0.002 +strand -75 : -69 CAAAAAT AC RSP01283 Mean Expected Number 0.000 -strand +27 : +11 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 -strand +25 : +9 GAGAGAGAGAGAGAGAg AC RSP01296 Mean Expected Number 0.000 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -35 : -26 CTATAAATAg AC RSP01708 Mean Expected Number 0.000 +strand -35 : -26 CTATAAATAG AC RSP01708 Mean Expected Number 0.000 -strand -26 : -35 CTATTTATAG Totally 19 motifs of 12 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 324. Group TF: SEF4 /AC: RSP00339//OS: Glycine max /GENE: beta-conglicinin alfa'/RE: SEF4 BScons /TF: SEF4 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1116_C08.114|complement(6247141..6247886) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +49 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.10 T - 0.31 C - 0.22 1 gcatatcaat ccacttttac caactttagt ccatatgatg cccacattag 51 gcgtggatca caattaatat tttatatgta tacaaaacca caagttaatc 101 tattagctca tgaacagcta aaacttttat gtcccttctt aaatcacttt 151 agtctttata gctataTATA AAACcaccaa tagatgaaga ccttaaacct 201 ATCCCTCTCA TACAAATTCA GACTAAAGAT TTTCTGCAAA CAAAAAGCCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01597 Mean Expected Number 0.001 -strand -156 : -166 GTGGGCATCaT Totally 1 motifs of 1 different REs have been found Description of REs found 1418. Group RE: Box II* /AC: RSP01597//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box II* /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0668C05.111|6956228..6957482 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.11 T - 0.19 C - 0.43 1 taaaggtaaa aaaaaagcag atgaacatca accgagtaac cgacagagga 51 cagacagacg accgaatatg ccgctgcagt gcttcttcct cctcctccac 101 cctccccata tccacctcga ccccccctct ccttcccacg aatcttctcc 151 attcccacct ccctctaTAT ATATCtccct cccacccccg ccgccactca 201 CATCCAACAA CCCACCACCC TCATTCCCTC AAGTCCCAAG ATCGAACACC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00677 Mean Expected Number 0.007 +strand -125 : -120 GCAGTG AC RSP00935 Mean Expected Number 0.001 +strand -75 : -62 CCTCTCCTTCCCaC AC RSP01237 Mean Expected Number 0.002 +strand -38 : -29 CTCTATATAT AC RSP01237 Mean Expected Number 0.002 +strand -36 : -27 CTaTATATAT Totally 4 motifs of 3 different REs have been found Description of REs found 646. Group RE: Box 1 /AC: RSP00677//OS: Hordeum vulgare /GENE: Amy32b/RE: Box 1 /TF: unknown 864. Group RE: CT element /AC: RSP00935//OS: Pinus sylvestris /GENE: GS1a/RE: CT element /TF: unknown 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0016A21.125|complement(7212821..7216473) |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +139 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.21 T - 0.18 C - 0.40 1 tctttctctt tttacgaaag agaagaagaa aaaaaaaacc tggaagcaga 51 gggctggcgg cccgggccca caccacctgg ataccgaaac gccctcggga 101 cgatcccagc cgtcggatcc cgccttatcc gcccacgtgt gcgtatcgga 151 ttcacccaac cccctccTAT AAATAtcccg cccccccctc ctccacccca 201 CCTCTTCCTC CTCCTCGAGG CTCGAGCTGC CACCGCCATT GGAGCGCCAC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00095 Mean Expected Number 0.005 -strand -130 : -138 GTGGGCCCG AC RSP00337 Mean Expected Number 0.000 -strand -25 : -33 ATATTTATA AC RSP00445 Mean Expected Number 0.001 -strand -187 : -196 tAAAAAGAGA AC RSP00695 Mean Expected Number 0.003 +strand -33 : -27 TATAAAT AC RSP01255 Mean Expected Number 0.004 -strand -61 : -68 ACACGTGG AC RSP01296 Mean Expected Number 0.000 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.004 +strand -34 : -25 CTATAAATAt AC RSP01497 Mean Expected Number 0.006 +strand -92 : -83 GCCGTCGGAT AC RSP01688 Mean Expected Number 0.005 -strand -184 : -190 TCGTAAA Totally 9 motifs of 9 different REs have been found Description of REs found 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 323. Group TF: SEF1 /AC: RSP00337//OS: Glycine max /GENE: beta-conglicinin (7S globulin) alpha' and beta subunits genes/RE: SEF1 BS /TF: SEF1 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1506. Group RE: CARE F /AC: RSP01688//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE F /TF: unknown ||Identical REs AC: RSP01695 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0016A21.128-1|complement(7221404..7223418) |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +204 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.21 T - 0.21 C - 0.32 1 attacacctg ttttaatagt tgggggttaa gatatcggta tcgtggttca 51 gggaaacaaa tcagatccgg tcactagtta agggagtaaa agtaaactta 101 ttcgtagtga agcccagaag cgggagatca aggcccatct aggcccgaca 151 cgagagagcc aTATAAACCc caccattctc ccacccgcct cttccccacc 201 TGCCCTCCTC GCGAAAACCC TAACCCTCCT CCTCCTCCGC CGCCGCCGCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00279 Mean Expected Number 0.002 -strand +23 : +15 TTAGGGTTT AC RSP00369 Mean Expected Number 0.002 +strand +15 : +23 AAACCCTAA AC RSP01021 Mean Expected Number 0.007 -strand -184 : -190 ATTAAAA AC RSP01303 Mean Expected Number 0.004 +strand +14 : +23 aAAACCCTAA Totally 4 motifs of 4 different REs have been found Description of REs found 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0086N05.119|complement(7312503..7317546) |SUPPORT|11 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +135 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.23 G - 0.22 T - 0.29 C - 0.26 1 gacttgatca acaccgccgt gtgaatacca cgtcagctaa aaccacctcc 51 aaaatcttgt ttgcaccggt tttaatagtt ggaggagccg atatacccgg 101 ttttatggtt ggaggttata aatcgaggga tagttgaggg agtcaaagta 151 tacattttcc ttctaTATAA AGCgaattgt tgggcctccg tctcttctcc 201 CTCGTCCTCC GTCCCCTGCT CGTCCTCTTC GGCAAGCCGA CAAATCTGCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00208 Mean Expected Number 0.000 +strand -174 : -163 aCCACGTCAGCT AC RSP00214 Mean Expected Number 0.004 -strand -166 : -173 TGACGTGG AC RSP00215 Mean Expected Number 0.004 +strand -173 : -166 CCACGTCA AC RSP00248 Mean Expected Number 0.006 +strand -174 : -165 aCCACGTCAG AC RSP01082 Mean Expected Number 0.000 -strand -84 : -95 AAcCTCCAACCA AC RSP01138 Mean Expected Number 0.000 -strand -167 : -178 GACGTGGTaTTC Totally 6 motifs of 6 different REs have been found Description of REs found 201. Group TF: MAT2 (ROM2) /AC: RSP00208//OS: French Phaseolus vulgaris /GENE: DLEC2/RE: DLEC2,A /TF: MAT2 (ROM2) 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 1000. Group TF: DcMYB1 /AC: RSP01082//OS: Daucus carota /GENE: DcPAL1/RE: box-L4 /TF: DcMYB1 1056. Group RE: Region C /AC: RSP01138//OS: Zea mays /GENE: Adh1/RE: Region C /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0418E08.127|7930982..7933128 |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +609 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.22 T - 0.18 C - 0.34 1 cccactcttg gcagtggcag aatgtccgat ttctcgtctg agaacgaagc 51 ctggaaggag atatcctggg ccggaggcca ctactgacaa gccgagccca 101 tttaagccca cataatgaaa atcccagccc atatatcttg tgcgtttggg 151 cccagcccat aaaagcccaT ATAAACGtag cacgaagcca cgaacacgaa 201 GCAATCCATC CCCACTCCCC GATCCCCATC CCCTCCGGGC TCCGGCGGCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00234 Mean Expected Number 0.003 -strand -35 : -44 GCTTTTATGG AC RSP01004 Mean Expected Number 0.004 -strand -94 : -103 gCTTAAATGG AC RSP01071 Mean Expected Number 0.002 -strand -53 : -62 CAAACGcACA Totally 3 motifs of 3 different REs have been found Description of REs found 227. Group RE: CArG Box 2 /AC: RSP00234//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CArG Box 2 /TF: unknown 929. Group TF: DEF/GLO /AC: RSP01004//OS: Antirrhinum majus /GENE: DEFH125/RE: CArG2 /TF: DEF/GLO 989. Group TF: PvAlf /AC: RSP01071//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1c /TF: PvAlf ||Identical REs AC: RSP01153 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1341_A08.114|complement(8020965..8022801) |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +70 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.22 T - 0.31 C - 0.12 1 ctgtgtttag ttcacgctag tttggaaatt tggttgaaat tggtacgatg 51 tgatagaaaa attgtgtgtg tatgaaaggt ttgatgtgac aaaaagttgg 101 aagtttagaa aaaaacttta gaactaaaca gggcctagaa aatataagca 151 tgtacatgtt tcatcaTATA AAACgcccat taattgtcta ggctagcttg 201 AAGGCCAACA TTTGAACTTA CGTTCAATAG CTTTGATATA ACTAGGTGCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01003 Mean Expected Number 0.010 -strand -14 : -23 ACAATTAAtG Totally 1 motifs of 1 different REs have been found Description of REs found 928. Group TF: DEF/GLO /AC: RSP01003//OS: Antirrhinum majus /GENE: DEFH125/RE: CArG1 /TF: DEF/GLO ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0003K21.13|8179262..8180805 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +79 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.19 T - 0.16 C - 0.30 1 taaaagtaaa caccaaaacg agacaggaag atagaaatgc aacatttgtc 51 acacagggca cactcccctc tcctaaaacc aaggtcagcc catgctaatg 101 cagggcaggg aaagaacaag tccctgacca ctcatggaca ccatatgcat 151 gcagcggtga gaagcgtagT ATAAAACccc atccaacccc tccccatttc 201 TGCCTCAACC ACTACAACAC AAAAAGCGAG AGAGATCTCT CCCGAGCTCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01651 Mean Expected Number 0.004 -strand -179 : -187 CTCGTTTTG Totally 1 motifs of 1 different REs have been found Description of REs found 1470. Group TF: TaVRT2 /AC: RSP01651//OS: Triticum aestivum /GENE: TaVRN1/RE: CArG motif /TF: TaVRT2 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1001_C01.122|9995138..9997145 |SUPPORT| 2 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +87 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.24 T - 0.22 C - 0.19 1 gagataagtc ttctcttaat cggcagctgc cgaacgcagc cttaagatat 51 atcttataga tagatagata tatagataat agatagatac acaaaacagc 101 acacgtagat gttttgaaaa atctggcaac tgacaaacaa gcagtgggtc 151 atatatccag cgcactgcta TATAAACAcc ataagtgtgt gaggtggtct 201 GCAAAACAAA AGTGCGAGAC GTGCCAAGCA AGGCGGGCGG AGATCGATCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00152 Mean Expected Number 0.000 -strand -124 : -136 ATCTATATATCTA AC RSP01237 Mean Expected Number 0.008 -strand -124 : -133 aTCTATATAT AC RSP01260 Mean Expected Number 0.005 -strand -93 : -100 CTACGTGT Totally 3 motifs of 3 different REs have been found Description of REs found 148. Group RE: ATCTA element /AC: RSP00152//OS: Arabidopsis thaliana /GENE: psy/RE: ATCTA element /TF: unknown 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1162. Group TF: GBF1 /AC: RSP01260//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS7 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0002J01.12|10040618..10044414 |SUPPORT| 5 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +675 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.20 T - 0.31 C - 0.19 1 aagatattag taattactac ataaaaacga gcgtgtagcg tgcaatgggt 51 aattttcaca gatagcgtgt gtaacaaaag actatattcg gatatcctat 101 gttaacaaAT TGGttatcct ctcctcgcag ttcgcttaaa aattgtctca 151 gtttaagtta aattgataAA TAAATCattt agcgttacgt tacggagtct 201 CGGTTGGGCT TAAACAACAA GCGAGCCTTC GCACGCCTTC GTTGGCCGAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00421 Mean Expected Number 0.010 -strand +4 : -3 ACCGAGA Totally 1 motifs of 1 different REs have been found Description of REs found 402. Group RE: DRE1 /AC: RSP00421//OS: Zea mays /GENE: rab17/RE: DRE1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0438G07.127|11217772..11218494 |SUPPORT| 1 exon(s)|Contig: NT_0798792.txt | -200:+51 from mRNA start|,5"-UTR: +84 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.12 T - 0.26 C - 0.26 1 caatgcacca ttgctttcag ttgtctactt ttgacaaacc gtgcaaatat 51 atgctttact accggaacgc actaacttaa ttgatcagtg gctacagcga 101 aatatctcaa gaaaaaataa agctgctgct cgtcattttc accctcgcca 151 acagtaggtt cttcccTATA AATAatccac gcatcctgac caaagactac 201 ACAAATCACA CTAAATAATT ACTCAAACCA TCATCAGTAA CAACCAGATT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00501 Mean Expected Number 0.005 -strand -69 : -75 CGAGCAG AC RSP00652 Mean Expected Number 0.002 -strand -136 : -143 CCGGTAGT AC RSP00709 Mean Expected Number 0.008 -strand +21 : +13 TAATTATTT AC RSP01296 Mean Expected Number 0.006 +strand -35 : -27 CTATAAATA Totally 4 motifs of 4 different REs have been found Description of REs found 477. Group TF: EmBP-1 /AC: RSP00501//OS: Triticum aestivum /GENE: Em/RE: Em2 /TF: EmBP-1 626. Group TF: C1 /AC: RSP00652//OS: Zea mays /GENE: a1/RE: C1 DBS /TF: C1 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0680C01.6|16823..17801 |SUPPORT| 1 exon(s)|Contig: NT_0798902.txt | -200:+51 from mRNA start|,5"-UTR: +91 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.14 T - 0.29 C - 0.26 1 gtcaccattt tcattcccta aataggggca attgcaaatt taccactact 51 ttgaatcgtt attacaaaac tgccactaga aaattacaaa aatgccacta 101 gaactgtcat tcgagtggta tccttGCAAT attcaaaaaa accggtggca 151 aatttgcaaa tgcccctTAT AAATAttgcc aagctttcac tcactagagc 201 TATAGCATTT GCGTCCTCGC TCGATCGATA TCGGCCTCTA CCACCACTCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00058 Mean Expected Number 0.000 -strand -51 : -59 TGCCACCGG AC RSP00404 Mean Expected Number 0.009 +strand +8 : +14 TTTGCGT AC RSP00743 Mean Expected Number 0.002 -strand -153 : -164 tAGTGGTAAATT Totally 3 motifs of 3 different REs have been found Description of REs found 57. Group RE: CE1 /AC: RSP00058//OS: Hordeum vulgare /GENE: HVA22/RE: CE1 /TF: unknown 386. Group RE: adja /AC: RSP00404//OS: Nicotiana tabacum /GENE: RNP2/RE: adja /TF: unknown 705. Group RE: box 3 /Group TF: GT-1 /AC: RSP00743//OS: Nicotiana plumbaginifolia /GENE: Cab-E/RE: box 3 /TF: GT-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0492E07.120|504144..505060 |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +95 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.27 T - 0.16 C - 0.33 1 ctcgcaggcc gcagaacggc ccagtaagtt tactattctt tcgtgcaaat 51 caagaaacgg acgcgaaacc tgagagaaaa ctgcagtggg agacggaagc 101 aaattccggc acgcctccgc tccaagcggg ctcagacccg aacccggcaa 151 gcgcggcgtc gtcgtcgtgT ATAAAACggc ggccacgccg atcattcttc 201 GTTCCACCTC GCCTCGCATC CACCGTGAGC GGAGCGCCAA CTCGCTAGCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00613 Mean Expected Number 0.003 +strand -152 : -145 ATCAAGAA AC RSP01605 Mean Expected Number 0.003 +strand -170 : -164 TACTATT Totally 2 motifs of 2 different REs have been found Description of REs found 589. Group RE: UN Z1 /AC: RSP00613//OS: Lycopersicon esculentum /GENE: rbcS2/RE: UN Z1 /TF: unknown 1426. Group TF: SPF1 /AC: RSP01605//OS: Ipomoea batatas /GENE: Sporamin; beta-amylase/RE: SP8b /TF: SPF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0710F09.102|complement(553444..554401) |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +104 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.21 C - 0.37 1 ctagtttgtc ctatgcagcc gccctacgtc agccaagtcc aacgacaacg 51 cccaaacttc caggttttca tgaccctaca tgtcatagtc atttgtcgac 101 gcgcgggccc caccgcaccg tcctggaaaa ttcgtcgccc acagagccac 151 ccaaccctct cggggctcta TATAAACCcc gcgctaattt aatccgctgc 201 CTTCCTGGAA AGGGAATAAT CAAACACGCC CCGTCACTTC GCCGCACACA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.007 -strand -26 : -32 TTATATA AC RSP00460 Mean Expected Number 0.003 +strand -124 : -115 tACATGTCAT AC RSP01020 Mean Expected Number 0.008 -strand -130 : -136 ATGAAAA AC RSP01236 Mean Expected Number 0.005 +strand -118 : -109 TCATAGTCAT Totally 4 motifs of 4 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1141. Group RE: 10 bp Z-BAC- /AC: RSP01236//OS: Phaseolus vulgaris /GENE: BAC/RE: 10 bp Z-BAC- /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0710F09.106|complement(574017..575508) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +71 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.15 T - 0.31 C - 0.29 1 ttaatacttg gtcccatctg tcatacacac actgcatctt ggagtccgtg 51 ctacagctgg ttacaaatct gtagcccgct gcccatctct ctctttattt 101 atcttcttaa aatatgttta cagctggctt atagcatgct ATTGTacatg 151 ctcttagcga gctctaTATA AACCtcgcta cccgattcgc tgccttcctg 201 GAACCAATCA GCAGCTAAAA GTCAATCCAC GCCACCATCG ATCTCTCTAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00635 Mean Expected Number 0.003 +strand -191 : -184 GGTCCCAT AC RSP00837 Mean Expected Number 0.010 -strand +44 : +35 AGATCGAtGG AC RSP00864 Mean Expected Number 0.006 -strand -107 : -115 AGAGAGAGA AC RSP01509 Mean Expected Number 0.001 +strand +3 : +11 ACCAATCAG Totally 4 motifs of 4 different REs have been found Description of REs found 611. Group RE: NDE Box 3 /AC: RSP00635//OS: Glycine max /GENE: SAUR 15A/RE: NDE Box 3 /TF: unknown 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1364. Group RE: CCAAT box /AC: RSP01509//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CCAAT box /TF: unknown ||Identical REs AC: RSP01510 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0025D09.112|1051014..1053313 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +112 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.17 T - 0.22 C - 0.34 1 cacgtgctcc ctagccagtc tgtctagaag ccttttgcat atatatccag 51 ccgttaccga aactgcttgc atcaccgctg atatcatcgc ctccaccacc 101 cgcctctcag tctctttccg accacgcata tatgtatact ggaaggtcaa 151 accggccacg ggcgccgcTA TAAATAcaac tttcgcctca cctcgagtct 201 CATAACACAG ACACACACCA ACACAAGCGA GAGACAAGCA GTCTCAAGCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00535 Mean Expected Number 0.001 +strand -171 : -156 GCCT-- +6 bp --TATATA AC RSP00961 Mean Expected Number 0.003 -strand -162 : -169 TGCAAAAG AC RSP01057 Mean Expected Number 0.002 +strand -151 : -141 GCCGTTACCgA AC RSP01296 Mean Expected Number 0.001 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -33 : -24 CTATAAATAC AC RSP01641 Mean Expected Number 0.004 -strand +39 : +30 gCTTGTCTCT Totally 6 motifs of 6 different REs have been found Description of REs found 511. Group RE: LRE-TATA AA1 /AC: RSP00535//OS: Lycopersicon esculentum /GENE: rbcS3C/RE: LRE-TATA AA1 /TF: unknown 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 977. Group TF: GT-3a /AC: RSP01057//OS: Arabidopsis thaliana /GENE: rbcS-1a/RE: GT-3a Box III /TF: GT-3a 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1123_B01.104|complement(1081319..1082375) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.25 T - 0.25 C - 0.24 1 ataccgttta tttggtgctt ttcctgatgg atctgaatgg gctggtgggc 51 gcgaaagtta cacggatcaa cgacgaagaa aaggtggatc actagtgaca 101 tgctaacgtt gccgatgaag caaagggagc atcacacgcg tctaccgcca 151 gttggctctc catgtcTATA AATCtcctag cctctccctg ccatttctgc 201 AACACACCTA GCTACCACAG CTTGTGTACT GTCAAGAGTG AGTAGTAGAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00143 Mean Expected Number 0.007 -strand -59 : -68 GACGCGTGTg AC RSP00836 Mean Expected Number 0.004 +strand -140 : -133 CACGGATC AC RSP00880 Mean Expected Number 0.007 -strand -84 : -93 CAtCGGCAAC AC RSP01507 Mean Expected Number 0.004 -strand -133 : -140 GATCCGTG Totally 4 motifs of 4 different REs have been found Description of REs found 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1123_B01.110|1093500..1094587 |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.23 T - 0.27 C - 0.24 1 tgccttttat ttggtacttt ttcctgatgg atctgaattg gctggtgggc 51 gtgaaagtta cacggatcaa cgacgaagaa aaggtggatc actagtgaca 101 tgctaacgtt gccgatgaag caaagggagc atcacacgcg tctaccgcca 151 gttggctctc catgtcTATA AATCtcctag cctctccctg ccatttctgc 201 AACACACCTA ACTACCACAG CTTGTGAACT ATCAAGAGTG AGTAGTAGAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00143 Mean Expected Number 0.006 -strand -59 : -68 GACGCGTGTg AC RSP00836 Mean Expected Number 0.003 +strand -140 : -133 CACGGATC AC RSP00880 Mean Expected Number 0.006 -strand -84 : -93 CAtCGGCAAC AC RSP01507 Mean Expected Number 0.003 -strand -133 : -140 GATCCGTG Totally 4 motifs of 4 different REs have been found Description of REs found 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0684A03.102-1|complement(1163848..1167278) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +2223 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.20 T - 0.10 C - 0.34 1 gaacgcaaac gagagagaga gagaggcggt acacctaacc cgattaaccc 51 ggcgcatgaa catatcgtcg gttcctataa ccgaccgaag gggaaaaaaa 101 aaaagaaaga aaatccgaaa cgaaaccaag aaagcaaatc ctcctccctt 151 cccctcgccc ccgtcTATAA AACcgcgacc tatgctctca cgcgcggacc 201 ACACAAACGC AAGCGCAACG CAAACGCAGC AAGCGACGCC ACCCCCCACC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00422 Mean Expected Number 0.007 -strand -129 : -134 ACCGAC AC RSP00444 Mean Expected Number 0.000 +strand -102 : -89 AAaAAAGAAAGAAA AC RSP00860 Mean Expected Number 0.007 +strand -97 : -89 AGAAAGAAA AC RSP00864 Mean Expected Number 0.002 +strand -189 : -181 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -187 : -179 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -185 : -177 AGAGAGAGA Totally 6 motifs of 4 different REs have been found Description of REs found 403. Group RE: DRE2 /AC: RSP00422//OS: Zea mays /GENE: rab17/RE: DRE2 /TF: unknown ||Identical REs AC: RSP00951 RSP01036 RSP01548 RSP01564 424. Group TF: Dof1 /AC: RSP00444//OS: Zea mays /GENE: cyPPDK1/RE: box d /TF: Dof1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: B1157F01.6|2558369..2560285 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +72 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.19 T - 0.28 C - 0.25 1 gctcgccaaa ttagctagtc accatcacta tatcttcctc tatgtgtaat 51 atgtacttgc aataactaat aagaagattt gcctcctaat cagacaacta 101 attagcttga tctgacagcg tgcattctga cgagtcgtac gtgcatcctg 151 acacggcgtc gatcgttcga ataTATAAAC Acagctgcgc tctacgccaa 201 CAACTAACTG TCCGTGTGCG AGTTGCGACC TTGCTGGAAA ACTTGTACCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00038 Mean Expected Number 0.001 -strand -18 : -29 TGTGtTTATATA AC RSP00072 Mean Expected Number 0.009 +strand -64 : -58 GTACGTG AC RSP00960 Mean Expected Number 0.007 +strand +1 : +8 CAACTAAC Totally 3 motifs of 3 different REs have been found Description of REs found 37. Group TF: GT-1 related TFs /AC: RSP00038//OS: Lycopersicon esculentum /GENE: LAT52; LAT56;/RE: 52/56 box /TF: GT-1 related TFs 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 885. Group TF: HvGAMYB /AC: RSP00960//OS: Hordeum vulgare /GENE: ITR1/RE: MYB BS /TF: HvGAMYB ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0475E07.131|2928455..2929887 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +94 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.38 G - 0.12 T - 0.23 C - 0.27 1 taaatatcgt cgaaacaact atatcgttat attcaaacaa cacgcgttaa 51 tgccagggaa gctccagaga atgccaggga attgggtata ttatataacc 101 aattcaaatt tcgattaaaa TCAATgaaac ataaacccta gaacaaatcc 151 cagtaccact gaaaccccTA TAAATAtaca tcccaacaca accagcaaac 201 CACAACACTT GCAAACCTCT CTCAAGCAGC TTAGCTCCTG CCTCCTCCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.006 +strand -33 : -25 CTATAAATA Totally 1 motifs of 1 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0475E07.134|2946412..2947785 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +86 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.11 T - 0.25 C - 0.31 1 tacatactac atggttcaca ggcacacaca gctcatggga tttgctgtac 51 aataatgttg acagctatag ccaagatcac tacaaagttt ccaaaattaa 101 gaaaaccaaa ttaaaccatA CAATaagacc atcctcttgt tcttctcaca 151 aaacccttaa accccTATAA ATAcctcccc catggcaccc aagattccac 201 AACACAAACA CTTGCAACCC CCAAGCATTT CCGTTTCTTG CTCTCCTCCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00104 Mean Expected Number 0.006 -strand -187 : -193 CCATGTA AC RSP00304 Mean Expected Number 0.003 +strand -142 : -135 TGACAGCT AC RSP01233 Mean Expected Number 0.009 -strand +42 : +36 AGCAAGA AC RSP01296 Mean Expected Number 0.005 +strand -36 : -28 CTATAAATA AC RSP01301 Mean Expected Number 0.002 +strand -36 : -27 CTATAAATAC Totally 5 motifs of 5 different REs have been found Description of REs found 102. Group RE: RY1 /AC: RSP00104//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY1 /TF: unknown 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 1138. Group RE: PLE-79 /AC: RSP01233//OS: Collettrichum lindemuthianum (bean pathogen) /GENE: CLPG2/RE: PLE-79 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0062P14.116-1|complement(3171521..3174057) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +114 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.16 T - 0.17 C - 0.41 1 ccaaatccat acccaatcca cacccaccta gtagtccccg gctcccagct 51 gggtcgccgg agagtgttcc ctgtaaaacg cagtctagtc tactactgtg 101 cgcccctccg cccacggaAC AATccagaac gcaactcgga cttctagata 151 tttcaatccc ccaccggctT ATAAACCcac cccgtacaca atagggtatc 201 ATCATCACAC CATCACGAGC ACCACCACCA CTCACCACGC GCCACCCACC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00941 Mean Expected Number 0.002 +strand -50 : -43 TTTCAATC AC RSP01594 Mean Expected Number 0.002 -strand -43 : -50 GATTGAAA Totally 2 motifs of 2 different REs have been found Description of REs found 870. Group TF: GBF /AC: RSP00941//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box I /TF: GBF 1416. Group RE: Box I /AC: RSP01594//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box I /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0040K22.111|3599091..3602882 |SUPPORT| 6 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +315 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.14 G - 0.19 T - 0.40 C - 0.27 1 gagcctctgg atccaagcat ttttttttat ttccggagcc cctctttagt 51 ctttacttgc gtgaagaaaa tttctcctgc tcctcctctt cttttttatt 101 ttttattttt atttttcgtc ctcctttcgg ttcgtgctcg tgttcgtgcg 151 ttgatgcgct tgcgcgagag cgTATAAATC ctcgcggatt ttcggatttg 201 GAGGGATTCT TCTCCGCTTC CCCCGCCCTC AAATCGCACC CCGGATTTAC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00253 Mean Expected Number 0.003 -strand -11 : -18 AATCCGCG AC RSP00695 Mean Expected Number 0.006 +strand -28 : -22 TATAAAT Totally 2 motifs of 2 different REs have been found Description of REs found 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0571D04.111|complement(4731746..4735195) |SUPPORT| 5 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +160 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.19 T - 0.27 C - 0.27 1 aacaaatata actaatatcg gtaaggtcca catatcaacg actacttacg 51 gccgtattat atactaatgt tggcctaatg ttggtgaggc cccacatgtc 101 agcgactaac tcgcgaccgg cttgtgtagg aagcgaATTG Tggctatagc 151 aatgggctca ccccatttgc TATAAACAcg cacacgcact ctcaaccctc 201 TCTCTCTCTC TTCCGTTTGC TATATATTGG CACTTAATTA ACACAGTGGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.002 -strand +11 : +3 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +9 : +1 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +7 : -2 AGAGAGAGA AC RSP01000 Mean Expected Number 0.010 +strand -114 : -105 AgGCCCCACA AC RSP01149 Mean Expected Number 0.000 -strand -183 : -195 ATATTAGTTATAT Totally 5 motifs of 3 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 1065. Group RE: C-DP BS1 /AC: RSP01149//OS: Cucumis sativus/GENE: POR/RE: C-DP BS1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0477A12.38|complement(5811105..5816401) |SUPPORT| 8 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +134 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.20 T - 0.23 C - 0.31 1 cagaagggat caggtaaatt ttaggggtat gaaaaggatt gagtgagttt 51 tcaggggtac acggggaatt tactccattc caaaagcctc accacgcggc 101 ccagcgaatc cacagctcac atcatcacgc cccttttgcc aaaagaaaaa 151 aaaaaggaaa caaataAATA AATCtcgccc acctctctct ctctctctcc 201 CCTGGTCTCT CGCTCTCTTC GCTCGCGGCG GCTTCTCCGC CTCCGCCTCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00030 Mean Expected Number 0.008 -strand +33 : +27 AGCCGCC AC RSP00063 Mean Expected Number 0.009 -strand -101 : -110 GCCGCGTGGt AC RSP00254 Mean Expected Number 0.009 -strand -164 : -170 CCTTTTC AC RSP00260 Mean Expected Number 0.006 +strand -181 : -175 TTTAGGG AC RSP00864 Mean Expected Number 0.001 -strand -3 : -11 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand -5 : -13 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand -7 : -15 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand -9 : -17 AGAGAGAGA AC RSP00865 Mean Expected Number 0.002 -strand -1 : -9 GGAGAGAGA AC RSP00915 Mean Expected Number 0.009 -strand -75 : -84 GATGATGTGA AC RSP00916 Mean Expected Number 0.006 -strand -75 : -84 GATGATGTGA AC RSP00948 Mean Expected Number 0.009 +strand -188 : -182 GGTAAAT AC RSP01283 Mean Expected Number 0.000 -strand -2 : -18 GAGAGAGAGAGAGAGAg AC RSP01499 Mean Expected Number 0.004 -strand -133 : -142 TTCCCCGTgT Totally 14 motifs of 11 different REs have been found Description of REs found 29. Group TF: EREBP /AC: RSP00030//OS: Nicotiana sylvestris /GENE: OLP/RE: ERRE /TF: EREBP ||Identical REs AC: RSP00082 RSP01344 RSP01523 RSP01764 RSP01775 62. Group RE: Motif III /AC: RSP00063//OS: Oryza sativa /GENE: rab16B/RE: Motif III /TF: unknown 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 253. Group RE: RTBP1 BS /AC: RSP00260//OS: Oryza sativa /GENE: Synthetic OLIGO/RE: RTBP1 BS /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 847. Group TF: Opaque-2 /AC: RSP00916//OS: Zea mays /GENE: b-32/RE: B4 /TF: Opaque-2 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0055I24.107|6330784..6332149 |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +469 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.09 T - 0.28 C - 0.36 1 tttgaaacaa aaaatcagcc taaaattaca tttaaagttc tcataaattg 51 aaactaaaaa ataccacaag atcattcctg tttcggccca aatggcccaa 101 ctatttctga ccgtcctatc tacgatctaa tggttctgat cgccgtccct 151 aaccctagcc ccaTATAAAA Ccctgctctc cacccctcct ctctctctct 201 ATCTCTCCAC CCTCAGCCGC CACACTTCTC CCATCCATTC CCCTCTCCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00030 Mean Expected Number 0.008 +strand +15 : +21 AGCCGCC AC RSP00559 Mean Expected Number 0.003 -strand -171 : -181 TGTAATTTtAG AC RSP00735 Mean Expected Number 0.010 +strand -191 : -184 AAAAATCA AC RSP00864 Mean Expected Number 0.007 -strand -1 : -9 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand -3 : -11 AGAGAGAGA AC RSP00958 Mean Expected Number 0.010 +strand -170 : -164 TTTAAAG AC RSP01476 Mean Expected Number 0.003 +strand -170 : -163 TTTAAAGT Totally 7 motifs of 6 different REs have been found Description of REs found 29. Group TF: EREBP /AC: RSP00030//OS: Nicotiana sylvestris /GENE: OLP/RE: ERRE /TF: EREBP ||Identical REs AC: RSP00082 RSP01344 RSP01523 RSP01764 RSP01775 535. Group RE: 2'/Box II J1 /AC: RSP00559//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: 2'/Box II J1 /TF: unknown 698. Group TF: DET1; CCA1 /AC: RSP00735//OS: Arabidopsis thaliana /GENE: CAB2/RE: CCA1 BS /TF: DET1; CCA1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 884. Group TF: BPBF /AC: RSP00958//OS: Hordeum vulgare /GENE: Hor2/RE: PB2 /TF: BPBF 1344. Group RE: E motif /AC: RSP01476//OS: Oryza sativa /GENE: GluA-3/RE: E motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1112_F06.6|complement(6443286..6445422) |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +165 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.18 T - 0.22 C - 0.36 1 catcccacct gcgcacccag cccggtaatc tccaattatt ctccattctc 51 ccccacggtt taagatcatt ccgttcgcca tgttcaacga gcacgtaaga 101 acacacatgt acaccccagc tacgtacgta cgctcgctcg ctagctgcga 151 gcgatggatc ggcacagTAT AAATAgagcc ccagtttcat cagctttctc 201 AAACCACGCA GCCACGACAC ATCGATCTCC CATCTCCTTG TGCAGCCGCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.009 +strand -33 : -27 TATAAAT Totally 1 motifs of 1 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0409B11.26|complement(7042789..7043549) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +248 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.29 T - 0.20 C - 0.20 1 ggggacaagc cgagtctgaa gggggggaga atgttacgct gcctgtagca 51 gatatcgaca aaggcaatcc gctgagaagc tatcggcgtc ctacgcgggc 101 taagaaacct aatgtccgtg tgagtgggcc agaatgggtc acagtCCAAT 151 gatgttctgg tatggtgTAT AAATAccaga gggctaagag agaagagggt 201 GTCGAAAGTG TAAACACAAA ACACAAAACT ATTCCCCAAA TCAAACCTTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00509 Mean Expected Number 0.001 +strand -33 : -22 TATAAATACCAG AC RSP01301 Mean Expected Number 0.007 +strand -34 : -25 gTATAAATAC AC RSP01621 Mean Expected Number 0.010 -strand +12 : +3 TACACTTTcG Totally 3 motifs of 3 different REs have been found Description of REs found 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1441. Group TF: GmDof4; GmDof22 /AC: RSP01621//OS: Glycine max /GENE: Synthetic OLIGO/RE: E4 /TF: GmDof4; GmDof22 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0007H12.40|complement(8250557..8252949) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +56 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.25 T - 0.22 C - 0.28 1 taagcatcca tcgatccacc gctggatcaa ccgcagcgcg cgagagatcg 51 atcaacgtac gtaacgccat gcaccgtagc caccaagttc catgcatgca 101 ccgatgcacg agtgatcgag tgagtgatct gatcgagtaa taagttgcag 151 gtttctggac gccatcgctc ggTATAAATA cggcgttttc tgcaggcgaa 201 GCAGCCAAGG CATGCATGCA CATTCGCTCT AGCCTTCCTC ATCGTTGACA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.004 +strand -110 : -103 CATGCATG AC RSP00108 Mean Expected Number 0.004 +strand +11 : +18 CATGCATG AC RSP00108 Mean Expected Number 0.004 -strand +18 : +11 CATGCATG AC RSP00108 Mean Expected Number 0.004 -strand -103 : -110 CATGCATG AC RSP00349 Mean Expected Number 0.001 +strand -112 : -104 TCCATGCAT AC RSP00695 Mean Expected Number 0.010 +strand -28 : -22 TATAAAT AC RSP01074 Mean Expected Number 0.002 +strand -111 : -102 cCATGCATGC AC RSP01074 Mean Expected Number 0.002 +strand +10 : +19 GCATGCATGC AC RSP01074 Mean Expected Number 0.002 -strand +19 : +10 GCATGCATGC AC RSP01074 Mean Expected Number 0.002 -strand -102 : -111 GCATGCATGg AC RSP01301 Mean Expected Number 0.006 +strand -29 : -20 gTATAAATAC Totally 11 motifs of 5 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 334. Group TF: VP1 (VIVAPAROUS1) /AC: RSP00349//OS: Zea mays, Zea mays /GENE: C1/RE: Sph-core /TF: VP1 (VIVAPAROUS1) 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0681F05.128|complement(8349263..8350133) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +132 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.14 T - 0.25 C - 0.28 1 cctgagcatg tacacttaaa tatagttaat taaactagct agctcctccg 51 atcctcttaa tccatcttca taaaaattcg tgcaaaagca tacacggcat 101 gcactgttcg tccgtacgct gccgtctcat ttcgctttcg tagaacttgc 151 tccagcaaac aaaccctgcT ATAAATAtgt acaccatact cttcgtctcc 201 ACTGCAAGCA AAGCTAGAAA AACCAAGTGA AAACCTCAAA GCTAGGCACC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00447 Mean Expected Number 0.008 +strand +7 : +16 AGCAAAGCtA AC RSP00503 Mean Expected Number 0.003 +strand -166 : -159 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -159 : -166 CTAGCTAG AC RSP00879 Mean Expected Number 0.007 -strand -61 : -67 CGAAAGC AC RSP00961 Mean Expected Number 0.004 +strand -120 : -113 TGCAAAAG AC RSP01296 Mean Expected Number 0.004 +strand -32 : -24 CTATAAATA AC RSP01601 Mean Expected Number 0.004 -strand +32 : +25 TTTCACTT Totally 7 motifs of 6 different REs have been found Description of REs found 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 815. Group RE: D2 /Group TF: Dof family /AC: RSP00879//OS: Hordeum vulgare /GENE: Al21/RE: D2 /TF: Dof family 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0681F05.131-1|8362729..8364786 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +90 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.22 T - 0.24 C - 0.22 1 acatgattgt aatacacgac cctatccatg actccatgtg cctgtggttg 51 ccttgctgga atcaggtagc taaaaacttg gtgaaggagg caaaaaaaaa 101 aagaaactct acagtgaaag tcaaagcctc gtCCAATtgc atccagcttc 151 gagcaggcac ttggacaaaa ctTATAAATA gctctgccaa gcatgacaga 201 GCATATTCAT CGAGAGATCG AATTCGGTTC TCGTCTCGAT CATCAGTTTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01076 Mean Expected Number 0.005 -strand -6 : -15 CATGCtTGGC AC RSP01191 Mean Expected Number 0.002 -strand -154 : -161 CCACAGGC Totally 2 motifs of 2 different REs have been found Description of REs found 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1102. Group RE: A-box /Group TF: A factor /AC: RSP01191//OS: Nicotiana tabacum /GENE: Adhl/RE: A-box /TF: A factor ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0458H05.105|complement(8839748..8842053) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +64 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.21 T - 0.25 C - 0.33 1 atccttggtc gacctagccc ggcccagttg caaattaacc tgtatctcta 51 gttctctaca cagactacac aaggccacta ggtcgcaggc acgggacggg 101 acgcatgcac atccagaaac gaaatcacga gtccatgtct ccatgagcct 151 tgttgctcgc TATAAATTcc catcgcgctc gcgtcttcca gtatagtcgt 201 CGTCATATTT TACCCTGCTT TCCTCTGCCA CTCGATCGCC ACGGCTCGCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.009 +strand -40 : -34 TATAAAT AC RSP01301 Mean Expected Number 0.006 +strand -41 : -32 CTATAAATtC Totally 2 motifs of 2 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1582_D10.7|complement(9135661..9138757) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +132 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.28 T - 0.19 C - 0.35 1 cagtgttatt ggactctgta tgggccgtag gtgcagcccg tgggctgaca 51 cggcacggct cggcgtgtcg gtcggcccga ctgatatctt gccttggtcg 101 tgcccagacc gggccgtgta tagcggccca tttgatcatc tgtagcctga 151 agcccacatt gccacggccc AATAAATCgc gcgatgacga ctcgaccacc 201 GGAAACCCCC TCTCCGCATC CCACAGCCAC AAGCGGCGCC GCACCACTTC 251 G Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1582_D10.12|9149245..9150343 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +149 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.18 T - 0.18 C - 0.47 1 gcgcgctccc aaaaaaatcc aaacgaaacc gcctcctcct actcccgccg 51 cttccggatc gaaaaccccc ctcgcatccg ccgtccgtcc aaacgcatcc 101 gacggtccac gtccgcgatc cgcgtgatcg cctcccATTG Gctgccgccc 151 cgaacccccc cgaccccTAT ATATCccagc atctcagctc ttcccttccc 201 TAGTCTTCTC GCGCCACGCG AATCCACGCC GCCGCCGCCT CTTGACCTAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00097 Mean Expected Number 0.004 +strand -99 : -92 ACGGTCCA AC RSP00272 Mean Expected Number 0.001 -strand -74 : -84 TCACGCGGATC AC RSP00839 Mean Expected Number 0.004 -strand -77 : -84 CGCGGATC AC RSP01237 Mean Expected Number 0.000 +strand -36 : -27 CcCTATATAT Totally 4 motifs of 4 different REs have been found Description of REs found 95. Group RE: 9-mer box /AC: RSP00097//OS: Zea mays /GENE: GapC4/RE: 9-mer box /TF: unknown 264. Group RE: Type II element /AC: RSP00272//OS: Nicotiana tabacum /GENE: artifical construction/RE: Type II element /TF: unknown 784. Group RE: OCT /AC: RSP00839//OS: Arabidopsis thaliana /GENE: H4A748/RE: OCT /TF: unknown ||Identical REs AC: RSP00845 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1612_A04.113|complement(9232068..9233579) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.23 G - 0.22 T - 0.27 C - 0.28 1 ggtttgagga aatttgtttg aattgaaatt tataaaaaaa taatgaaaaa 51 attaaaacgg ggacactatt ttccctcatg ggccggcggc ctaggtcata 101 ctgggccgtc tggattaatg ggcccgaggg tagtatgttt gcttgctccc 151 ccacccctcc caTATAAAGC aagtagggtt cccgtctcgc tcgcctcctc 201 GATCGTCTTC TCCACCTGCG CCGCCGCAGC CTCCTCAACT CAACTCTCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01020 Mean Expected Number 0.009 +strand -158 : -152 ATGAAAA AC RSP01250 Mean Expected Number 0.008 -strand -170 : -179 AAAtTTCAAT Totally 2 motifs of 2 different REs have been found Description of REs found 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0406F06.10|complement(9970653..9972496) |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +785 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.28 T - 0.25 C - 0.25 1 gccctccacc taggacgtgg gctgcttggt gcggaagatt ccggcgaccc 51 agaaagcttt ggataccggc ggttgctacg attttctaga aacccccctc 101 gcggcgagat ttttctaggc aggttcgcct cgcgagcagc agcagcagaa 151 aaaaatggga gctcctaTAT AAACAagcgg tagaggtggc cagctgtttc 201 TATTTTTACC ACTTCATTCT CCATTCAGTT TGCTTAGCGA GTTAGGGGGG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.006 -strand -11 : -18 GCCACCTC AC RSP00146 Mean Expected Number 0.009 -strand -29 : -35 TTATATA AC RSP00629 Mean Expected Number 0.003 -strand -87 : -94 AAAAATCT AC RSP00821 Mean Expected Number 0.006 -strand -180 : -189 cCCACGTCCT Totally 4 motifs of 4 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0406F06.29|10033985..10035791 |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.15 T - 0.33 C - 0.18 1 tcccttagta ataggcacgt aaatactctt ttctactgta aaaacataaa 51 aatatgttta tatgccaaga aaaatgcttc aattttagtt gtattatgat 101 gtaaactttt tatgaataat tatcacttat ttagtttaaa tcctggATTG 151 Cagtattgca ccgtcttgac aTATAAATAc tgaagtaccc ctagcaagtt 201 CCATCGATCG TGAGGAAGAT CAGTAGAGAG CGCACTCAAC TTCGCCAAAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00572 Mean Expected Number 0.009 -strand -27 : -34 ATATGTCA AC RSP01757 Mean Expected Number 0.002 -strand -31 : -38 GTCAAGAC Totally 2 motifs of 2 different REs have been found Description of REs found 548. Group RE: 3'/AT-rich J1 /AC: RSP00572//OS: Lycopersicon esculentum /GENE: rbcS1/RE: 3'/AT-rich J1 /TF: unknown 1562. Group TF: B /AC: RSP01757//OS: Glycine max /GENE: a2/RE: BBS /TF: B ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1773_H01.131|complement(10333575..10334613) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +252 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.16 T - 0.25 C - 0.29 1 tctgatcttt ggattgataa tactactcaa agcgaaatct gactattaaa 51 ataacaaatt tccccgcccg gggactgtgc gcggataact tactcagtac 101 tttcatgtca taattaaaat gttcccatgc gcgcgcgatg cgaccatgac 151 caccccgaac ccaatccttT ATAAACGcat gcatgccggc ccatcccctc 201 ATCCACATAT CAGGCATCAC AATTCACAAA CTAACTCGTA GCGATCGATC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -23 : -16 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -16 : -23 CATGCATG AC RSP01074 Mean Expected Number 0.001 +strand -24 : -15 GCATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand -15 : -24 GCATGCATGC Totally 4 motifs of 2 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1301_C12.3|11141696..11143756 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.27 T - 0.18 C - 0.35 1 tcggccacca cgtccaattc ccggcggcta tgcaacggcc ggggacaggt 51 catacctggg cccaccttac cagaggctgt caagatgggc ccacacgcca 101 ttcggATTGT agtcggaggg ctcggaggtg atccgaccct gctgcctcct 151 cgcctcgcgc cgtcTATAAA TGctggccga tttccactga ctcctctgcc 201 ACACAGAAGG CGAGCTCTCG ACCGCCACTA CTGTACACGG CCCAGAGCGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00460 Mean Expected Number 0.002 +strand -157 : -148 GACAgGTCAT AC RSP00695 Mean Expected Number 0.002 +strand -36 : -30 TATAAAT AC RSP01301 Mean Expected Number 0.002 +strand -37 : -28 CTATAAATgC AC RSP01351 Mean Expected Number 0.009 +strand -145 : -135 CTGGGCCCaCC Totally 4 motifs of 4 different REs have been found Description of REs found 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1233. Group TF: CPRF1 /AC: RSP01351//OS: Arabidopsis thaliana /GENE: APX1/RE: DNase I footprint /TF: CPRF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1127_E01.118|11232482..11235795 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +338 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.21 T - 0.16 C - 0.26 1 atcgatcgat tcaattccca atctttggtt tgatttccgc atgtggcttt 51 gcccactgat cctccagacc tccaccaacc aaccccaaaa caaccggcga 101 cgacgaaatg acaaaataaa gaaaaaagaa aagtgccgtc gcgtacgaag 151 gcaagctatc tacggtcacc cccTATAAAT Tcggaaagag gcgagcgaaa 201 GACGAAAAAA ACAGCCCGAA AACAGAAGCA ATCGCGACAG AGAAGAAGAG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00316 Mean Expected Number 0.006 -strand -171 : -176 AACCAA AC RSP00651 Mean Expected Number 0.007 +strand -127 : -117 ACCaACCAACC AC RSP01185 Mean Expected Number 0.007 +strand -126 : -115 CCAACcAACCCC Totally 3 motifs of 3 different REs have been found Description of REs found 302. Group RE: REalpha /AC: RSP00316//OS: Lemna gibba /GENE: Lhcb2*1/RE: REalpha /TF: unknown 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 1097. Group RE: box 2 /AC: RSP01185//OS: Petunia hybrida /GENE: chsA/RE: box 2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1127_E01.120|11237289..11239345 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.16 G - 0.25 T - 0.19 C - 0.40 1 tccgccgtag accgtagcgc tatacggacg tagtacgagt acaaatacgt 51 cacaggcttg tactcctata ccggctctgc ctggtgcagg cgcttacctg 101 cgggtggccc aaccgcgacg caccacgcgt tcacacggcc acgtcagcct 151 actacgcctg tctccgcgTA TAAATAgccg ccgcccccga tttcgccgct 201 GCTGCTAACC TCGCCCCACT TTCCCCGCCT CGGGTCGCGC CGCCGCGTCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.006 -strand -27 : -32 TTTATA AC RSP00113 Mean Expected Number 0.002 -strand -55 : -63 TGACGTGGC AC RSP00147 Mean Expected Number 0.006 +strand -32 : -27 TATAAA AC RSP00208 Mean Expected Number 0.001 +strand -63 : -52 GCCACGTCAGCc AC RSP00214 Mean Expected Number 0.008 -strand -55 : -62 TGACGTGG AC RSP00215 Mean Expected Number 0.008 +strand -62 : -55 CCACGTCA AC RSP00247 Mean Expected Number 0.007 +strand -63 : -54 GCCACGTcAG AC RSP00248 Mean Expected Number 0.000 +strand -63 : -54 GCCACGTCAG AC RSP00695 Mean Expected Number 0.001 +strand -32 : -26 TATAAAT AC RSP00896 Mean Expected Number 0.002 +strand -186 : -179 TAGCGCTA AC RSP00896 Mean Expected Number 0.002 -strand -179 : -186 TAGCGCTA AC RSP01280 Mean Expected Number 0.005 -strand -53 : -63 GcTGACGTGGC AC RSP01662 Mean Expected Number 0.000 -strand -147 : -158 TGTGACGTaTTT Totally 13 motifs of 12 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 201. Group TF: MAT2 (ROM2) /AC: RSP00208//OS: French Phaseolus vulgaris /GENE: DLEC2/RE: DLEC2,A /TF: MAT2 (ROM2) 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 827. Group RE: PAL01 /AC: RSP00896//OS: Abutilon mosaic-A virus (Begomovirus) /GENE: Intergenic Region/RE: PAL01 /TF: unknown 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1480. Group TF: HY5 /AC: RSP01662//OS: Arabidopsis thaliana /GENE: ARR8 (At2g41310)/RE: C/G-box /TF: HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1060_D03.124|11341586..11343253 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +61 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.23 T - 0.18 C - 0.29 1 agccatccac cgtaatataa tcagagttgg ggtccaggcc gaaggctcga 51 ggaaattacc atatcgccca ccaccccggg ccacgttcgg gacgcggttg 101 cctaaaaagc gaaaatatat tcccggaaca aaGCAATaat aacccgtcac 151 gattcgccca cacggcctat cTATAAAGCc gcccccgtct ccgcaaggtg 201 ATCGTATTCA ATCAGTTTAT TCGATCGCCG GATACCCGAG GAAGAAGAAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00891 Mean Expected Number 0.001 +strand -89 : -81 AAAATATAT Totally 1 motifs of 1 different REs have been found Description of REs found 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1710_H11.110|complement(11709143..11711500) |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +159 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.16 G - 0.21 T - 0.18 C - 0.45 1 aggccccggc cgcccccacc gtgccggccg ttgtccacct cccgacggga 51 caccgggccc cgccgttgcc gcgccgtgga ccgacagcca ctgacgtcac 101 cccatgtcct tcttctcggc tagctcttct cctcctcgcc cgtgaccagc 151 agctcgcctc gccctcTATA AATAcccggc cattcgaagg cgttccgact 201 CAGGCCACAC ACCACCAACA CAAAACATTT CCTTGTCCCT CGCCTTCCTC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.005 -strand -29 : -34 TTTATA AC RSP00147 Mean Expected Number 0.005 +strand -34 : -29 TATAAA AC RSP00509 Mean Expected Number 0.000 +strand -34 : -23 TATAAATACCcG AC RSP00695 Mean Expected Number 0.001 +strand -34 : -28 TATAAAT AC RSP01296 Mean Expected Number 0.000 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -35 : -26 CTATAAATAC AC RSP01654 Mean Expected Number 0.008 -strand -100 : -109 GGTGACGTCA Totally 7 motifs of 7 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0453E05.118|complement(11877127..11880389) |SUPPORT| 6 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +245 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.26 T - 0.20 C - 0.33 1 cgtacacgtg tcccgatccc cagaccgaat cgacggctgc gactctcgta 51 acacgccacc accgcctcgc tcacagacag gtggggacgg gtcgttccgg 101 gacccaccgt cagtgtcaca ggtggtgtct ccgcgggtga gagggtgagg 151 cggaaacgtt gttagcagcg TATAAATGta accaaaccct aggattccaa 201 CGCGAGCTTA TCACTTATCA TCAATCGGCG CCTCCCTCTC TCTCGCTCAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00012 Mean Expected Number 0.009 -strand +19 : +8 GATA-- +3 bp --GATA AC RSP00340 Mean Expected Number 0.010 +strand -198 : -189 TaCACGTGTC AC RSP00536 Mean Expected Number 0.009 -strand +14 : +8 GTGATAA AC RSP00695 Mean Expected Number 0.004 +strand -30 : -24 TATAAAT AC RSP01256 Mean Expected Number 0.003 +strand -197 : -190 ACACGTGT AC RSP01256 Mean Expected Number 0.003 -strand -190 : -197 ACACGTGT Totally 6 motifs of 5 different REs have been found Description of REs found 12. Group RE: GATA /AC: RSP00012//OS: petunia /GENE: Cab22R/RE: GATA /TF: unknown ||Identical REs AC: RSP00013 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 512. Group RE: LRE-TATA AA2 /AC: RSP00536//OS: Lycopersicon esculentum /GENE: rbcS3C/RE: LRE-TATA AA2 /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1159. Group TF: GBF1 /AC: RSP01256//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS3 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1634_B10.112|complement(12029533..12030540) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +71 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.19 T - 0.24 C - 0.22 1 gggagatcac acactgagtc actgactgac taaatcgaaa caagtcaaac 51 aaccaaaaag gggtgcagat cacctacgta cctaccagta attaatcagc 101 aggctcactg taatcaaata taatcatgca ttagtagctt aactgcttaa 151 gtaaggtgca gtttagcagT ATAAATAtct ggcttgcttg cctttctccc 201 AGCCATCACA GAGTGCTTAG CTAGCTCACA CTAAAAGATA TAGAGATAGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00681 Mean Expected Number 0.003 +strand -112 : -104 TAATTAATC AC RSP00756 Mean Expected Number 0.004 +strand +25 : +32 CTCACACT AC RSP01150 Mean Expected Number 0.010 +strand -85 : -75 AAaTATAATCA AC RSP01167 Mean Expected Number 0.003 +strand -29 : -21 TAAATATCT Totally 4 motifs of 4 different REs have been found Description of REs found 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 718. Group RE: submotif B /AC: RSP00756//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif B /TF: unknown 1066. Group RE: C-DP BS2 /AC: RSP01150//OS: Cucumis sativus/GENE: POR/RE: C-DP BS2 /TF: unknown 1079. Group RE: TATA box /Group TF: HMG proteins /AC: RSP01167//OS: Zea mays /GENE: pMS1/RE: TATA box /TF: HMG proteins ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1634_B10.113|complement(12031934..12033005) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +51 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.18 T - 0.25 C - 0.25 1 atcagggctc aggggagatc acactcacac atcgaaacag gtcgaacaac 51 caatggagtg cagttcacct acctacaagt aattaatcaa cacatcagca 101 ggctagctcc tgtaattaat catgcattaa ttaatttATT GAtcttgatt 151 aatgttcagt ttagcacTAT AAATAccagg cttgcctgcc ttctccaaac 201 CATCAAAGCA CACTAGCTCA CACAGTGAGG TAGCATAGCT AGCTAAGCCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00509 Mean Expected Number 0.002 +strand -33 : -22 TATAAATACCAG AC RSP00681 Mean Expected Number 0.003 +strand -121 : -113 TAATTAATC AC RSP00681 Mean Expected Number 0.003 +strand -88 : -80 TAATTAATC AC RSP01296 Mean Expected Number 0.004 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -34 : -25 CTATAAATAC Totally 5 motifs of 4 different REs have been found Description of REs found 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1634_B10.115|complement(12036805..12037580) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +114 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.14 T - 0.22 C - 0.29 1 ataatcccaa ccaactaaac catagtacat gaaactgaaa tcatcagaga 51 tcagagacac agaccatagt aaacaaccac caaaatacag atcacctgcc 101 actgctgcca gccaccaaag atcagagact cctgcaaATT GAtgatgcat 151 ctaagctccc attcatcacT ATAAATGcca gcatcgtctt cttagtttct 201 CACCCAGCCA TCTTCACACA GACTGATCAA GTGATCATCA GCTAGTGCCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00509 Mean Expected Number 0.002 +strand -31 : -20 TATAAATgCCAG AC RSP01024 Mean Expected Number 0.007 -strand -1 : -7 AGAAACT AC RSP01640 Mean Expected Number 0.005 -strand -139 : -148 CTgTGTCTCT Totally 3 motifs of 3 different REs have been found Description of REs found 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 949. Group RE: R1 /AC: RSP01024//OS: Arabidopsis thaliana /GENE: GapB/RE: R1 /TF: unknown 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1634_B10.117|complement(12040685..12041362) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.12 T - 0.25 C - 0.28 1 aactctgaat attcccagct aattaagcca tcctcaaata tatattagga 51 aaccaattga tcaccaaatt actgatgcag atgacctacc aagcaccaaa 101 gatcagaaga gacttccatg cacattcagc aagctaacat tccttaaatt 151 tttgctcTAT AAATAccagc ttcctcttgc ctctcaaccc atcacacaaa 201 GAACTAGCTC TCTCACCGTC ACTGATACAC CGAGACGAGC TAGAAATTAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00018 Mean Expected Number 0.010 +strand -53 : -47 ATTTTTG AC RSP00426 Mean Expected Number 0.001 +strand +29 : +39 ACCGAGACGaG AC RSP00509 Mean Expected Number 0.002 +strand -43 : -32 TATAAATACCAG AC RSP00595 Mean Expected Number 0.002 -strand -173 : -181 GCTTAATTA AC RSP01115 Mean Expected Number 0.010 -strand -47 : -53 CAAAAAT AC RSP01296 Mean Expected Number 0.006 +strand -44 : -36 CTATAAATA AC RSP01301 Mean Expected Number 0.002 +strand -44 : -35 CTATAAATAC Totally 7 motifs of 7 different REs have been found Description of REs found 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 407. Group RE: DRE1/ABRE1 /AC: RSP00426//OS: Zea mays /GENE: rab17/RE: DRE1/ABRE1 /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1634_B10.118|complement(12042912..12044345) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +72 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.24 T - 0.20 C - 0.31 1 cacacggtgg caggtacata accggacggt gtacatgcag cgaggagtaa 51 ataacgagtg tgagtgacac gaacacgcag ctgagcttgc ctccacgcga 101 cgcccaaccg tgcacccaca gtgcatgcAT TGCcagcgat agctaccatt 151 ctggccgccg cgaggcTATA AATAcacctc gccagcatcg gcttctcatc 201 ACCGATCCAG CTCAAACACA TCTTCTTCTT CCTGAGCTTA GCATAGTTAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00016 Mean Expected Number 0.010 -strand -74 : -80 CATGCAC AC RSP00695 Mean Expected Number 0.008 +strand -34 : -28 TATAAAT AC RSP00756 Mean Expected Number 0.002 -strand -137 : -144 CTCACACT AC RSP01296 Mean Expected Number 0.001 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.006 +strand -35 : -26 CTATAAATAC Totally 5 motifs of 5 different REs have been found Description of REs found 15. Group RE: RY /AC: RSP00016//OS: Glycine max /GENE: beta-conglycinin/RE: RY /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 718. Group RE: submotif B /AC: RSP00756//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif B /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1634_B10.120|complement(12047246..12047874) |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +79 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.16 T - 0.22 C - 0.28 1 tgtacacagg atctgcgcgg cgctctcgcc aacccgacta gcttctttct 51 caaccaaatc atagacaaaa acacacagaa accaaccact actaagaatt 101 taagtaagaa cacttgcaga tcaaccacta ctccatcaac gcgcgtgtgt 151 ttgcgctttc cgcggccTAT AAATTaatta caccacgcat ttgtcaattc 201 ACATTGCAAA ACATCTCAGG ACAGAAATAG AGGCAAACTG ATCAGTGAAC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.003 -strand -179 : -185 CGCCGCG AC RSP00523 Mean Expected Number 0.004 -strand -53 : -59 ACACGCG AC RSP00950 Mean Expected Number 0.008 +strand -176 : -166 CTCgCCAACCC AC RSP00996 Mean Expected Number 0.009 -strand -76 : -85 GTTGATCTGC AC RSP01083 Mean Expected Number 0.002 +strand -177 : -166 TCTCgCCAACCC Totally 5 motifs of 5 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 499. Group TF: DPBF-1; DPBF-2 /AC: RSP00523//OS: Daucus carota /GENE: Dc3/RE: E3-core /TF: DPBF-1; DPBF-2 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) 1001. Group TF: DcMYB1 /AC: RSP01083//OS: Daucus carota /GENE: DcPAL1/RE: box-L5 /TF: DcMYB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0018H10.27|complement(12214332..12219273) |SUPPORT|10 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +979 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.25 T - 0.17 C - 0.39 1 agcgggccca cacagcccac cacaaaacca acaagcttct catgggcctg 51 gaggcggccc atggcgggac gcacgaggga aggactccac caccgctggg 101 tggggggccc acagcgcagt gacacgcggt ggccgcgtgg ggcccaccaa 151 aaacccttcc accttcctcg cTATAAACCc ctctctcttt ctctctcgcc 201 GCCTCCTCTC TCCGTCTCGC TTCGGTTCCT TCCTCGAGTC GAAACCTCGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.007 -strand -24 : -29 TTTATA AC RSP00095 Mean Expected Number 0.007 -strand -190 : -198 GTGGGCCCG AC RSP00147 Mean Expected Number 0.007 +strand -29 : -24 TATAAA AC RSP00471 Mean Expected Number 0.003 +strand -66 : -56 GcGTGGGGCCC AC RSP00716 Mean Expected Number 0.000 +strand -178 : -170 CAAAACCAA AC RSP00861 Mean Expected Number 0.000 -strand -9 : -17 AGAAAGAGA Totally 6 motifs of 6 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0039M16.4|12258882..12263068 |SUPPORT| 6 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +3198 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.31 C - 0.26 1 ttttatggtg ctttcggatg atcttctcaa ccaacgtgcc acattttcgc 51 aggagggaga aattcttttt tttttgtcaa cggtcaacac taaccaccag 101 caactgaaac tctaatttcg tcaaaagatg aggtcctttt tgcaaaagag 151 agtagtagcc accagaagTA TAAATTttcg tatgcttttc ctgccatttc 201 TGCCGCGCCA TCTCTCTCTC TTGCGCCTTC TCCGACTCGG ACTCCGACGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00653 Mean Expected Number 0.000 -strand -140 : -150 TTCTCcCTCCT AC RSP00864 Mean Expected Number 0.003 -strand +21 : +13 AGAGAGAGA AC RSP00864 Mean Expected Number 0.003 -strand +19 : +11 AGAGAGAGA AC RSP00866 Mean Expected Number 0.003 -strand -162 : -169 GCACGTTG AC RSP00961 Mean Expected Number 0.002 +strand -60 : -53 TGCAAAAG AC RSP01221 Mean Expected Number 0.005 +strand -110 : -103 TAACCACC Totally 6 motifs of 5 different REs have been found Description of REs found 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 802. Group RE: G-box /AC: RSP00866//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: G-box /TF: unknown 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 1128. Group RE: GARE /AC: RSP01221//OS: Oryza sativa /GENE: Amy3E (Amy8)/RE: GARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBb0040H10.18|12325107..12326138 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +97 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.27 T - 0.20 C - 0.20 1 cttgggaaaa attaaactag actttgacag ggatatatgg atcaatggaa 51 gctgcgaaaa cagcaggcag ctcatggttt cgagctcgaa cgattcgcag 101 agagcgagca gaggcaaaaa ctcttgtcag cccacaggaa aatttgctgc 151 catgccggcg tgcgtaTATA TATCgcatgc aagctggttt gcatggcatt 201 GTGCAGTGAA CAAGAACAAG GACAAGAACA AGCTAGCCGG TCGAGATCAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00331 Mean Expected Number 0.007 -strand -120 : -128 GAAACCATG AC RSP00987 Mean Expected Number 0.008 -strand -147 : -156 CAGCTtCCAT Totally 2 motifs of 2 different REs have been found Description of REs found 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 908. Group RE: H-box-like motif /AC: RSP00987//OS: Antirrhinum majus /GENE: CHS/RE: H-box-like motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0616D06.105|12814490..12819386 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +144 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.11 T - 0.16 C - 0.38 1 catcacaaaa acaaatcaaa tcccctccaa atttataacc cattaatcaa 51 aattaaaaat atcccccaat ggtcaacaca cacacaaaaa cacacacgag 101 atgatcaaag gccattccat cccgccctga caggtgggcc ccacctgcag 151 cctctcgcct tcgccTATAT ATCcactcgt gacacacaca gccccctctc 201 GCTTGCCACG CACACCACCA AATCGCCAAC CAAAAAGCAA ACCCCCGCGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00109 Mean Expected Number 0.007 -strand -65 : -70 CACCTG AC RSP00174 Mean Expected Number 0.010 -strand -96 : -101 ATCATC AC RSP00187 Mean Expected Number 0.006 -strand -64 : -68 CCACC AC RSP00304 Mean Expected Number 0.002 +strand -73 : -66 TGACAGGT AC RSP00695 Mean Expected Number 0.007 -strand -164 : -170 TATAAAT AC RSP01068 Mean Expected Number 0.010 +strand -75 : -67 CCTGACAGG AC RSP01082 Mean Expected Number 0.006 +strand +21 : +32 AATCgCCAACCA Totally 7 motifs of 7 different REs have been found Description of REs found 107. Group RE: E-site /AC: RSP00109//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: E-site /TF: unknown ||Identical REs AC: RSP00309 RSP01147 168. Group RE: ATCATC motif /AC: RSP00174//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: ATCATC motif /TF: unknown 181. Group RE: CCACC box /AC: RSP00187//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: CCACC box /TF: unknown 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 987. Group TF: HvH21 /AC: RSP01068//OS: Hordeum vulgare /GENE: Synthetic OLIGOs/RE: HvH21 BS /TF: HvH21 1000. Group TF: DcMYB1 /AC: RSP01082//OS: Daucus carota /GENE: DcPAL1/RE: box-L4 /TF: DcMYB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0616D06.125|12907482..12909667 |SUPPORT| 5 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +186 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.26 T - 0.24 C - 0.22 1 ttaaagttgg acacgaaaat atatagggtt tgtttttttt ggagggagga 51 agtaggtaat taggagaaga aaaaaatggg aagaaagaaa atccgcgagg 101 ttaaattgaa tcgaATTGAg tggtgaccag aaaccgcagc ggctgcgtcg 151 tctccgtctc ctctccttgc tTATAAACGc tcgcgcacga gcctctctct 201 CTCTAGCTCT CGCTCTCGCA GCTCAACCAC TAGCAGCAGC GGCAGGAAGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00253 Mean Expected Number 0.003 +strand -111 : -104 AATCCGCG AC RSP00858 Mean Expected Number 0.005 +strand -146 : -139 GGTAATTA AC RSP00860 Mean Expected Number 0.002 +strand -119 : -111 AGAAAGAAA AC RSP00864 Mean Expected Number 0.000 -strand +4 : -5 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand +2 : -7 AGAGAGAGA AC RSP00891 Mean Expected Number 0.002 +strand -185 : -177 AAAATATAT AC RSP00988 Mean Expected Number 0.001 -strand -153 : -164 CTCCCtCCAAAA AC RSP01237 Mean Expected Number 0.004 -strand -173 : -182 CcCTATATAT Totally 8 motifs of 7 different REs have been found Description of REs found 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 794. Group TF: DF1 /AC: RSP00858//OS: Pisum sativum /GENE: pra2/RE: GT2 /TF: DF1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family 909. Group TF: E2F/DP /AC: RSP00988//OS: Zea mays /GENE: RBR3/RE: E2F/DP I /TF: E2F/DP 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0616D06.128|complement(12922998..12923985) |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +34 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.13 T - 0.20 C - 0.37 1 ctaccagcgc cgccaccgcc aaacaaagcc tcccaagcac ataataactt 51 gtgtacactc ttggtgttgc tttagccgcg ccgaaagtac caacaaaatt 101 aaaggaagca acaaataaag gcatttagaa ttcctcacca agcaaccccc 151 ttctcccccc aaagctaTAT AAACCcacac cgcctcaccc tcccaatctc 201 ACCATTTTCA CTCACTCACT CACACTGAAC TCCTATGGCC TCCGCCGTCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00042 Mean Expected Number 0.007 -strand -69 : -75 AATTCTA AC RSP00228 Mean Expected Number 0.001 +strand +1 : +12 AcCATTTTCACT AC RSP00270 Mean Expected Number 0.001 +strand -147 : -137 TACACTcTTGG AC RSP00543 Mean Expected Number 0.005 +strand -82 : -76 AGGCATT Totally 4 motifs of 4 different REs have been found Description of REs found 41. Group RE: Motif h /AC: RSP00042//OS: Pisum sativum /GENE: PSPAL2/RE: Motif h /TF: unknown 221. Group TF: GT-1 /AC: RSP00228//OS: Pisum sativum /GENE: rbcS-3A/RE: BOX III /TF: GT-1 262. Group TF: OBP1 /AC: RSP00270//OS: Arabidopsis thaliana /GENE: GST6/RE: OBP1 BS /TF: OBP1 519. Group RE: GT-1-like K /AC: RSP00543//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: GT-1-like K /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: B1056G08.113|complement(12972857..12975111) |SUPPORT| 5 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +97 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.17 T - 0.24 C - 0.37 1 ttcaatttgc ctataatttt tggtatcaaa ccaaaacggc cgattatttg 51 cacattagac ctttttagtt ggcagaaacc catataggcc ctcctgctta 101 tcaggaaagc ccaggccgca gaagatccgg agctagggtt ttatcccaaa 151 cgagagccca cctcggccca TATAAATTct cccatccccc ccaacccctc 201 GCGACCTCTC CCGCCGCCGC CGCCGTCCTC CTCCACCTCC TCCGCTCTCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00018 Mean Expected Number 0.007 +strand -185 : -179 ATTTTTG AC RSP00695 Mean Expected Number 0.008 +strand -30 : -24 TATAAAT AC RSP00989 Mean Expected Number 0.006 +strand +7 : +15 TCTCCCGCC AC RSP01115 Mean Expected Number 0.007 -strand -179 : -185 CAAAAAT Totally 4 motifs of 4 different REs have been found Description of REs found 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 910. Group TF: E2F/DP /AC: RSP00989//OS: Zea mays /GENE: RBR3/RE: E2F/DP IV /TF: E2F/DP 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: B1056G08.118|12989063..12994557 |SUPPORT|16 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +960 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.24 T - 0.24 C - 0.25 1 cttttacgat ccccatacag ccgttgctgc aaacctgcca agaaagagca 51 gcagaaacag gtgtcatttt gtggtggaaa gccaagtaaa gtaaacagaa 101 gatggaagat agtgaggacc agggagtgag gcaggggaca catggcccac 151 gcctccctgc acattttcgt gTATAAATAc aggtggatgc atcgctctcc 201 CAGCATCCAT CGGTTCTCTG CTCTGTTCAT CCATAGAGTT TCCTCCTCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01301 Mean Expected Number 0.008 +strand -30 : -21 gTATAAATAC AC RSP01598 Mean Expected Number 0.003 +strand -139 : -132 TGTCATTT Totally 2 motifs of 2 different REs have been found Description of REs found 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1419. Group RE: Inr /AC: RSP01598//OS: Spinacia oleracea /GENE: RPL21/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0594D10.113|complement(13205421..13208586) |SUPPORT| 7 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +782 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.22 T - 0.33 C - 0.16 1 aaaaatttac atcactcata gtactttaag tgtgatttat atattatata 51 tttgcataaa atttttgaat aagacgaatg gttaaacatg tgagaaaaag 101 TCAATgtcgt catctttttt ttaaaaaaag gagggagtat aatttttact 151 tctttcgagg ggggattcgT ATAAAACctt tttcgcgtga tacagtggcg 201 GTCTCCTCTC CTGTCGTGCG TGCGTGCCGG AGACGACGAG GCGAACGCAC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00021 Mean Expected Number 0.003 -strand -47 : -58 AAgAAGTAAAAA AC RSP00158 Mean Expected Number 0.008 +strand -152 : -142 TATTTGCaTAA AC RSP00397 Mean Expected Number 0.002 +strand -7 : +1 AGTGGCGG AC RSP01174 Mean Expected Number 0.000 +strand +5 : +15 CCTCTCCtGTC AC RSP01469 Mean Expected Number 0.008 -strand -108 : -117 TCACATGTtT Totally 5 motifs of 5 different REs have been found Description of REs found 20. Group TF: GT-1 /AC: RSP00021//OS: Catharantus roseus /GENE: TDC/RE: GT-1#Box7 /TF: GT-1 153. Group RE: D3 /AC: RSP00158//OS: Glycine max /GENE: GmAux28/RE: D3 /TF: unknown 379. Group RE: CDE /AC: RSP00397//OS: Nicotiana tabacum /GENE: RNP2/RE: CDE /TF: unknown 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0594D10.119|complement(13222333..13224741) |SUPPORT| 6 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +305 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.18 T - 0.26 C - 0.39 1 ttgaattcgt tcggtacact aggaaatgtt attactatcg ccacgtctct 51 cccggctccc tctattttgg ccttaagttg gcacgcctcg gtgcagcgca 101 gcgtgtgggt gcaccaccgc acacggatcc acctcctgtc tcgtcgcacg 151 cgcacgcgca cgcccTATAA AACtgccacg ccccaaaaac ccctcctcct 201 CTCTTCCCCA GGAGACCTCT CCTCTGTCTC TCCCCTCCTT TTTCCACTTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00204 Mean Expected Number 0.007 -strand -152 : -161 GAgACGTGGC AC RSP00426 Mean Expected Number 0.003 -strand -109 : -119 ACCGAGgCGTG AC RSP00819 Mean Expected Number 0.009 +strand -161 : -152 GCCACGTCTc AC RSP00836 Mean Expected Number 0.004 +strand -79 : -72 CACGGATC AC RSP01114 Mean Expected Number 0.006 -strand -131 : -137 CCAAAAT AC RSP01507 Mean Expected Number 0.004 -strand -72 : -79 GATCCGTG AC RSP01640 Mean Expected Number 0.009 +strand +22 : +31 CTcTGTCTCT Totally 7 motifs of 7 different REs have been found Description of REs found 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 407. Group RE: DRE1/ABRE1 /AC: RSP00426//OS: Zea mays /GENE: rab17/RE: DRE1/ABRE1 /TF: unknown 765. Group TF: ACE-binding TF /AC: RSP00819//OS: Arabidopsis thaliana /GENE: F3H/RE: ACE-core (AtF3H) /TF: ACE-binding TF 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 1033. Group RE: CCAAT box-like motif 1 /AC: RSP01114//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 1 /TF: unknown 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0594D10.136|complement(13285862..13289453) |SUPPORT| 5 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.09 T - 0.19 C - 0.50 1 ctaaagtatc ttttccaagt caggtcatat agatacgaag aaaaactacg 51 aaactaccct tccccaccac cccttcttcc tccctcctct cacaccctcg 101 tcgccgccaa ccaccatcca acccatccac caacccctcc tcctcccctt 151 cgccgtcgac cccgccTATA AATAcccctc accccaccca cctccacctt 201 CAGAGGAGCC CCGCCTACCG CCGCCCTCAC GCCTCCTCCC ACCTACCTCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00265 Mean Expected Number 0.009 -strand -194 : -199 ACTTTA AC RSP00695 Mean Expected Number 0.004 +strand -34 : -28 TATAAAT AC RSP01296 Mean Expected Number 0.000 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.007 +strand -35 : -26 CTATAAATAC Totally 4 motifs of 4 different REs have been found Description of REs found 257. Group TF: NtBBF1 /AC: RSP00265//OS: Agrobacterium rhizogenes /GENE: rolB/RE: "ACTTA" motif /TF: NtBBF1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0524E08.130|13426637..13430657 |SUPPORT|11 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +138 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.13 T - 0.24 C - 0.31 1 gacctcattc ctccaaaaat aaaataaata gaaaagaaaa catttctttt 51 attattgtat aacgtgttta ccaacctcaa aaaaaatctg tgagaatctg 101 tctctagaaa acgatgagga aaaaaaaata aaggaaactg cggtggtggg 151 ccattcctct acctaTATAA ACCcccctcc ccccaccgtc caaagccccc 201 ACCTTCCCCT GTCATCTCCT CCTCCTCCAC CACCACCTCG CCGTCGCCGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00022 Mean Expected Number 0.001 -strand -146 : -154 ATAATAAAA AC RSP00913 Mean Expected Number 0.008 -strand +16 : +7 GATGACAGGG AC RSP01072 Mean Expected Number 0.003 +strand -142 : -133 ATaACGTGTT AC RSP01735 Mean Expected Number 0.001 -strand -102 : -110 AGATTCTCA Totally 4 motifs of 4 different REs have been found Description of REs found 21. Group TF: PCF1 /AC: RSP00022//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX1 /TF: PCF1 844. Group TF: Opaque-2 /AC: RSP00913//OS: Zea mays /GENE: b-32/RE: B1 /TF: Opaque-2 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1543. Group TF: CAMTA3 /AC: RSP01735//OS: Arabidopsis thaliana /GENE: CBF2/RE: CM6 /TF: CAMTA3 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0524E08.133|complement(13437993..13441828) |SUPPORT|10 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +1009 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.14 G - 0.25 T - 0.16 C - 0.45 1 gggctccgct tccctcagga gccagggccg ctcgctccgc caccgggtgt 51 ctggtgtggc tgcgccgacg cgcgccccct cccacgacca atcaacgcgc 101 ttcccgcggc gcgaccccgc gtgggcccca cctgccagag gaggattcat 151 ccccgccccg cgcgcgcgTA TAAACGgaca cctctcctcc cccctctccc 201 TATCTCGTGT GAATTGTGAT CTCTCCACCA CCATCACCAC CACCACGACG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.003 -strand -27 : -32 TTTATA AC RSP00147 Mean Expected Number 0.003 +strand -32 : -27 TATAAA Totally 2 motifs of 2 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1339_F05.111|13464190..13465035 |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +70 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.29 T - 0.16 C - 0.31 1 ctcctctggg ccgtacccag cccaacctac tggcccagca aggcctgcaa 51 atcacagtac tctcctactc ttggagaaga ggaaatgcaa cggccgccgc 101 gaaggcgaag gcgaacacgt ctccgtctcc gggctgcgcc tttaaccaga 151 acacgtgagc cggcggcTAT ATATCggcga ccccatctgc ttccggcgat 201 CGCTAAGGTA ATCAGTTTCC GAGAGCGAGC GAGAGAGAGA GAGAGAGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00426 Mean Expected Number 0.002 -strand -75 : -85 ACgGAGACGTG AC RSP00864 Mean Expected Number 0.002 +strand +32 : +40 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +34 : +42 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +36 : +44 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +38 : +46 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +40 : +48 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +42 : +50 AGAGAGAGA AC RSP00978 Mean Expected Number 0.003 -strand -42 : -51 cTCACGTGTT AC RSP01283 Mean Expected Number 0.000 +strand +31 : +47 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +33 : +49 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +35 : +51 GAGAGAGAGAGAGAGAg Totally 11 motifs of 4 different REs have been found Description of REs found 407. Group RE: DRE1/ABRE1 /AC: RSP00426//OS: Zea mays /GENE: rab17/RE: DRE1/ABRE1 /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 900. Group RE: G-box /AC: RSP00978//OS: Glycine max /GENE: vspA/RE: G-box /TF: unknown 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0519E12.113|13771174..13773267 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +64 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.08 T - 0.22 C - 0.41 1 tccgttatcc tatccaatcc taatcctaac acactccctc aaaatctgaa 51 taatacaacc ctcctctagc taaacagcct ggccgccgac gtcccaccta 101 cactgacagt gggccacacc taaaaaatat ctgcgacaca aatatcagca 151 attaccccca cacactaTAT AAACCcccac ctctttctcc actcctcctc 201 GAGCCCCAAA ACCTTATCTT CCCAAAGCCT CATCTCCTCC TTCCTCCCAC 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1340_C08.108|14111099..14112403 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +107 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.23 T - 0.28 C - 0.23 1 gcgagagcag agtcgatgca gtgtgttttg agtaggggtg tgaacgcagc 51 tgaacagcaa gcagagttgg cagattcgaa ttcttgtccc gtaaattttt 101 ccttgcctta tcctacaccc aggcctagat gcttgctttt tataatcctc 151 tagtggcaac acagcctcac cTATAAATGc tgtgactgat gataagtcca 201 GTGCATTCCA TCACAGACAG TTCGCAGAAT CGCAGCAGCT TAGCTTAATT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00595 Mean Expected Number 0.001 +strand +43 : +51 GCTTAATTA AC RSP01073 Mean Expected Number 0.001 +strand -143 : -135 CAAGCAGAG AC RSP01301 Mean Expected Number 0.010 +strand -30 : -21 CTATAAATgC Totally 3 motifs of 3 different REs have been found Description of REs found 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1340_C08.125|14163061..14164389 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +48 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.25 T - 0.27 C - 0.25 1 taattcctag ctccaaagtc agcgagcctc gcatgctagc tgagctgttc 51 ttgcatgtgt tcttcccgcg ctgtccgcgc agacaaaaac cctgcaaatt 101 tcttccggat tccgaccact agtctgtcac tagctagctc tctgtccatc 151 tgatcgattc ggatttgtgc TATAAATGga cgtgcaatgg agagcttagc 201 CATTCAGACA ACGGTAGTGG AGTGTGTGAG TAGCTGAGGA GGTCGACCAT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.004 +strand -71 : -64 CTAGCTAG AC RSP00503 Mean Expected Number 0.004 -strand -64 : -71 CTAGCTAG AC RSP00857 Mean Expected Number 0.007 +strand -55 : -46 CCATCTGAtC AC RSP00987 Mean Expected Number 0.007 -strand -159 : -168 CAGCTAgCAT AC RSP01076 Mean Expected Number 0.007 -strand -166 : -175 CATGCGaGGC AC RSP01470 Mean Expected Number 0.008 +strand -152 : -143 TCtTGCATGT Totally 6 motifs of 5 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 793. Group RE: NON /AC: RSP00857//OS: Zea mays /GENE: H4C7/RE: NON /TF: unknown 908. Group RE: H-box-like motif /AC: RSP00987//OS: Antirrhinum majus /GENE: CHS/RE: H-box-like motif /TF: unknown 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0453E03.111|15501185..15503561 |SUPPORT| 6 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +95 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.28 T - 0.18 C - 0.32 1 taaagaaaag gtaattcaag tgatgatgaa aagctcagaa tccgggccgt 51 acactgcctc gagatccgat ccgacggcca ggaggctccc agcggtgccc 101 ccgggaatat ccccaccgta gatgcctcat cccacgggta gaaggctaga 151 tgccgcggga gccggggTAT AAATAggcca ctcgtccttc tcctctcggt 201 CTCTAGGGTT TGGGATTTTA GCCGCCGCCG CCGCCGCCGC CGCTCACCCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00044 Mean Expected Number 0.007 -strand -14 : -24 GGACGaGTGGC AC RSP00056 Mean Expected Number 0.009 +strand -24 : -15 GCCACTcGTC AC RSP00695 Mean Expected Number 0.003 +strand -33 : -27 TATAAAT AC RSP00854 Mean Expected Number 0.002 -strand -44 : -52 CGCGGCATC AC RSP00894 Mean Expected Number 0.001 +strand -188 : -181 AATTCAAG AC RSP00940 Mean Expected Number 0.008 -strand -78 : -87 aTCTACGGTG AC RSP01020 Mean Expected Number 0.005 +strand -175 : -169 ATGAAAA AC RSP01497 Mean Expected Number 0.000 -strand -123 : -132 GCCGTCGGAT AC RSP01511 Mean Expected Number 0.007 -strand -45 : -52 GCGGCATC Totally 9 motifs of 9 different REs have been found Description of REs found 43. Group TF: ASF1 /AC: RSP00044//OS: Triticum aestivum /GENE: H3/RE: hex3 /TF: ASF1 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 791. Group RE: OCT /AC: RSP00854//OS: Zea mays /GENE: H4C7/RE: OCT /TF: unknown 825. Group TF: Dof family /AC: RSP00894//OS: Solanum melongena /GENE: SmCP/RE: ERE 2 /TF: Dof family 869. Group TF: GBF /AC: RSP00940//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box II* /TF: GBF 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1365. Group RE: OLS /AC: RSP01511//OS: Triticum aestivum /GENE: H1 (TH315)/RE: OLS /TF: unknown ||Identical REs AC: RSP01512 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0470D12.119|15941983..15943550 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +112 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.21 T - 0.25 C - 0.30 1 tggatatgat cattgcgtac aaatatattt atgtggttct gatgtcacca 51 tcctgggtcc ttcaaggatt gacgtgtaca gggtaccagt agacctgggc 101 ccacaggtca gtgacacgct ggcactttgc aaatagcacc ctcaactagt 151 acagtgctac acttgttggc catTATAAAG Ctcagcttcc ctaagcaaca 201 CACCCCCTCC TGGCTTAGCT TCCCTTCTCA CTCGCACGCG CCGCCGCCAC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00792 Mean Expected Number 0.009 +strand -10 : -1 CtAAGCAACA AC RSP01088 Mean Expected Number 0.003 +strand -120 : -113 GGGTACCA AC RSP01258 Mean Expected Number 0.003 +strand -131 : -124 TGACGTGT Totally 3 motifs of 3 different REs have been found Description of REs found 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 1006. Group TF: CRR1 /AC: RSP01088//OS: Helianthus annuus /GENE: CYC6; CPX1; CRD1; CTR; CTH1locus;/RE: CuRE 2 /TF: CRR1 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0470D12.138|complement(16007984..16010629) |SUPPORT| 9 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +57 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.22 T - 0.23 C - 0.29 1 gtattgtggt tgaaggagat gaaattatga atcaaattcg cacactagct 51 aagggagaca atgtgaactt agcccacctc acatagcggt actacctgca 101 aagcccaaga catcATTGGt gaggcccata tagctctcat gggctaacac 151 tcaggaggcc caagagagct TATAAATCcc gaagcgaggc ctcttttttc 201 CTCCTTTCCT CCTCCCCCAC CCAAAGCTCG AGCTCCCGCT AGGGTTTCGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.002 +strand -181 : -171 TGAAATTaTGA AC RSP00445 Mean Expected Number 0.003 -strand -2 : -11 AAAAAAGAGg Totally 2 motifs of 2 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0618H09.13|16093690..16094754 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +60 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.39 G - 0.16 T - 0.22 C - 0.23 1 cagtggctaa ctactcaaca tgcacttggt tcattcgccg tcagaagcac 51 aggataaaga acaatatatc aacgaacttt aattcctagt ggataatcga 101 cctaattaag gcgataagaa taaccacact taactatgaa tcaaatcgta 151 ccttggcctt gtaacatcaT ATAAAACaat cggtcacgca caacaaacgc 201 AAGAACCGAG AACTCGGACT GATCAAACAC ATCAGAGTAT TAGCAGATAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00093 Mean Expected Number 0.008 -strand -106 : -112 TATCCAC AC RSP00631 Mean Expected Number 0.002 -strand -73 : -85 TGTGGTTATTcTT AC RSP01058 Mean Expected Number 0.002 +strand -114 : -107 TAGTGGAT Totally 3 motifs of 3 different REs have been found Description of REs found 91. Group RE: TATCCAC box /AC: RSP00093//OS: Hordeum vulgare /GENE: Amy pHV19/RE: TATCCAC box /TF: unknown ||Identical REs AC: RSP01050 607. Group TF: S2F /AC: RSP00631//OS: Spinacia oleracea /GENE: RPL21/RE: CII /TF: S2F 978. Group TF: GT-3a /AC: RSP01058//OS: Brassica napus /GENE: extA/RE: GT-3a Box III /TF: GT-3a ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1167_G06.110|16219614..16221219 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +47 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.17 T - 0.25 C - 0.24 1 ttgccgtcgt gtggcttcca tgtccatgca ttgtgatagt aaccatacta 51 aaaccatgaa caaaacgcat cataagtaca tcacatctct aaaaaatatg 101 cagcatatgg ctgacatgct accaacagac tgtcacgggc gcaaaaatga 151 caacacattt agctctcaca TATAAATGca catatgcaac acatgcaatt 201 CAGGCCATTG CATACACACA CAGAGTTGTT TGCATTGTAG ATTGACAATG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00349 Mean Expected Number 0.001 +strand -178 : -170 TCCATGCAT AC RSP00350 Mean Expected Number 0.001 +strand -180 : -170 tGTCCATGCAT AC RSP00450 Mean Expected Number 0.002 +strand -111 : -100 TaAAAAATATGC AC RSP00642 Mean Expected Number 0.009 +strand -28 : -21 TAAATGCA AC RSP00734 Mean Expected Number 0.008 +strand -140 : -133 CAAAACGC Totally 5 motifs of 5 different REs have been found Description of REs found 334. Group TF: VP1 (VIVAPAROUS1) /AC: RSP00349//OS: Zea mays, Zea mays /GENE: C1/RE: Sph-core /TF: VP1 (VIVAPAROUS1) 335. Group RE: VP1 RE /AC: RSP00350//OS: Zea mays /GENE: C1/RE: VP1 RE /TF: unknown 429. Group RE: AIV /AC: RSP00450//OS: Phaseolus vulgaris /GENE: CHS/RE: AIV /TF: unknown 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 697. Group TF: DET1; CDA-1 /AC: RSP00734//OS: Arabidopsis thaliana /GENE: cab2/RE: CDA-1 BS /TF: DET1; CDA-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1167_G06.112|16228923..16230811 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.20 T - 0.28 C - 0.20 1 tgtcatgcaa gttgaagaag caatcataga tatatcgtat atatttttca 51 gatgttcatt tgactccatg cacaacactc cacagaatgc agaattctac 101 gattctatat ctgctatcaa aatagcacga aatggccatg tggccaaaaa 151 cgacattacg atatggaggg ctaTATATAT Ctgcatgcga cgcaggcatt 201 GCATTGCATC GCATCGCATT GCATCTGCAA GAGTAGTAGT AGTGGTGCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00073 Mean Expected Number 0.002 +strand -66 : -57 GCCAtGTGGC AC RSP00073 Mean Expected Number 0.002 -strand -57 : -66 GCCACaTGGC AC RSP00153 Mean Expected Number 0.002 +strand -65 : -56 CCAtGTGGCC AC RSP00153 Mean Expected Number 0.002 -strand -58 : -67 CCACaTGGCC AC RSP00891 Mean Expected Number 0.004 -strand -154 : -162 AAAATATAT AC RSP01014 Mean Expected Number 0.006 -strand -139 : -148 CAAATGAAcA AC RSP01237 Mean Expected Number 0.006 +strand -30 : -21 CTaTATATAT AC RSP01470 Mean Expected Number 0.008 +strand -198 : -189 TCATGCAaGT Totally 8 motifs of 6 different REs have been found Description of REs found 72. Group TF: TAF-1 /AC: RSP00073//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: PA /TF: TAF-1 ||Identical REs AC: RSP00274 149. Group RE: Box II /AC: RSP00153//OS: Petroselinum crispum /GENE: CHS/RE: Box II /TF: CPRF-1; CPRF-2; CPRF-3; ||Identical REs AC: RSP00154 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family 939. Group TF: GAPF /AC: RSP01014//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 2 /TF: GAPF 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1167_G06.113|16233177..16234778 |SUPPORT| 4 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +72 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.26 T - 0.26 C - 0.21 1 tgccggatgg gggcatgtat gcagatgacg aaacttctat tgttcaggtt 51 gaacgtcttg tacgtacgct tgtatgccaa tgtggacaag ttggacttgg 101 tggtcacaaa gtttggatgt ttatatccct acaagagtgg catgctcgtg 151 gcagcgtaca aaatctctgg cTATAAATAt gcatgcaatg cagcaatctc 201 TTGCAAGCCA CAACGGCCAA GCAGAAAGTG CAATTAGCCT GCAGGCAGCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00337 Mean Expected Number 0.006 -strand -21 : -29 ATATTTATA AC RSP01296 Mean Expected Number 0.001 +strand -30 : -22 CTATAAATA AC RSP01301 Mean Expected Number 0.008 +strand -30 : -21 CTATAAATAt Totally 3 motifs of 3 different REs have been found Description of REs found 323. Group TF: SEF1 /AC: RSP00337//OS: Glycine max /GENE: beta-conglicinin (7S globulin) alpha' and beta subunits genes/RE: SEF1 BS /TF: SEF1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1409_C08.26|16323852..16328508 |SUPPORT|15 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +89 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.26 T - 0.23 C - 0.24 1 tgctgccacg tgtacttata aaattgtccc ctcgagaaac tattattttt 51 cgtcgtcaaa acacataatc ttgtgactgg ataaagcagc attatggtac 101 ggTCAATggc aggtgggtcc cagaagagtg cagagaacac tgacatgtgg 151 gccccacaat ttcgccgcaT ATAAACGgca gccgtaacga gctcggaaat 201 CGCCTGCACA GCTGTTTCAA CGACGGCTGC TCGGAATTCG GAGGGAGGGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00002 Mean Expected Number 0.001 -strand -188 : -196 ACACGTGGC AC RSP00024 Mean Expected Number 0.003 +strand -160 : -153 TATTATTT AC RSP00079 Mean Expected Number 0.009 -strand -84 : -93 CCCACCTgCC AC RSP00175 Mean Expected Number 0.004 -strand -189 : -196 CACGTGGC AC RSP00204 Mean Expected Number 0.004 -strand -187 : -196 tACACGTGGC AC RSP00471 Mean Expected Number 0.001 -strand -42 : -52 tTGTGGGGCCC AC RSP00682 Mean Expected Number 0.005 +strand -196 : -187 GCCACGTGtA AC RSP00783 Mean Expected Number 0.000 -strand -187 : -196 TACACGTGGC AC RSP01072 Mean Expected Number 0.009 -strand -132 : -141 ATTAtGTGTT AC RSP01255 Mean Expected Number 0.003 -strand -188 : -195 ACACGTGG AC RSP01593 Mean Expected Number 0.000 -strand -187 : -198 TACACGTGGCAg Totally 11 motifs of 11 different REs have been found Description of REs found 2. Group RE: ABRE-3 /AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /TF: unknown 23. Group TF: PCF1 /AC: RSP00024//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX3 /TF: PCF1 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 738. Group TF: G-box binding TF /AC: RSP00783//OS: Nicotiana tabacum /GENE: OLIGO-GUS/RE: G-box 7 /TF: G-box binding TF 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1415. Group TF: GBF /AC: RSP01593//OS: Pisum sativum /GENE: rbcS-3.6/RE: G box /TF: GBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0008J01.12|complement(16408321..16411664) |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +1109 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.12 T - 0.32 C - 0.37 1 agccagccac tcgctatcgc ggaagcggtc agacttcttc tccaccccat 51 cgcatataaa tatttctcca ccacgccgct tcatttttac atcaccccaa 101 accccatcat ttcttgcttc ctcagctgct tcttcctcct tcctcttcac 151 acgacgctcc catttttatt taTATATATC agcatcgttt ctcctggcgt 201 CACTGCACCC ATAACTGCCA AGAATTGGAG CTGTCTCTTC TCCCTCTCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00157 Mean Expected Number 0.001 +strand -33 : -22 ATTTATATAtAT AC RSP00157 Mean Expected Number 0.001 -strand -22 : -33 ATaTATATAAAT AC RSP00337 Mean Expected Number 0.003 -strand -138 : -146 ATATTTATA AC RSP00713 Mean Expected Number 0.009 -strand -73 : -79 CAGCTGA Totally 4 motifs of 3 different REs have been found Description of REs found 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 323. Group TF: SEF1 /AC: RSP00337//OS: Glycine max /GENE: beta-conglicinin (7S globulin) alpha' and beta subunits genes/RE: SEF1 BS /TF: SEF1 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0008J01.24|16448667..16451457 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +52 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.27 T - 0.19 C - 0.25 1 aattaaggtc gatggaattt ctcagattaa atggcgcttt aaaatggaga 51 tgggtatggt aggcaatcaa tttcccgggg gaaaaagaag aagaaaagaa 101 actgacatgt cgctaaaaaa actgctccgc ctccgcgtcc cccggccgca 151 cgcgtcgcgc tctgtgctgc TATAAACGac gagagcctcg ccgcgcactc 201 GACGCGCATC TTCCGAAATA GAGAAATTGC CACGGATCGA GGGCGACCGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.006 +strand -54 : -45 CGCACGcGTC AC RSP00460 Mean Expected Number 0.004 -strand -90 : -99 GACATGTCAg AC RSP00836 Mean Expected Number 0.004 +strand +31 : +38 CACGGATC AC RSP01013 Mean Expected Number 0.008 +strand -160 : -151 aAAATGGAGA AC RSP01507 Mean Expected Number 0.004 -strand +38 : +31 GATCCGTG AC SP017556 Mean Expected Number 0.003 -strand -186 : -193 CCATCGAC Totally 6 motifs of 6 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 938. Group TF: GAPF /AC: RSP01013//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 1 /TF: GAPF 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 1561. Group TF: C1 /AC: SP017556//OS: Glycine max /GENE: a2/RE: C1BS2 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0008J01.29|16479013..16480201 |SUPPORT| 3 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.32 C - 0.21 1 ctctaattat ggagcactag gttgttgttc ggaatcttct acttgaataa 51 gagggattag gttttcagca cgttgaagtg accaatcatg gtagactcct 101 cttcaccgac gATTGAccgc aatgtaaagt actagtcgat tatagtattg 151 caatgaccaa caacccTATA AATTtcactc ctttttggca acatgcctcc 201 ACTCGAACTT GCTGAACTTT GTTAGGATTA TATTGTTGGA TCCATCATGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00467 Mean Expected Number 0.003 -strand -117 : -126 TGGTCAcTTC AC RSP00468 Mean Expected Number 0.001 -strand -116 : -126 TTGGTCAcTTC AC RSP00495 Mean Expected Number 0.006 +strand -78 : -71 TGTAAAGT AC RSP00866 Mean Expected Number 0.002 +strand -133 : -126 GCACGTTG AC RSP00881 Mean Expected Number 0.007 +strand -45 : -36 AcCAACAACC AC RSP00917 Mean Expected Number 0.003 +strand -129 : -120 GTTGAAGTGA AC RSP01482 Mean Expected Number 0.001 +strand -126 : -116 GAAgTGACCAA Totally 7 motifs of 7 different REs have been found Description of REs found 445. Group RE: ERE1 /AC: RSP00467//OS: Dianthus caryophyylus /GENE: hcbt2/RE: ERE1 /TF: unknown 446. Group RE: ERE2 /AC: RSP00468//OS: Dianthus caryophyylus /GENE: hcbt2/RE: ERE2 /TF: unknown 471. Group RE: P-box 2 /AC: RSP00495//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 2 /TF: unknown ||Identical REs AC: RSP00686 802. Group RE: G-box /AC: RSP00866//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: G-box /TF: unknown 817. Group TF: Dof family /AC: RSP00881//OS: Hordeum vulgare /GENE: Al21/RE: M2 /TF: Dof family 848. Group TF: Opaque-2 /AC: RSP00917//OS: Zea mays /GENE: b-32/RE: B5 /TF: Opaque-2 1350. Group RE: ERE2 /AC: RSP01482//OS: carnation (Dianthus caryophillus) /GENE: hcbt2/RE: ERE2 /TF: unknown ||Identical REs AC: RSP01483 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0060O17.11-1|16563643..16565635 |SUPPORT| 6 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +80 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.23 G - 0.30 T - 0.18 C - 0.29 1 aaacggctag aatgcaaaac atacacgcac gcatgtcacg cgtttgagcc 51 agtcgaggac caccggtggg cccagctgtc agcgaacgtg ggagttggca 101 caggagagcg cgtcatcgag ccgagccgat cgatcagtgg gtgagggtga 151 gagtggccgg ccttggcctt cTATAAAACg tggcacctct cgctcctcct 201 CGCATCATCG CTCGCAGTCG CAGCACAAAA ACATTTCTCT CGCGAGTCGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.006 -strand -120 : -127 TGACAGCT AC RSP00358 Mean Expected Number 0.004 -strand -104 : -111 CAACTCCC AC RSP00819 Mean Expected Number 0.006 -strand -17 : -26 GCCACGTtTT AC RSP01351 Mean Expected Number 0.007 -strand -126 : -136 CTGGGCCCaCC Totally 4 motifs of 4 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 343. Group RE: CARE2 /AC: RSP00358//OS: Oryza sativa /GENE: Rep-1/RE: CARE2 /TF: unknown 765. Group TF: ACE-binding TF /AC: RSP00819//OS: Arabidopsis thaliana /GENE: F3H/RE: ACE-core (AtF3H) /TF: ACE-binding TF 1233. Group TF: CPRF1 /AC: RSP01351//OS: Arabidopsis thaliana /GENE: APX1/RE: DNase I footprint /TF: CPRF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OSJNBa0060O17.13|16568301..16569370 |SUPPORT| 2 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +99 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.21 T - 0.19 C - 0.26 1 gaaagcgcaa gtgtggaatg gcatcatcta tcctaccaag ttcctaagcc 51 cctgaccatg cagtgcacga ataatgcaca tcgatcagct atctagagag 101 agagagagag agagagagag agatagatag catctcgatc agtgctactg 151 atcaatcgat catccccTAT AAATCcccca tcccattgcc atgcatagag 201 GCAGCACATC AACGATCGAA CGAACAACGC ACTCTGCAGC TAGCTATACA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.002 +strand -106 : -98 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -104 : -96 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -102 : -94 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -100 : -92 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -98 : -90 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -96 : -88 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -94 : -86 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -92 : -84 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -90 : -82 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -88 : -80 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -86 : -78 AGAGAGAGA AC RSP01065 Mean Expected Number 0.001 -strand -167 : -177 AGGATaGATGA AC RSP01283 Mean Expected Number 0.000 +strand -105 : -89 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -103 : -87 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -101 : -85 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -99 : -83 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -97 : -81 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -95 : -79 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -93 : -77 GAGAGAGAGAGAGAGAt Totally 19 motifs of 3 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 984. Group RE: Fungus RE /Group TF: homeodomain TF /AC: RSP01065//OS: Arabidopsis thaliana /GENE: At5g64250/RE: Fungus RE /TF: homeodomain TF 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: OJ1165_F02.129|16882521..16884034 |SUPPORT| 1 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +91 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.18 T - 0.25 C - 0.21 1 aaagatatgt ttttaaaatt aaaaactaaa ataatttttt ttaaaaaaaa 51 tcgtaggtac tccgtagata gatagatgct atatctcaaa acaaaaagtt 101 agatataggg gcagcttaga gataggtacc cgctgacacg tgggccaccc 151 atccaaaccg tcctatgcTA TAAATAatgg cgcccccgcg gctcaccatt 201 GCACTCCAAT CCAAAAGTAT AATCAAGCAA AGCAGCTCGA TCGAGTGTTC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.003 -strand -57 : -66 CcCACGTGTC AC RSP00204 Mean Expected Number 0.002 +strand -66 : -57 GACACGTGGg AC RSP00270 Mean Expected Number 0.004 -strand +21 : +11 TAtACTTTTGG AC RSP00340 Mean Expected Number 0.005 -strand -57 : -66 cCCACGTGTC AC RSP01176 Mean Expected Number 0.001 -strand -85 : -95 AGCTGCcCCTA AC RSP01255 Mean Expected Number 0.002 +strand -65 : -58 ACACGTGG AC RSP01296 Mean Expected Number 0.005 +strand -33 : -25 CTATAAATA Totally 7 motifs of 7 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 262. Group TF: OBP1 /AC: RSP00270//OS: Arabidopsis thaliana /GENE: GST6/RE: OBP1 BS /TF: OBP1 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 1087. Group TF: Zmhox1a /AC: RSP01176//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 3 /TF: Zmhox1a 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 7 ( 3 contigs)|GENE: P0034A04.123|17038184..17043026 |SUPPORT| 7 exon(s)|Contig: NT_0798992.txt | -200:+51 from mRNA start|,5"-UTR: +346 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.14 G - 0.37 T - 0.23 C - 0.27 1 gctagggcgt tggaggagga ggggatttcg ggggcggggc ggccgcggcg 51 cggggtttgg gtttttcggt ggagggggag tcgtgtcgag ttcaagtgtt 101 atctgtcgca cgctcgctcg cTCAATaatg tgtgcgtgac ctgggcaagt 151 ggcggtagca agaggagggT ATAAATAggc gagggtctca tcaccgccgc 201 CGCCGCCGCC GCCTCCTCCT CCTCTACACT GCTTCTTCCT CTCTCACTCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.005 -strand -26 : -31 TTTATA AC RSP00056 Mean Expected Number 0.007 -strand -48 : -57 GCCACTTGcC AC RSP00147 Mean Expected Number 0.005 +strand -31 : -26 TATAAA AC RSP00621 Mean Expected Number 0.004 -strand -177 : -185 CCCCTCCTC AC RSP00695 Mean Expected Number 0.001 +strand -31 : -25 TATAAAT AC RSP00863 Mean Expected Number 0.001 -strand +44 : +36 AGAGAGGAA AC RSP01233 Mean Expected Number 0.003 +strand -44 : -38 AGCAAGA Totally 7 motifs of 7 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 1138. Group RE: PLE-79 /AC: RSP01233//OS: Collettrichum lindemuthianum (bean pathogen) /GENE: CLPG2/RE: PLE-79 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1147B12.16|80041..81507 |SUPPORT| 1 exon(s)|Contig: NT_0799302.txt | -200:+51 from mRNA start|,5"-UTR: +11 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.31 T - 0.25 C - 0.14 1 ttatgagagt ttttctaata ataaatttgt taacggcatt ttcacggaat 51 ttaggaggac atacttgtgt ttggagggtg tagttgacga gaagttatac 101 tgtattagtt gaccatggca gaaatacatc atcagtgaca aatactagag 151 acaggtagga tccTATAAAT Cctgcgcggc gagcagagaa gagaagagac 201 GAGCAGCGGT GATGGCCGGC GTGGGCGTGG TAGTAGATCC GGAGGCGGTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00114 Mean Expected Number 0.009 -strand -107 : -116 CTTcTCGTCA AC RSP00142 Mean Expected Number 0.007 -strand -20 : -26 CGCCGCG AC RSP00917 Mean Expected Number 0.008 +strand -118 : -109 GTTGACGaGA AC RSP01301 Mean Expected Number 0.006 +strand -38 : -29 CTATAAATcC Totally 4 motifs of 4 different REs have been found Description of REs found 112. Group RE: B2 /AC: RSP00114//OS: Glycine max /GENE: GmAux28/RE: B2 /TF: unknown 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 848. Group TF: Opaque-2 /AC: RSP00917//OS: Zea mays /GENE: b-32/RE: B5 /TF: Opaque-2 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0015C07.40|complement(227469..228117) |SUPPORT| 1 exon(s)|Contig: NT_0799302.txt | -200:+51 from mRNA start|,5"-UTR: +41 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.22 T - 0.26 C - 0.21 1 agagagtgta cgtaggcgcg taaatcaaca ggtagcgtcc acgtcgctgc 51 tgcgtgtcct cgcatcagct ttcatcactt caattcccta tatatatatg 101 tgtgtgtatt ctgttccttc atagcaaatt aaaggcgatc atcgatcgct 151 taactaatta taTATATATC cagccagccg catcaggaga gatcgatcat 201 ATACATCGAT CGAAGAGAGA GAGAGAGAGA GAGTAATTAA CATGGCGACG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00057 Mean Expected Number 0.004 +strand -163 : -154 TCCACGTCgC AC RSP00189 Mean Expected Number 0.003 +strand -163 : -154 TCCACGTcGC AC RSP00320 Mean Expected Number 0.002 +strand -64 : -54 GATCATCGATC AC RSP00682 Mean Expected Number 0.002 -strand -154 : -163 GCgACGTGGA AC RSP00864 Mean Expected Number 0.002 +strand +14 : +22 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +16 : +24 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +18 : +26 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +20 : +28 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +22 : +30 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +24 : +32 AGAGAGAGA AC RSP00986 Mean Expected Number 0.002 +strand -162 : -155 CCACGTCG AC RSP01237 Mean Expected Number 0.004 +strand -115 : -106 CcCTATATAT AC RSP01237 Mean Expected Number 0.004 +strand -113 : -104 CTaTATATAT AC RSP01283 Mean Expected Number 0.000 +strand +15 : +31 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +17 : +33 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +19 : +35 GAGAGAGAGAGAGAGtA Totally 16 motifs of 8 different REs have been found Description of REs found 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0450B04.30|complement(149887..150864) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +164 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.11 T - 0.27 C - 0.33 1 ctattactag ctgctaatta acaacgcact aactataata aacatgctaa 51 gtggactagc tagctaagct aagctactac agtactcctc tcccacttga 101 ccacctcagc ttcctcctcc tttctcatac taagaaagaa ttcagagtca 151 aatttctcag ccacctcgcc tataTATACA TCccatgcct agcttaattc 201 CATCATCCAT CATCACACAG CTCACTGACC AGCAGCTCAG CCTCATCACT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.008 +strand -41 : -34 GCCACCTC AC RSP00210 Mean Expected Number 0.001 +strand -101 : -90 ACCACCTCAGCT AC RSP00503 Mean Expected Number 0.002 +strand -145 : -138 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand -138 : -145 CTAGCTAG AC RSP00683 Mean Expected Number 0.001 +strand -155 : -146 GCtAAGTGGA AC RSP01711 Mean Expected Number 0.006 -strand -191 : -200 CTAGTAATAG Totally 6 motifs of 5 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 203. Group TF: MAT2 (ROM2) /AC: RSP00210//OS: French Phaseolus vulgaris /GENE: DLEC2/RE: DLEC2,B /TF: MAT2 (ROM2) 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 1519. Group TF: RIN /AC: RSP01711//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Others /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0498H04.27|457258..458655 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +60 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.16 T - 0.32 C - 0.27 1 gccgctatct tcagagaggc acagagagct tttttgactc ttgctacaac 51 atgatctctc caccgtttag tgctctggtt tttggattca tccatgtcgt 101 gcactacgta cattaatcaA TTGTgcataa ttcaaatcaa tcgacatcgt 151 tcatgtgctt cagcttcagc TATAAATAcc gcatcataca tgtgatcact 201 CACTCACTCT CACACACACT CTCATCTTCT TCATCGCAAG CTAGTAAGAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01023 Mean Expected Number 0.003 +strand -9 : -2 GTGATCAC AC RSP01023 Mean Expected Number 0.003 -strand -2 : -9 GTGATCAC AC RSP01296 Mean Expected Number 0.002 +strand -31 : -23 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -31 : -22 CTATAAATAC AC RSP01469 Mean Expected Number 0.006 -strand -6 : -15 TCACATGTaT AC RSP01470 Mean Expected Number 0.009 +strand -113 : -104 TCATcCATGT AC RSP01470 Mean Expected Number 0.009 +strand -17 : -8 TCATaCATGT Totally 7 motifs of 5 different REs have been found Description of REs found 948. Group RE: PI /AC: RSP01023//OS: Arabidopsis thaliana /GENE: GapB/RE: PI /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0498H04.29|461330..464071 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.30 C - 0.28 1 ccgttgagtc gcgggtagta attctttttt tactcggaga gaagagaaaa 51 atccaaatta gggtgagatt attacggatc cgaaggggta attagtctcg 101 gattaagact aattacgcga taatccctct tcgtctcggg ctaagcctta 151 tcgcccccaa agcccttTAT AAACAcccac cccctcctct tcttcctcct 201 CATCGCTTCT CATCGCAAAT CGCATCGACT TCGATTCGCT TCGTTTCGTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00530 Mean Expected Number 0.002 +strand -178 : -167 TCTTTTTTtACT AC RSP00621 Mean Expected Number 0.003 +strand -20 : -12 CCCCTCCTC AC RSP00858 Mean Expected Number 0.003 +strand -114 : -107 GGTAATTA Totally 3 motifs of 3 different REs have been found Description of REs found 506. Group RE: AT-rich F /AC: RSP00530//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich F /TF: unknown 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 794. Group TF: DF1 /AC: RSP00858//OS: Pisum sativum /GENE: pra2/RE: GT2 /TF: DF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0427G12.36|616188..618319 |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +285 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.17 T - 0.25 C - 0.26 1 ctctctcaag ggtgggtggc aaaactaacc ccacttggca ctgacaagct 51 agatgagaga gagagaaaga aagaaagagt cagagaggtg agatagctag 101 ctagtatatg ctgtagccac acacACAATt actactactt ctacgtacat 151 catcatgtaa tgatggcaaT ATATATCgat ctcctcctct ctaatttctt 201 TCGTCCATCC TTCTCCCAAT CAAGCATCCA TCCATCCTCC CCAACTATAT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00313 Mean Expected Number 0.002 +strand -169 : -159 CACtTGGCACT AC RSP00444 Mean Expected Number 0.000 +strand -138 : -125 gAGAAAGAAAGAAA AC RSP00503 Mean Expected Number 0.003 +strand -104 : -97 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -97 : -104 CTAGCTAG AC RSP00683 Mean Expected Number 0.006 -strand -162 : -171 GCCAAGTGGg AC RSP00860 Mean Expected Number 0.002 +strand -137 : -129 AGAAAGAAA AC RSP00860 Mean Expected Number 0.002 +strand -133 : -125 AGAAAGAAA AC RSP00864 Mean Expected Number 0.001 +strand -145 : -137 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -143 : -135 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 +strand -146 : -130 GAGAGAGAGAGAaAGAA AC RSP01435 Mean Expected Number 0.009 +strand +38 : +47 TCCCCAACtA Totally 11 motifs of 8 different REs have been found Description of REs found 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 424. Group TF: Dof1 /AC: RSP00444//OS: Zea mays /GENE: cyPPDK1/RE: box d /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1308. Group TF: RNFG2 /AC: RSP01435//OS: Oryza sativa /GENE: RSs1/RE: BoxII /TF: RNFG2 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0470F10.11|664209..665690 |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +187 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.21 T - 0.14 C - 0.43 1 atactcacgg cccaccgtat cctatcgtgc cctatccaaa cacgcgcaaa 51 caccgcacgt gcctgaccca aactccgcaa acgggccgga tccgaaccag 101 acgaggccca cgatccggcc caagaggaga aaccctagcg aggaagggag 151 tgcctcctac ccgcTATAAA TTcccagcca cgccgcctcc tcccaaaccc 201 TAGAAGCCCC CCTGCCTCCT GCGCCTCCGC CGCCGCCGCC TTCTTCGTCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00012 Mean Expected Number 0.004 -strand -165 : -178 GATA-- +6 bp --GATA AC RSP00379 Mean Expected Number 0.009 -strand -163 : -172 tGGATAGGGC AC RSP00695 Mean Expected Number 0.002 +strand -36 : -30 TATAAAT AC RSP01301 Mean Expected Number 0.003 +strand -37 : -28 CTATAAATtC Totally 4 motifs of 4 different REs have been found Description of REs found 12. Group RE: GATA /AC: RSP00012//OS: petunia /GENE: Cab22R/RE: GATA /TF: unknown ||Identical REs AC: RSP00013 364. Group RE: LS7 /AC: RSP00379//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS7 /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0470F10.23|734369..738991 |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +40 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.09 T - 0.31 C - 0.35 1 atacatctca gacaagatag acatgcacag gttcatgtac tgtacataca 51 tgcaacaatc ccaataaaac ccctcctttt tttcaccttt taccatccat 101 CCAATatttc catttttcct ctttttacca gttaccacga tcactttttt 151 ttttaccgta aacccccTAT AAACCtccga attctcactc ctccgctctc 201 CACACGCCTC CAGCCTCCGA GCTTGTCGCT TCCACCTCCC ATGGCGTCCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00741 Mean Expected Number 0.004 -strand -110 : -121 AAAAGGTgAAAA Totally 1 motifs of 1 different REs have been found Description of REs found 703. Group RE: box 1 /Group TF: GT-1 /AC: RSP00741//OS: Nicotiana plumbaginifolia /GENE: Cab-E/RE: box 1 /TF: GT-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1203H11.17|909024..910636 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.28 C - 0.23 1 tggcttgaag tgcttcctta caaaaagatt agttttgtcg atcaagctga 51 agcaaagcaa catgcttgag ccatcagtct tagtatcagc tgctgacaga 101 tagctcgaga gtgtacctta tacgtacatc tcactcgatc ccagagagtt 151 ccatgcatgc ttgatagcTA TAAATAcctg ccgcgacagc ctagaaactg 201 AAACTACATA TCTACTCCAT TAATTAGCTT ATTACCGTCA ATCTTGAATA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -49 : -42 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -42 : -49 CATGCATG AC RSP00200 Mean Expected Number 0.001 +strand +18 : +27 CATTAATTAG AC RSP00349 Mean Expected Number 0.001 +strand -51 : -43 TCCATGCAT AC RSP00447 Mean Expected Number 0.007 +strand -150 : -141 AGCAAAGCAA AC RSP00509 Mean Expected Number 0.001 +strand -32 : -21 TATAAATACCtG AC RSP00559 Mean Expected Number 0.004 -strand +8 : -3 TGTAgTTTCAG AC RSP00837 Mean Expected Number 0.005 -strand +44 : +35 AGATtGACGG AC RSP01074 Mean Expected Number 0.001 +strand -50 : -41 cCATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand -41 : -50 GCATGCATGg AC RSP01296 Mean Expected Number 0.003 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -33 : -24 CTATAAATAC AC RSP01470 Mean Expected Number 0.009 -strand -132 : -141 TCAaGCATGT Totally 13 motifs of 11 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 193. Group TF: GmHdl56; GmHdl57 /AC: RSP00200//OS: Glycine max /GENE: vspB/RE: PRD motif 1 /TF: GmHdl56; GmHdl57 334. Group TF: VP1 (VIVAPAROUS1) /AC: RSP00349//OS: Zea mays, Zea mays /GENE: C1/RE: Sph-core /TF: VP1 (VIVAPAROUS1) 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 535. Group RE: 2'/Box II J1 /AC: RSP00559//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: 2'/Box II J1 /TF: unknown 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1203H11.32-2|complement(957267..960169) |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +213 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.29 T - 0.18 C - 0.31 1 ttctattttt taataagata caaacagaaa ctcagagcga caagtctcac 51 tgacaggttg tccccgtggg acccacctgt cattggcacc caccgcgccg 101 cgtggagcgc ctgccatttg ggtcaccgac atgtggggac aggtgtggac 151 cggcgtgcgc gcgggTATAA ACGgcaacca ccgccgcttc ggattcggag 201 CCTCCGCCTC CTCGCCATTT ACGGCAGCAA CCGCGGCGGA GAGAGACGAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.006 +strand -150 : -143 TGACAGGT AC RSP00304 Mean Expected Number 0.006 -strand -119 : -126 TGACAGGT AC RSP00865 Mean Expected Number 0.001 +strand +38 : +46 GGAGAGAGA AC RSP01021 Mean Expected Number 0.002 -strand -187 : -193 ATTAAAA AC RSP01024 Mean Expected Number 0.009 +strand -175 : -169 AGAAACT AC RSP01755 Mean Expected Number 0.008 +strand -26 : -19 CAACCACC Totally 6 motifs of 5 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 949. Group RE: R1 /AC: RSP01024//OS: Arabidopsis thaliana /GENE: GapB/RE: R1 /TF: unknown 1560. Group TF: C1 /AC: RSP01755//OS: Glycine max /GENE: a2/RE: C1BS1 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1499_A07.20|1229603..1234406 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +231 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.31 T - 0.23 C - 0.20 1 agctgatccg gacgacgcgg gaatgcaacg gtgtgtaacg gtgtggcgag 51 atgcccgggc aaaggagatc ggtggcgact agttcgtgca gcgcaggaag 101 cgcgatgaag cagagtgcat gacggggagt aacctcgtcg tttccacatt 151 tgtaggatca aagttgttag ccTATAAATA gttggtggta acagaatttg 201 TACGCGCGCA TTCAGTTTTC ATTTCAGTTC GAAATAAACA CCGAAAGTTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00355 Mean Expected Number 0.004 +strand -12 : -5 TAACAGAA AC RSP01020 Mean Expected Number 0.008 -strand +22 : +16 ATGAAAA AC RSP01296 Mean Expected Number 0.001 +strand -29 : -21 CTATAAATA AC RSP01301 Mean Expected Number 0.005 +strand -29 : -20 CTATAAATAg AC RSP01708 Mean Expected Number 0.003 +strand -29 : -20 CTATAAATAG AC RSP01708 Mean Expected Number 0.003 -strand -20 : -29 CTATTTATAG Totally 6 motifs of 5 different REs have been found Description of REs found 340. Group RE: GARE2 /AC: RSP00355//OS: Oryza sativa /GENE: Rep-1/RE: GARE2 /TF: unknown 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1163_G08.30|complement(1350387..1351389) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.19 C - 0.39 1 agccagacag gttggagcta ggcagctgct agccaactgc cattcccaca 51 ccaaccaacc aaagaaggaa tgcgcagtca accacatagc gtgagtctta 101 cccgccaaaa ccgccgaaag ccatcccccg cctcctcctc acgccacccc 151 ctctcgccat cgccgcTATA AAGCtcctct cctcccatgg cggcgtctcc 201 TACTTCGATC TACACGCTGC TTTCAACTCT CTGAGAGCTA GCTAGCATGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00431 Mean Expected Number 0.008 -strand -157 : -168 AATGGCAGTTGG AC RSP00503 Mean Expected Number 0.003 +strand +38 : +45 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +45 : +38 CTAGCTAG AC RSP00877 Mean Expected Number 0.005 +strand -100 : -92 CCCGCCAAA AC RSP01033 Mean Expected Number 0.005 -strand -133 : -142 CCTTCTTTGG Totally 5 motifs of 4 different REs have been found Description of REs found 411. Group TF: AtMYB77 /AC: RSP00431//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB77 BS /TF: AtMYB77 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 813. Group TF: AtE2F /AC: RSP00877//OS: Arabidopsis thaliana /GENE: MCM3/RE: Site 2 E2F (D2) /TF: AtE2F 958. Group TF: FLC /AC: RSP01033//OS: Arabidopsis thaliana /GENE: FT/RE: CArG box /TF: FLC ||Identical REs AC: RSP01204 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1163_G08.32|1358420..1360682 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +39 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.13 T - 0.20 C - 0.37 1 gcacgtatct aattaaccca aaatttttaa tatgtgagtg tgtacgttct 51 atgaatctgt cacaagtcat gacgccgcga gccgcgtcca gctacaaacc 101 actcaaccca aacgcatcca aaacccctcg ctgagctgcc atgcatgcac 151 tccccctcct cccacTATAA ATTatcacca cctcattccc gccatgtctc 201 ACCACCACCA CCACCAACAC TGCAACACAA CACACCACCA TGAAGACGGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.002 +strand -61 : -54 CATGCATG AC RSP00108 Mean Expected Number 0.002 -strand -54 : -61 CATGCATG AC RSP00621 Mean Expected Number 0.009 +strand -48 : -40 CCCCTCCTC AC RSP01019 Mean Expected Number 0.007 +strand +40 : +46 ATGAAGA AC RSP01021 Mean Expected Number 0.007 -strand -170 : -176 ATTAAAA AC RSP01074 Mean Expected Number 0.001 +strand -62 : -53 CCATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand -53 : -62 GCATGCATGg AC RSP01076 Mean Expected Number 0.007 -strand -54 : -63 CATGCaTGGC AC RSP01767 Mean Expected Number 0.001 -strand -172 : -180 TAAAAATTT Totally 9 motifs of 7 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 944. Group TF: GAPF /AC: RSP01019//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 1 /TF: GAPF 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf 994. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01076//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE III /TF: CpbZIP1; CpbZIP2 (short) 1570. Group RE: AT-rich element /AC: RSP01767//OS: Zea mays /GENE: Bz1/RE: AT-rich element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0582D05.130-1|complement(1481603..1484320) |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +129 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.19 T - 0.14 C - 0.42 1 aaaagaaatt tggttccttg ggcaaccgtg ccctctgcag actctggcaa 51 ggcccatacg ccggagagcc caataaggcc catctcctga gaccgcaacc 101 gccacgaaac cctaaaacca agcccatcag gcccaccaac ccgaagccac 151 acccatccct ctcccacTAT AAATAcccgc accccccacc ctggaaaccc 201 TAGGTTAAAG CGACGCCGCC GCCGCAAGCC GTCCGCCTTG CTCCTCCTCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00182 Mean Expected Number 0.006 -strand -188 : -193 CCAAAT AC RSP00229 Mean Expected Number 0.001 +strand -132 : -123 CCCAATAAGG AC RSP00279 Mean Expected Number 0.003 -strand -86 : -94 TTAGGGTTT AC RSP00316 Mean Expected Number 0.003 -strand -186 : -191 AACCAA AC RSP00369 Mean Expected Number 0.003 +strand -94 : -86 AAACCCTAA AC RSP00509 Mean Expected Number 0.000 +strand -33 : -22 TATAAATACCcG AC RSP00695 Mean Expected Number 0.003 +strand -33 : -27 TATAAAT AC RSP00873 Mean Expected Number 0.008 +strand +3 : +13 GGTTAAAGCGA AC RSP01296 Mean Expected Number 0.000 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.005 +strand -34 : -25 CTATAAATAC AC RSP01303 Mean Expected Number 0.005 +strand -95 : -86 gAAACCCTAA Totally 11 motifs of 11 different REs have been found Description of REs found 176. Group TF: ROM1; ROM2 /AC: RSP00182//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: CCAAAT box /TF: ROM1; ROM2 222. Group RE: CArG Box 1 /AC: RSP00229//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CArG Box 1 /TF: unknown 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 302. Group RE: REalpha /AC: RSP00316//OS: Lemna gibba /GENE: Lhcb2*1/RE: REalpha /TF: unknown 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 809. Group TF: Dof2 /AC: RSP00873//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof2 BSopt /TF: Dof2 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1119_D01.19|complement(1944052..1945951) |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +61 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.15 T - 0.26 C - 0.26 1 gggagtactc ctaattgata acccaaaata catcggtgaa aaaaagagaa 51 ggaattaaat gagttttttt atacgggtag aattaaatga ctttttgcct 101 caaaaaatga attaaatgag atttaattta gacccaaatg gacatggcga 151 agacctctcc ccacagcTAT AAATGcccca agtcctccct cctccctccc 201 CACATCGCAA TCCCAGCTCC CTTCTTCCCA CCGATTCCAA TCTCCAGAAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.001 +strand -161 : -152 AAAAAAGAGA AC RSP01013 Mean Expected Number 0.004 +strand -66 : -57 CAAATGGAcA Totally 2 motifs of 2 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 938. Group TF: GAPF /AC: RSP01013//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 1 /TF: GAPF ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0473D02.20|complement(2083729..2084821) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +42 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.38 G - 0.13 T - 0.29 C - 0.19 1 tattttttaa aaaaaatatt atagtaagtt agtacttttg accattcaac 51 cggttagcat ttatctgata atgctcagcc ggtgcaggta ttgattggtt 101 ttgagaccac tgtcaaaaat agcatcacat caacaaataa ttcaaatcca 151 ctcgtagttg caaaacacct ataTATAAAG Cccatttcta ccatgtaatt 201 CAATCTATAA ACAAACACTC AAGACAATTA ACACGACAAA TCATGGAGAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00231 Mean Expected Number 0.005 -strand -103 : -109 CCAATCA AC RSP00716 Mean Expected Number 0.000 -strand -98 : -106 CAAAACCAA AC RSP00917 Mean Expected Number 0.004 -strand -67 : -76 GTTGATGTGA AC RSP00996 Mean Expected Number 0.007 -strand -67 : -76 GTTGATGTGA Totally 4 motifs of 4 different REs have been found Description of REs found 224. Group RE: CCAAT box 1 /AC: RSP00231//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CCAAT box 1 /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 848. Group TF: Opaque-2 /AC: RSP00917//OS: Zea mays /GENE: b-32/RE: B5 /TF: Opaque-2 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1349_D05.116|complement(2770875..2773709) |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +257 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.23 G - 0.10 T - 0.38 C - 0.29 1 atttcgtgtt gtagccggct acgaacttgt agtccgcttt tttctctctc 51 ctcttctatc ttatccacat aagcataaat atgatgtggc aatatatata 101 aaccgcttac atcatatatt atattatttt actcgctcta atcctactat 151 tttcttttac caaataAATA AATCtccacc cttcatctga attttctgaa 201 CCCACCCACC CTTCTTCCTT CTCCAGCTCT CGCCTCTCGC CTCGTCCTTG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00596 Mean Expected Number 0.009 -strand -111 : -116 GCCACA AC RSP00653 Mean Expected Number 0.002 +strand -159 : -149 TTCTCTCTCCT AC RSP00868 Mean Expected Number 0.005 +strand -84 : -73 TATTATATTATt AC RSP01053 Mean Expected Number 0.009 -strand -136 : -144 GATAAGATA Totally 4 motifs of 4 different REs have been found Description of REs found 572. Group RE: Box II EE2 /AC: RSP00596//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE2 /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 973. Group TF: HvMCB1 /AC: RSP01053//OS: Hordeum vulgare /GENE: ITR1/RE: GATA-core /TF: HvMCB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0438H08.29|complement(3098986..3102101) |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +82 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.19 T - 0.26 C - 0.25 1 tctttcttcc ttccttctcc taattaattc ccctaaaaaa ttgaaggtga 51 agagaagaag aaggaaaaga aagcaaaaca aattaattaa agaaaagaaa 101 agaaaagaaa aaggtgagtt ggtggtgtca tatatagtgt gtggtggttg 151 gtgaaggctt gagctcccaT ATAAACCccc tcctccctct ccattgcctt 201 CACCTCACTC GCCGCCGGTG ATCAGCCTCC TCCTCCTTCT TCTCCATCGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00357 Mean Expected Number 0.002 -strand -80 : -87 CAACTCAC AC RSP00621 Mean Expected Number 0.001 +strand -24 : -16 CCCCTCCTC AC RSP01237 Mean Expected Number 0.005 -strand -62 : -71 CaCTATATAT AC RSP01454 Mean Expected Number 0.005 -strand -49 : -55 ACCAACC AC RSP01755 Mean Expected Number 0.001 -strand -51 : -58 CAACCACC Totally 5 motifs of 5 different REs have been found Description of REs found 342. Group RE: CARE1 /AC: RSP00357//OS: Oryza sativa /GENE: Rep-1/RE: CARE1 /TF: unknown 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1325. Group RE: AC-II /Group TF: PtMYB4 /AC: RSP01454//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-II /TF: PtMYB4 1560. Group TF: C1 /AC: RSP01755//OS: Glycine max /GENE: a2/RE: C1BS1 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0498E12.107|complement(3169458..3171151) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +21 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.14 T - 0.26 C - 0.30 1 ctttaaccct cctctctcca cacaaatgct tagaaaactg ccaccactga 51 gcccactccc atgagagcaa tttccagaac cacaaaagtt ggaccattca 101 attctgtagt ggtggtttag tcaaagtctt ccctgaaaGC AATctgcagt 151 ctgtacaaaa cacagcTATA TATCtgtgtg ctcactacca caacaaacct 201 CAACCTATCT CTCATGAAGT CATGAGTCCC ACCATTTCAC CTGTCCTGGT 251 T Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0577B11.140|complement(3459512..3461679) |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.39 G - 0.18 T - 0.24 C - 0.20 1 ctggtacaag aacagcaaca tttatctctc tcttaaaaaa aaaaaagaaa 51 tcacgctgag ggctttcctg aaaaaaaaaa taaaattgtg cttcaggcta 101 aggacttgtt cataagtaga ataaaaatca gggattttgg tgctatgcta 151 cacattccca gacctcgcTA TAAAACagat ccgatcactc tcctgatcgg 201 CGCCGGCGTT AATTCCAAGA AAAGAAGAAG AGAAGAATCT GAAAAACTTT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.000 -strand -168 : -176 AGAGAGAGA AC RSP01114 Mean Expected Number 0.010 -strand -61 : -67 CCAAAAT Totally 2 motifs of 2 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1033. Group RE: CCAAT box-like motif 1 /AC: RSP01114//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0583B06.11|complement(4257867..4263424) |SUPPORT|12 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +522 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.33 C - 0.18 1 gtgcacatgg cattttagac ccaaccctca aattttcgcc cattattacc 51 atgcatgtgc acctgactgt ttgggcttag ttgctacaat ggttttagaa 101 acaaaACAAT tatatagtat tatattttat gtgttgatta aaccaaaatt 151 ctcTATAAAT Aaaatatact agtataaatt gattatttta ttgaaccgat 201 GGTTGAAGTG AACCAAAATC CGTAGGTCGT ATCGTAGGGA GGGCCTGCGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -151 : -144 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -144 : -151 CATGCATG AC RSP00313 Mean Expected Number 0.001 +strand -197 : -187 CACATGGCAtT AC RSP00868 Mean Expected Number 0.008 +strand -83 : -72 TATTATATTtTA AC RSP00917 Mean Expected Number 0.003 +strand +2 : +11 GTTGAaGTGA AC RSP01017 Mean Expected Number 0.007 +strand -104 : -97 AGAAACAA AC RSP01296 Mean Expected Number 0.005 +strand -48 : -40 CTATAAATA AC RSP01470 Mean Expected Number 0.009 +strand -152 : -143 cCATGCATGT AC RSP01678 Mean Expected Number 0.005 -strand -8 : -19 CAATAAAATAaT Totally 9 motifs of 8 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 848. Group TF: Opaque-2 /AC: RSP00917//OS: Zea mays /GENE: b-32/RE: B5 /TF: Opaque-2 942. Group TF: AEF /AC: RSP01017//OS: Arabidopsis thaliana /GENE: GapA/RE: AE box 2 /TF: AEF 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) 1496. Group TF: AT-Hook TFs /AC: RSP01678//OS: Catharanthus roseus /GENE: ORSA3/RE: JRE (Quant. Seq.) /TF: AT-Hook TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1734_E04.11|6029007..6032088 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +34 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.23 T - 0.15 C - 0.33 1 ggtaaattat taagcgcaaa cttaagagag gtatttgaat aattgccaaa 51 tctaaaagtg gcaaatagtt aaattccccc aaatttaaag cagcgaagca 101 gtggaggcga caaaaagatg agcacacgat ggcacacccg cgatgccgcg 151 cgcgcgcgcg ccaccTATAA AACgcccgcg cgccccgcgc cgcctccctc 201 CCCCTCCTCC CCACACGCCA CCCGCACGCG CGCCATGGAC GCCATGAGGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00179 Mean Expected Number 0.005 -strand -112 : -118 TTTAAAT AC RSP00621 Mean Expected Number 0.002 +strand +1 : +9 CCCCTCCTC AC RSP00854 Mean Expected Number 0.001 -strand -51 : -59 CGCGGCATC AC RSP00870 Mean Expected Number 0.002 +strand -150 : -141 TcTAAAAGTG AC RSP00874 Mean Expected Number 0.007 +strand -150 : -140 TCTaAAAGTGG AC RSP00948 Mean Expected Number 0.007 +strand -200 : -194 GGTAAAT AC RSP00958 Mean Expected Number 0.004 +strand -117 : -111 TTTAAAG AC RSP01511 Mean Expected Number 0.005 -strand -52 : -59 GCGGCATC Totally 8 motifs of 8 different REs have been found Description of REs found 173. Group RE: AT-rich motif /AC: RSP00179//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: AT-rich motif /TF: unknown 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 791. Group RE: OCT /AC: RSP00854//OS: Zea mays /GENE: H4C7/RE: OCT /TF: unknown 806. Group RE: EM2 /AC: RSP00870//OS: Triticum aestivum /GENE: LMWG-1D1/RE: EM2 /TF: unknown 810. Group TF: Dof3 /AC: RSP00874//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof3 BSopt /TF: Dof3 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 884. Group TF: BPBF /AC: RSP00958//OS: Hordeum vulgare /GENE: Hor2/RE: PB2 /TF: BPBF 1365. Group RE: OLS /AC: RSP01511//OS: Triticum aestivum /GENE: H1 (TH315)/RE: OLS /TF: unknown ||Identical REs AC: RSP01512 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBa0002E10.45|6652282..6654855 |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +1823 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.18 T - 0.32 C - 0.30 1 aggggaaata ttcctcttat cctcctctat ctttaccccc aagaatcgga 51 gcaaaccgtt gagtatttta tccgaatcga actcgttttt gagtttatct 101 ccaaaaccga gtttttgttt tcccggatcg atttcttgcg ggaggagtcc 151 gatctcttca atccaaggcT ATAAATAgga ccccgtagtc ctcctctttc 201 GTTTGCCCCC TCTCCCGTCC TCTTCCGTGC TCCGTAGCTC CGTCGCCACT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00701 Mean Expected Number 0.004 +strand -79 : -72 CCCGGATC AC RSP01174 Mean Expected Number 0.010 +strand +9 : +19 CCTCTCCCGTC AC RSP01296 Mean Expected Number 0.001 +strand -32 : -24 CTATAAATA AC RSP01301 Mean Expected Number 0.006 +strand -32 : -23 CTATAAATAg AC RSP01708 Mean Expected Number 0.004 +strand -32 : -23 CTATAAATAG AC RSP01708 Mean Expected Number 0.004 -strand -23 : -32 CTATTTATAG Totally 6 motifs of 5 different REs have been found Description of REs found 667. Group RE: Oct (d) /AC: RSP00701//OS: Triticum aestivum /GENE: H3/RE: Oct (d) /TF: unknown 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1049E04.7-1|complement(6926655..6927733) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.22 T - 0.26 C - 0.15 1 ggctgtctat atatggacaa ttagttgcat taatatagta gtttataatt 51 gcaagcatgg cactacatca caacacctaa aagacatgcc gtgatgctag 101 aacagccATT GAataaatta gaaagaaagg ttgtggttaa ttagttaacg 151 accaatcgag cctactagTA TAAATTgtac ctcgttgtta tgaagtaatt 201 CATCCTGTAG TAACGAAACA AGCAGAGAGA GAGAGAGGCG GAGAGATAAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.004 +strand +24 : +32 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 +strand +26 : +34 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 +strand +28 : +36 AGAGAGAGA AC RSP01073 Mean Expected Number 0.001 +strand +19 : +27 CAAGCAGAG AC RSP01237 Mean Expected Number 0.005 +strand -196 : -187 gTCTATATAT Totally 5 motifs of 3 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0691F12.18|complement(7086341..7088938) |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.29 T - 0.23 C - 0.21 1 cttcaataga aagagaaaga gaggaagcaa gacatgcaaa tgcatgggga 51 ccccggccgg ccggccggcc tcagtcgtag ttgttggttc cattagtaac 101 atgcagtgca catagctttc tccagccctt gttgggcatg catatgcagc 151 atgaagagtt ggagtggttg TATAAATAgg taggcagtgg tggactgcga 201 GGCGCTGCAA GACAGACAGA TACATCGATC GATCGATCAG AGCTTTTTCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00861 Mean Expected Number 0.002 +strand -193 : -185 AGAAAGAGA AC RSP00861 Mean Expected Number 0.002 +strand -187 : -179 AGAAAGAGA AC RSP00863 Mean Expected Number 0.003 +strand -183 : -175 AGAGAGGAA AC RSP01214 Mean Expected Number 0.003 +strand -74 : -65 CCTTGTTGGG Totally 4 motifs of 3 different REs have been found Description of REs found 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 1122. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01214//OS: Brassica oleracea /GENE: BoCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1119_E09.5|7171363..7172572 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.21 T - 0.26 C - 0.19 1 ttagaatagc tgatgtatgc cattagaaac gcatagagga tcacggatca 51 ccagctagtt gtatcaaaat gaatgcaagc atgccgtgat gctatcacag 101 ccattgaaga aattagaaag gttgacaatt agtactgaCC AATcgatcga 151 gctagcctag ctagctagTA TAAATTaatt tgtacctcat cgattgatca 201 TATAGATGCA CTAATCCATC CTGTAGCTTC TAATCAAACT GAGAGGGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand -44 : -37 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 +strand -40 : -33 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -33 : -40 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -37 : -44 CTAGCTAG AC RSP00836 Mean Expected Number 0.002 +strand -159 : -152 CACGGATC AC RSP01507 Mean Expected Number 0.002 -strand -152 : -159 GATCCGTG Totally 6 motifs of 3 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 781. Group RE: dOCT /AC: RSP00836//OS: Arabidopsis thaliana /GENE: H4A748/RE: dOCT /TF: unknown ||Identical REs AC: RSP00852 1363. Group RE: Oct-p /AC: RSP01507//OS: Triticum aestivum /GENE: H1 (TH315)/RE: Oct-p /TF: unknown ||Identical REs AC: RSP01508 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0461A06.7|7733965..7734661 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +148 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.14 T - 0.36 C - 0.23 1 ctacgtgcat cgaccggtga ttaggttttc aagacaatgt tgtattttcc 51 tttttttttt aatctaaggg aatgttgaaa aagatgatga cttcgacttt 101 taaagtggta gagataagtc ggagttgttg tacttttaca aattacaact 151 cgctttgcct tctTATATAT Ccctactact actacagcat catctactac 201 ACACATGACA CATTCCCATC TTTCCAATGT CCACTTCCAT CCCTCTCATC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00874 Mean Expected Number 0.008 +strand -103 : -93 TTTTAAAGTGG Totally 1 motifs of 1 different REs have been found Description of REs found 810. Group TF: Dof3 /AC: RSP00874//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof3 BSopt /TF: Dof3 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1047A05.37|7914571..7916998 |SUPPORT| 7 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +132 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.16 G - 0.14 T - 0.21 C - 0.50 1 gtcacatttc cgcacacccc ctcggaagat ctcccattcg ccatttccca 51 tccctcccag agccctcctc acccgtccga tcacgcggcc gcggcaacca 101 cagccgtccg atccacaccc cgagccgcgc ccgaaaccct aaccctaaaa 151 cctcccgcct ccccCATAAA TCcccttctc cctcctcgcc gccgcctctt 201 CCTCTCTCTC TCCCCTCTCG ATCTCGTCTT CTCTCTCTCG CAGGACTCGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00279 Mean Expected Number 0.001 -strand -59 : -67 TTAGGGTTT AC RSP00369 Mean Expected Number 0.001 +strand -67 : -59 AAACCCTAA AC RSP00863 Mean Expected Number 0.006 -strand +7 : -2 AGAGAGGAA AC RSP00864 Mean Expected Number 0.006 -strand +38 : +30 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +11 : +3 AGAGAGAGA AC RSP01303 Mean Expected Number 0.002 +strand -68 : -59 gAAACCCTAA AC RSP01497 Mean Expected Number 0.003 +strand -98 : -89 GCCGTCcGAT AC RSP01505 Mean Expected Number 0.002 -strand -88 : -96 GATCGGACG AC RSP01505 Mean Expected Number 0.002 -strand -119 : -127 GATCGGACG Totally 9 motifs of 7 different REs have been found Description of REs found 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0682A06.17|8089195..8090424 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +48 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.16 T - 0.19 C - 0.40 1 cccaacatta gcgctaatca tctttattta tttgctaatt atcattgtta 51 acgtagtaga ttagccacag cccacaagcc ttcgtcccca cccgacagcg 101 acgtcaccaa accgcgccac caccaccacc acccgccgcc ggagcagcgc 151 ctcctcctcc tcctcgcgcc agTATAAATC cggcctcccc ctcgccgtgc 201 CACTCACTCA TCCACCACCC AAAGACAAAG CAAGCAAGTA CAGTAGCCAT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00354 Mean Expected Number 0.001 +strand -152 : -145 TAACGTAG AC RSP00695 Mean Expected Number 0.007 +strand -28 : -22 TATAAAT AC RSP00896 Mean Expected Number 0.002 +strand -192 : -185 TAGCGCTA AC RSP00896 Mean Expected Number 0.002 -strand -185 : -192 TAGCGCTA AC RSP01280 Mean Expected Number 0.005 -strand -93 : -103 GGTGACGTcGC AC RSP01729 Mean Expected Number 0.001 -strand -93 : -104 GGTGACGTCGCT Totally 6 motifs of 5 different REs have been found Description of REs found 339. Group RE: GARE1 /AC: RSP00354//OS: Oryza sativa /GENE: Rep-1/RE: GARE1 /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 827. Group RE: PAL01 /AC: RSP00896//OS: Abutilon mosaic-A virus (Begomovirus) /GENE: Intergenic Region/RE: PAL01 /TF: unknown 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1537. Group TF: STF1/HY5 /AC: RSP01729//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBb0070J06.9|8464982..8470071 |SUPPORT| 8 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +2 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.21 T - 0.16 C - 0.41 1 ttttccaaaa aaaaaaaaaa atcctcctgc cttgccacgt gtctgagccc 51 ccctatacta ctagaggcgg agatcccaag ggcagcttgt cgggcggtca 101 gcaaaaacca accaaccagc cgtccttcgc tttttaattc cgatggcccc 151 gccgccgccg gcccgcgTAT AAACCacagt ccgccccgcc cccgcccgac 201 GAATGCACCA CCGCCTCCTC CTCCGCCGCG GCGCGATGCC CGTCCCCCCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00002 Mean Expected Number 0.001 -strand -159 : -167 ACACGTGGC AC RSP00056 Mean Expected Number 0.010 +strand -167 : -158 GCCACgTGTC AC RSP00175 Mean Expected Number 0.006 -strand -160 : -167 CACGTGGC AC RSP00204 Mean Expected Number 0.007 -strand -158 : -167 GACACGTGGC AC RSP00219 Mean Expected Number 0.001 -strand -157 : -168 aGACACGTGGCA AC RSP00340 Mean Expected Number 0.010 +strand -167 : -158 gCCACGTGTC AC RSP00936 Mean Expected Number 0.001 +strand -168 : -157 TGCCACGTGTCt AC RSP01021 Mean Expected Number 0.001 -strand -63 : -69 ATTAAAA AC RSP01255 Mean Expected Number 0.004 -strand -159 : -166 ACACGTGG Totally 9 motifs of 9 different REs have been found Description of REs found 2. Group RE: ABRE-3 /AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /TF: unknown 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 212. Group TF: HY5 /AC: RSP00219//OS: Arabidopsis thaliana /GENE: RBCS-1A/RE: G box-1 /TF: HY5 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 865. Group TF: GBF /AC: RSP00936//OS: Lycopersicon esculentum /GENE: RbcS-3A/RE: G box /TF: GBF 946. Group TF: GAPF /AC: RSP01021//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 3 /TF: GAPF 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBa0005L24.22|9299308..9300939 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +641 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.34 C - 0.17 1 atttacatgt aaactgtgca attggttttt tttcgtccat atttaatgct 51 ccatgcatgt gtccaaacat ttgatgtgac ggaaaaattg aaagtttgaa 101 gaaaaaaatt ttaatctaaa cacggcctta cATTGTaagc taaagtcgtt 151 caaattggat gcagttagta TATAAATAtg acaggatcaa ttcgttatcc 201 GTGCACCATC ATTAGCCAAT TTGTCCCTAG CTCGTCCTGG TGGTACTGGT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -149 : -142 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -142 : -149 CATGCATG AC RSP00195 Mean Expected Number 0.001 +strand -3 : +8 TCCGTGcACCA AC RSP00349 Mean Expected Number 0.001 +strand -151 : -143 TCCATGCAT AC RSP01470 Mean Expected Number 0.009 +strand -150 : -141 cCATGCATGT Totally 5 motifs of 4 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 188. Group RE: Box II /AC: RSP00195//OS: Oryza sativa /GENE: Gt2/RE: Box II /TF: unknown 334. Group TF: VP1 (VIVAPAROUS1) /AC: RSP00349//OS: Zea mays, Zea mays /GENE: C1/RE: Sph-core /TF: VP1 (VIVAPAROUS1) 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBb0005C03.18|9682705..9684401 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +7 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.14 T - 0.35 C - 0.20 1 tattgtaatt agatgcaatt tataatataa ttatactata ttatattgta 51 tttatatttg ataaatttct gagagaaaat ttatcgaccg atgcccttaa 101 tcgatcagtt gcaaacgacg ctggtctggt gaaggagaca ttaattcgat 151 gctgtagtac tcttccccTA TAAATCaatc catccttcct ctctttgtcc 201 ATCACACATG CACCTAATTA TTAGTAGCAT ACACACATAT ACCATAATGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00016 Mean Expected Number 0.009 +strand +7 : +13 CATGCAC AC RSP00863 Mean Expected Number 0.002 -strand -7 : -15 AGAGAGGAA AC RSP01642 Mean Expected Number 0.004 -strand -58 : -67 tAATGTCTCC Totally 3 motifs of 3 different REs have been found Description of REs found 15. Group RE: RY /AC: RSP00016//OS: Glycine max /GENE: beta-conglycinin/RE: RY /TF: unknown 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 1462. Group RE: ARE /AC: RSP01642//OS: Nicotiana tabacum /GENE: WIPK/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1114E07.25-2|11240391..11241900 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +138 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.15 G - 0.21 T - 0.27 C - 0.37 1 acccgagtgc gaagtggatc cccgatgcct ttacaccgag ccggactgtg 51 agagacggtg ggtggggccc acatgtcagc gtgcgaggtc taccaacacc 101 cggtctacgc ggcggccgag aagcgcccgt ccctttcagg tttttttttc 151 ctcctcctcc tcctcccTAT AAATGcttct ctcgcctctc tcgcctctcc 201 CTTTCCAAGA AACCACCAAT CTCTCTCTCT CTCTCTCTTT CTCTCTCGCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.009 -strand -28 : -33 TTTATA AC RSP00079 Mean Expected Number 0.002 -strand -135 : -144 CCCACCcACC AC RSP00147 Mean Expected Number 0.009 +strand -33 : -28 TATAAA AC RSP00171 Mean Expected Number 0.008 +strand -151 : -146 GAGAGA AC RSP00471 Mean Expected Number 0.002 +strand -141 : -131 GgGTGGGGCCC AC RSP00683 Mean Expected Number 0.002 +strand -192 : -183 GCgAAGTGGA AC RSP00695 Mean Expected Number 0.002 +strand -33 : -27 TATAAAT AC RSP00861 Mean Expected Number 0.005 -strand +42 : +34 AGAAAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +38 : +30 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +36 : +28 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +34 : +26 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +32 : +24 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +30 : +22 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand +28 : +20 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 -strand +37 : +21 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 -strand +35 : +19 GAGAGAGAGAGAGAGAt AC RSP01301 Mean Expected Number 0.002 +strand -34 : -25 CTATAAATgC Totally 17 motifs of 11 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 165. Group RE: GAGAGA motif /AC: RSP00171//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GAGAGA motif /TF: unknown 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0467G09.22|11360465..11361888 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +31 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.22 T - 0.29 C - 0.17 1 gtgtgttata tggtgaaatt aataatgaca ggtggcatac cagttagtgg 51 agggttgcag ggtaaaatta atggtgacag atgtcatgct agctagtgga 101 ccattgcatt cattttcttg gcttggATTG Aggtagcaaa gaccttgtgt 151 ttatcaagtt caaggcTATA AATCactccc ttctcatcat aacaactaca 201 CATACAGAAA ACATCTTGGC TAGCAATTTC CATGGAGAAA ATCCAAGTGA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00056 Mean Expected Number 0.005 -strand -165 : -174 GCCACcTGTC AC RSP00219 Mean Expected Number 0.000 +strand -175 : -164 TGACAgGTGGCA AC RSP00304 Mean Expected Number 0.007 +strand -175 : -168 TGACAGGT AC RSP00503 Mean Expected Number 0.003 +strand -112 : -105 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -105 : -112 CTAGCTAG AC RSP00936 Mean Expected Number 0.000 -strand -164 : -175 TGCCACcTGTCA AC RSP01294 Mean Expected Number 0.001 +strand +27 : +38 TTTCCATGGAGa Totally 7 motifs of 6 different REs have been found Description of REs found 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 212. Group TF: HY5 /AC: RSP00219//OS: Arabidopsis thaliana /GENE: RBCS-1A/RE: G box-1 /TF: HY5 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 865. Group TF: GBF /AC: RSP00936//OS: Lycopersicon esculentum /GENE: RbcS-3A/RE: G box /TF: GBF 1191. Group RE: Box 5 /AC: RSP01294//OS: Avena fatua /GENE: Amy2/D/RE: Box 5 /TF: unknown ||Identical REs AC: RSP01299 RSP01300 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBb0075O18.125|complement(11526810..11527593) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +53 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.12 T - 0.25 C - 0.41 1 atcatcctcc ctgtttctct tttataaaaa aaataataat aatcatcctc 51 cgctccgcga cgctcgcgcc cacggggaag ccaaacccag ccactttccc 101 cgtctccttc ctcccctact ccggcgccct cccctcctta tccatccgca 151 cccacctcct ccatcctgcT ATAAACCaac cccaagattt gtcaccctcc 201 GGTAGGTAGT ACCACTCCAA TCCCAATCCA AGCCTGAATC CTCTTTTGAT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00024 Mean Expected Number 0.002 -strand -163 : -170 TATTATTT AC RSP00445 Mean Expected Number 0.010 -strand -176 : -185 AtAAAAGAGA AC RSP01150 Mean Expected Number 0.002 +strand -166 : -156 AATaATAATCA AC RSP01453 Mean Expected Number 0.001 -strand +7 : +1 ACCTACC AC RSP01499 Mean Expected Number 0.001 +strand -105 : -96 TTCCCCGTCT Totally 5 motifs of 5 different REs have been found Description of REs found 23. Group TF: PCF1 /AC: RSP00024//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX3 /TF: PCF1 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 1066. Group RE: C-DP BS2 /AC: RSP01150//OS: Cucumis sativus/GENE: POR/RE: C-DP BS2 /TF: unknown 1324. Group RE: AC-I /Group TF: PtMYB4 /AC: RSP01453//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-I /TF: PtMYB4 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBb0075O18.126|11533455..11535276 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +584 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.12 T - 0.35 C - 0.19 1 ttggtcattt ttacaacact atattttgtc atttctatgc tagaaagact 51 actaaactgg gataccatct acaaattata acatataaac atgctaaata 101 attatttctt atataactct tataatatct taatataaaa cgatcctaat 151 ttttatattt gacatatatt cataTATAAA TCtgtaagtc ctatagtaaa 201 GTAGCCGAAT CCTGATTGCC GCTGCAACGA CCGCGACTCG ACTCCGCGAG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00572 Mean Expected Number 0.009 -strand -34 : -41 ATATGTCA AC RSP00710 Mean Expected Number 0.004 +strand -102 : -90 TAATTATTTCTTA AC RSP01598 Mean Expected Number 0.009 +strand -174 : -167 TGTCATTT Totally 3 motifs of 3 different REs have been found Description of REs found 548. Group RE: 3'/AT-rich J1 /AC: RSP00572//OS: Lycopersicon esculentum /GENE: rbcS1/RE: 3'/AT-rich J1 /TF: unknown 676. Group RE: AT1-box /AC: RSP00710//OS: Pisum sativum /GENE: TOP2/RE: AT1-box /TF: unknown 1419. Group RE: Inr /AC: RSP01598//OS: Spinacia oleracea /GENE: RPL21/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1705_A03.28|complement(11602222..11603110) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +390 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.18 T - 0.27 C - 0.18 1 atggacagga aacaaacaac gatcaagtct aaataatgac tattattagt 51 tgcatcgaaa tagtggtata taactaagca tgccgtgatg atatcacagc 101 cattgaagaa attatattgg aaaggttgac aatttgtaat gaCCAATcga 151 gccagcctag caagctagTA TAAATTaact ggtacctcat cgattgaaca 201 TATATATGCA TTAATCCATC CTGTAGCTGG CTACTAACTA AACTCAGAGA 251 G Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0670E08.20|14204841..14205564 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.15 T - 0.29 C - 0.33 1 gataacaaga aacttgttta gagcgtacct gcttcccaag cgtgtcgccc 51 ttatccggct gcctcgtgtc cagacacctg gcacaacaca catcgcccat 101 cttacacgtg cacatgctcc cgtgtcacct cctcaacact tgcacgagtt 151 cttcgttgct tgccgctcTA TAAATTtcca gcttcctttc gatcctcttc 201 AACAATTACA ATAATCATCA AGCTTCTTCT TATGTTCATC CAAATCCACA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00524 Mean Expected Number 0.009 +strand -97 : -91 ACACGTG AC RSP00817 Mean Expected Number 0.005 +strand -98 : -89 TACACGTGCa AC RSP00974 Mean Expected Number 0.002 +strand -98 : -89 TACACGTGCA AC RSP01030 Mean Expected Number 0.003 +strand -193 : -186 AGAAACTT Totally 4 motifs of 4 different REs have been found Description of REs found 500. Group TF: DPBF-1; DPBF-2 /AC: RSP00524//OS: Daucus carota /GENE: Dc3/RE: E4-core /TF: DPBF-1; DPBF-2 763. Group TF: ACE-binding TF /AC: RSP00817//OS: Arabidopsis thaliana /GENE: CFI/RE: ACE-core (AtCFI) /TF: ACE-binding TF 897. Group RE: G-box /AC: RSP00974//OS: Glycine max /GENE: vspB/RE: G-box /TF: unknown ||Identical REs AC: RSP00981 955. Group TF: AEF /AC: RSP01030//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 1 /TF: AEF ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1119_B10.28|15308810..15313816 |SUPPORT| 6 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +72 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.44 G - 0.18 T - 0.19 C - 0.19 1 aaaaggtaaa aattacaata atatgccatt ttttcaaaaa aaaagttaat 51 gcaaaatgtc gaaaaataac caatgcagaa aacctataaa ttctatgacg 101 tgtagggtga aaaggaaaaa aagaagggaa aaactgaatc cctctgtccc 151 tcccgtctcc ttgccttggc TATAAACCcc cggaaaccac aaggcagaga 201 GAAGGTCCTT CCCTTCCCAC AAGGGGAAAA AAGGGGAAAA AAAAAAGAAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00232 Mean Expected Number 0.003 -strand -100 : -109 ACGTCATAGA AC RSP00741 Mean Expected Number 0.009 +strand -200 : -189 AAAAGGTaAAAA AC RSP01258 Mean Expected Number 0.001 +strand -105 : -98 TGACGTGT AC RSP01275 Mean Expected Number 0.003 -strand -97 : -106 TaCACGTCAT Totally 4 motifs of 4 different REs have been found Description of REs found 225. Group RE: LS7 /Group TF: TGA2 & NPR1/NIM1 /AC: RSP00232//OS: Arabidopsis thaliana /GENE: PR-1/RE: LS7 /TF: TGA2 & NPR1/NIM1 703. Group RE: box 1 /Group TF: GT-1 /AC: RSP00741//OS: Nicotiana plumbaginifolia /GENE: Cab-E/RE: box 1 /TF: GT-1 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0410E11.123-1|complement(15421060..15427259) |SUPPORT|10 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +112 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.15 T - 0.29 C - 0.25 1 ctaaaattac aacaaaaacg gcacgctttg caaaccatgg tgtaacgttt 51 gcccacaaca acctgtataa gaaaacaagc tttacagctt cgtacaactc 101 tggttagcaa actaattttg tcacgctaag gaatcagttt ctcatagcac 151 cgaccagttt caccTATAAA TTagaggata ctgcacagcc cttgatcaca 201 ATACAGTGCA TTTCTACAAT CTTTTGTTGC CCATTCATCT GGGTTTTCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00259 Mean Expected Number 0.006 +strand -100 : -94 TGGTTAG AC RSP00559 Mean Expected Number 0.005 -strand -190 : -200 TGTAATTTtAG Totally 2 motifs of 2 different REs have been found Description of REs found 252. Group TF: ATMyb2 /AC: RSP00259//OS: Arabidopsis thaliana /GENE: rd22/RE: ATMyb2 BS /TF: ATMyb2 535. Group RE: 2'/Box II J1 /AC: RSP00559//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: 2'/Box II J1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0436B06.30-1|17389461..17393074 |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +27 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.19 T - 0.29 C - 0.22 1 catcatacga attacaccct agcatgtaca tattcttcta taatgtgtta 51 attgtatttc gatgaaatcc gtgtttatgc gattatatga tgatcaattt 101 agaaaattta gaaaggatgg agcatatttt aggacgggga cagtacacca 151 gcgtagcatt gctgtatTAT AAATGgagac cgtctacact gtacacgacc 201 GCGCAGACCC AAGTGCCAAA GCTTTCCATG TCCACCGATC TCACCATCCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00439 Mean Expected Number 0.010 +strand -171 : -164 ATATTCTT AC RSP00950 Mean Expected Number 0.002 +strand +40 : +50 CTCACCAtCCC AC RSP01013 Mean Expected Number 0.005 +strand -31 : -22 tAAATGGAGA AC RSP01083 Mean Expected Number 0.000 +strand +39 : +50 TCTCACCAtCCC Totally 4 motifs of 4 different REs have been found Description of REs found 419. Group RE: -624-box /AC: RSP00439//OS: Arabidopsis thaliana /GENE: PR-1/RE: -624-box /TF: unknown 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 938. Group TF: GAPF /AC: RSP01013//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 1 /TF: GAPF 1001. Group TF: DcMYB1 /AC: RSP01083//OS: Daucus carota /GENE: DcPAL1/RE: box-L5 /TF: DcMYB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1090H08.28|17844420..17846634 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +1341 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.15 T - 0.35 C - 0.20 1 attaaaataa gttattcccc aaacagtttg gatattttct tggatgtctc 51 ttgcaagatg tctcttgcaa ctttcaacct tatttcaacc taagggatat 101 tggttgtaaa aaatagctga aatttctccc tttctggatc taatcACAAT 151 atgcatattt ttTATATATC agagttcatc aacctcctat cttctgaatc 201 CAATGAAGTT TGCAGCCGAG AGGACAAGAA AACTATTGCT CCTGAGCATG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00319 Mean Expected Number 0.002 -strand -5 : -13 CAGAAGATA AC RSP00450 Mean Expected Number 0.002 -strand -37 : -48 TaAAAAATATGC AC RSP01435 Mean Expected Number 0.002 +strand -185 : -176 TCCCCAAaCA Totally 3 motifs of 3 different REs have been found Description of REs found 305. Group TF: R-GATA /AC: RSP00319//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: GATA motif /TF: R-GATA 429. Group RE: AIV /AC: RSP00450//OS: Phaseolus vulgaris /GENE: CHS/RE: AIV /TF: unknown 1308. Group TF: RNFG2 /AC: RSP01435//OS: Oryza sativa /GENE: RSs1/RE: BoxII /TF: RNFG2 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0434E03.25|18060035..18064035 |SUPPORT| 7 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +122 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.14 T - 0.26 C - 0.26 1 cctaactgtt ggatgatcag ataattaatt aactaagcta gcttagggca 51 tagtaattgt gtacaagtcc tacactcttt gctaattagc tagtttgccc 101 caacacacca cacactacac atgcacatac acagttaagc ttgatatctc 151 tctctcgctc atcgatcaca cTATAAATAc gttgccctag ccatggcaat 201 TTTGCATCAC AAGATCATCA ACTAAGCGAA GAACACACAC ACAAACACAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00320 Mean Expected Number 0.002 +strand -44 : -34 GcTCATCGATC AC RSP00864 Mean Expected Number 0.001 -strand -46 : -54 AGAGAGAGA AC RSP01296 Mean Expected Number 0.005 +strand -30 : -22 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -30 : -21 CTATAAATAC AC RSP01604 Mean Expected Number 0.006 -strand -66 : -73 ACTGTGTA Totally 5 motifs of 5 different REs have been found Description of REs found 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1425. Group TF: SPF1 /AC: RSP01604//OS: Ipomoea batatas /GENE: Sporamin; beta-amylase/RE: SP8a /TF: SPF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1198_B10.6|complement(18705103..18705878) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +301 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.19 T - 0.25 C - 0.31 1 gattggtgac gtgggccgtc agtgaagatg aagccatttt cgctatcgga 51 cctcctaaaa ccctaccaga aaaatatatt ttttgtggcg gacctcctaa 101 gaccctgcca gcgaaaatct atttttgctg gtggtaggaa tagtgttttc 151 ccgtattaaa agcctaccta cccaCATAAA TCcatgcccg cagaaacccc 201 CACCCATAGA AATCCGCGCC GCTCCACCTT TCTCACTCTC TCCCTCCGTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00214 Mean Expected Number 0.002 +strand -194 : -187 TGACGTGG AC RSP00215 Mean Expected Number 0.002 -strand -187 : -194 CCACGTCA AC RSP00253 Mean Expected Number 0.004 +strand +11 : +18 AATCCGCG AC RSP00755 Mean Expected Number 0.009 +strand -65 : -59 AGGAATA AC RSP00824 Mean Expected Number 0.002 +strand -38 : -28 cCTACCTACCC AC RSP00891 Mean Expected Number 0.001 +strand -130 : -122 AAAATATAT AC RSP00891 Mean Expected Number 0.001 -strand -119 : -127 AAAATATAT AC RSP01280 Mean Expected Number 0.000 +strand -196 : -186 GGTGACGTGGg AC RSP01472 Mean Expected Number 0.006 +strand -38 : -28 cCTACCTACCC Totally 9 motifs of 8 different REs have been found Description of REs found 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown 770. Group TF: R2R3-type MYB /AC: RSP00824//OS: Arabidopsis thaliana /GENE: CFI/RE: MRE-core (AtCFI) /TF: R2R3-type MYB 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1341. Group RE: Box-I /AC: RSP01472//OS: Pisum sativum /GENE: PsCHS1/RE: Box-I /TF: unknown ||Identical REs AC: RSP01528 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1198_B10.9|complement(18714798..18721001) |SUPPORT|16 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +59 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.23 G - 0.18 T - 0.18 C - 0.41 1 tgcagtgcag tccgttcact gacacgtggg ccccacagac ccccgggtcc 51 acgtgccagt gagcagcact gaagcactgg agatgatctc cacggcaagc 101 agcagcagca gcgcccgtta cctcctcccc actgcggccg ttttcttaca 151 aatccccccc TATAAATAcc ccaattcacc aacgccccct tcttcttctc 201 CAACTCCCTC CCCCTCCAAG AAGCGAACAA GCCAAGAACT CCTCCAACTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.006 -strand -171 : -180 CcCACGTGTC AC RSP00204 Mean Expected Number 0.003 +strand -180 : -171 GACACGTGGg AC RSP00340 Mean Expected Number 0.010 +strand -153 : -144 TCCACGTGcC AC RSP00340 Mean Expected Number 0.003 -strand -171 : -180 cCCACGTGTC AC RSP00471 Mean Expected Number 0.008 -strand -163 : -173 cTGTGGGGCCC AC RSP00682 Mean Expected Number 0.006 -strand -144 : -153 GgCACGTGGA AC RSP00695 Mean Expected Number 0.004 +strand -40 : -34 TATAAAT AC RSP01228 Mean Expected Number 0.000 +strand -27 : -14 ATTCACCAACgCCC AC RSP01255 Mean Expected Number 0.002 +strand -179 : -172 ACACGTGG AC RSP01296 Mean Expected Number 0.000 +strand -41 : -33 CTATAAATA AC RSP01301 Mean Expected Number 0.005 +strand -41 : -32 CTATAAATAC Totally 11 motifs of 10 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1133. Group RE: P-box 3 /AC: RSP01228//OS: Arabidopsis thaliana /GENE: C4H/RE: P-box 3 /TF: unknown 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1198_B10.18|complement(18771921..18773134) |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +209 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.14 T - 0.34 C - 0.20 1 ttttcttgct agctagtagt actacagaag gaaaaataaa atgatgctat 51 tcttagctga atgagacttt cactcttatc ctcacaacag catgcccaaa 101 tccatacact atcctaatta tagagcTCAA Ttttagtttg tatatatcca 151 tagaactcaa ttttagtttg TATATATCcg tactacttga aattggtttt 201 GTTGTCCACA AGAGTCAAGG CTCACAGAAA TCTCACCACA GATAATCTTG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00115 Mean Expected Number 0.008 +strand -51 : -41 ATAGAAcTCAA AC RSP00503 Mean Expected Number 0.002 +strand -192 : -185 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand -185 : -192 CTAGCTAG AC RSP00716 Mean Expected Number 0.001 -strand +1 : -8 CAAAACCAA Totally 4 motifs of 3 different REs have been found Description of REs found 113. Group TF: ATBP-1 /AC: RSP00115//OS: Pisum sativum /GENE: GS2/RE: BOX 1 /TF: ATBP-1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0685B10.33|19137624..19141246 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +108 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.15 G - 0.16 T - 0.30 C - 0.39 1 cacgcaatct caccagcgcc cgcgcgcgcg cgcgagtacg tgttgtcgag 51 acgagacgag agaaccatgc tactaaaccc cctccattaa ttccaccgtg 101 attccatctc ctttgtcctc ctcctcctcc accgcttcgt ctctctctct 151 ctctcgcttt cctctctTAT ATATCgcctc ctctcctcct cctcctctgc 201 ATCGCCATTG CTGCCTAGCT ATTCTACTAG CTTTGTTTCT CTCTTGGCGA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00072 Mean Expected Number 0.005 +strand -165 : -159 GTACGTG AC RSP00146 Mean Expected Number 0.007 +strand -34 : -28 TTATATA AC RSP00171 Mean Expected Number 0.003 +strand -143 : -138 GAGAGA AC RSP01072 Mean Expected Number 0.005 +strand -166 : -157 AgTACGTGTT AC RSP01283 Mean Expected Number 0.000 -strand -46 : -62 GAGAGAGAGAGAGAGAc AC RSP01546 Mean Expected Number 0.008 +strand -150 : -145 ACGAGA AC RSP01546 Mean Expected Number 0.008 +strand -145 : -140 ACGAGA AC RSP01702 Mean Expected Number 0.002 -strand -157 : -166 AACACGTAcT Totally 8 motifs of 7 different REs have been found Description of REs found 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 165. Group RE: GAGAGA motif /AC: RSP00171//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GAGAGA motif /TF: unknown 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1388. Group RE: DRE1 /AC: RSP01546//OS: Sorghum bicolor; Sorghum vulgare /GENE: Sbdhn2/RE: DRE1 /TF: unknown 1511. Group RE: ACGT1 /AC: RSP01702//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBa0007M04.21|complement(19502114..19503507) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +1 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.27 C - 0.26 1 caatttaatt cagtcaagtt catggcttga ccgcggcagt atacgtttct 51 ctttgataac accaacaaat taaatttcac ggaaatggcc acagtgcgac 101 acgtgccatg aatctcagct gtgaatatat atatactctc cagttgtctt 151 ctactAATAA ATCcagaccg ttaaatattc ttcatcagaa gttactcagc 201 AATGTACGCA ACCAAGCCGC TCTCGGCGTT CGCGGGCCAC CCGGATGCCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.004 -strand -94 : -103 gGCACGTGTC AC RSP00204 Mean Expected Number 0.002 +strand -103 : -94 GACACGTGcC AC RSP00439 Mean Expected Number 0.008 +strand -26 : -19 ATATTCTT AC RSP01086 Mean Expected Number 0.006 +strand -161 : -152 TaTACGTTTC AC RSP01152 Mean Expected Number 0.004 +strand -103 : -94 gACACGTGCC Totally 5 motifs of 5 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 419. Group RE: -624-box /AC: RSP00439//OS: Arabidopsis thaliana /GENE: PR-1/RE: -624-box /TF: unknown 1004. Group TF: bZIP TF /AC: RSP01086//OS: Helianthus annuus /GENE: sHSP/RE: bZIP BS /TF: bZIP TF 1067. Group TF: EmBP-1 (+VP1) /AC: RSP01152//OS: Zea mays /GENE: Em/RE: Em1b /TF: EmBP-1 (+VP1) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0456B03.116|complement(20204704..20206942) |SUPPORT| 7 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +248 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.25 T - 0.31 C - 0.17 1 tttgccgttt acaatgtaaa tccgtaatga tgtgagaaaa tgacagggag 51 atcgagtaaa ccataagctg gttcgatggc tttgtttggt catgtttcat 101 gaaagagaag cggctggttt tttttttttt gtgaggtcca aggtcacaca 151 cacttagtga aatTATAAAC Ctgcagatgc aggcgactcg acaactccct 201 CACCGAATGT GTGGTTGGAT GCTTGACATG TAGTAGTAGT AGTATCTCGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00358 Mean Expected Number 0.001 +strand -9 : -2 CAACTCCC AC RSP00872 Mean Expected Number 0.005 -strand -51 : -60 TGTGTGACcT AC RSP01598 Mean Expected Number 0.004 -strand -156 : -163 TGTCATTT Totally 3 motifs of 3 different REs have been found Description of REs found 343. Group RE: CARE2 /AC: RSP00358//OS: Oryza sativa /GENE: Rep-1/RE: CARE2 /TF: unknown 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown 1419. Group RE: Inr /AC: RSP01598//OS: Spinacia oleracea /GENE: RPL21/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0431A03.26|20805379..20807517 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +87 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.16 T - 0.27 C - 0.25 1 ttgcaagatt gatgagtagc caattattac tcctcccaat cccaaagaaa 51 aataagttgg caattattca caccttgaaa tgcaaacatc gcaatttgcc 101 atccatgcag aaTCAATgca gcgttctacc catgcttttc tttctgtact 151 tcctgcctaa actttgccTA TAAATCtgca catccatggc tcgtttcttg 201 CAACAAAGCC ACAGCCTTCA TCATCATCAG AGAGAGAAGG AGAGAGAGGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00653 Mean Expected Number 0.001 -strand +48 : +38 cTCTCTCTCCT AC RSP00860 Mean Expected Number 0.002 -strand -56 : -64 AGAAAGAAA AC RSP00863 Mean Expected Number 0.001 +strand +43 : +51 AGAGAGGAA AC RSP00864 Mean Expected Number 0.001 +strand +29 : +37 AGAGAGAGA AC RSP00865 Mean Expected Number 0.000 +strand +39 : +47 GGAGAGAGA AC RSP00953 Mean Expected Number 0.003 +strand -180 : -172 CAATTATTA AC RSP00962 Mean Expected Number 0.008 +strand -188 : -182 TGAGTAG Totally 7 motifs of 7 different REs have been found Description of REs found 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 880. Group TF: ATHB6 /AC: RSP00953//OS: Arabidopsis thaliana /GENE: ATHB6/RE: ATHB6 BS /TF: ATHB6 887. Group RE: GLM1 /AC: RSP00962//OS: Hordeum vulgare /GENE: ITR1/RE: GLM1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0528B09.35-1|complement(21261145..21268328) |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +170 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.22 T - 0.21 C - 0.38 1 ctcacctaac cccgggtcgc cgtcgcgggc cacccggcca cacgcggtgc 51 gcgcgtccga tccatctcct ctccgtttct ctcagctact ctcgcctgta 101 cacacactcg cgggtaggga gccggagcga gttggctttg ttgtgttgag 151 ccctttcctg ggccTATAAA TTcggcatca cgcccaacgc atcccctccc 201 CAGAAGAATC CCAGCTACCA AATCGAACCT ACCAACTCAT TCCCGATCGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00014 Mean Expected Number 0.001 +strand +23 : +33 TCgAACCTACC AC RSP00489 Mean Expected Number 0.009 +strand +26 : +35 aACCTACCAA AC RSP00651 Mean Expected Number 0.006 +strand +27 : +37 ACCTACCAACt AC RSP00695 Mean Expected Number 0.003 +strand -36 : -30 TATAAAT AC RSP01301 Mean Expected Number 0.003 +strand -37 : -28 CTATAAATtC AC RSP01505 Mean Expected Number 0.002 -strand -139 : -147 GATCGGACG Totally 6 motifs of 6 different REs have been found Description of REs found 13. Group RE: MRE-core /AC: RSP00014//OS: Arabidopsis thaliana /GENE: CHS/RE: MRE-core /TF: unknown 465. Group RE: UVLRE2 /AC: RSP00489//OS: Glycine max /GENE: chs1/RE: UVLRE2 /TF: unknown 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0708B04.12|complement(21345674..21346711) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +119 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.19 T - 0.13 C - 0.41 1 gcgcccaaat ctgcgggaca ggccggattg ctccactacg cgacgccctc 51 cgccggccgc ggccacaacc tcgcgacacc gacgcaaatc ccactaaaac 101 cttacgacac gacgagccgc gctagctacc gcacgcatgc gtaccaccac 151 aaccgcgcgc gctcccTATA AATTtcaccg ctaaatccca ccacgaactc 201 ATCAATCCAT CAAGCCATCA GTTCATCACA CCACACACAG CAGTACAGCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.003 +strand -34 : -28 TATAAAT Totally 1 motifs of 1 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0429B05.38|complement(21627748..21630170) |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +106 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.17 T - 0.25 C - 0.28 1 atacaaactt tttataaaaa tacaccattt aattaattga aaagtgtgtg 51 tgtaaaataa ggaagatggg ttgggaagaa ggaccggtga tctggtcttc 101 gtcctcctca agaagtcaaa aacacaacca ttccgagctc ccccaccaaa 151 caccatttgc ctccacTATA AATCcgagct ctccagctgc ttccactcct 201 CAGGAATCGG TAGTTGTCAT CACGCGCACT TCCATTCCGC TCACCTACCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00286 Mean Expected Number 0.005 +strand +39 : +49 gCTCACCTACC AC RSP00601 Mean Expected Number 0.003 +strand -60 : -52 CCCCACCAA AC RSP00950 Mean Expected Number 0.006 +strand +40 : +50 CTCACCtACCC Totally 3 motifs of 3 different REs have been found Description of REs found 277. Group RE: Box L /AC: RSP00286//OS: Petroselinum crispum /GENE: PAL-1/RE: Box L /TF: unknown ||Identical REs AC: RSP01754 577. Group RE: C-rich R /AC: RSP00601//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich R /TF: unknown 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1005_H01.19|21732740..21736228 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +61 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.17 T - 0.26 C - 0.24 1 caaaagttcc ggtactattt gaattttatc aaatttgaaa agccattcaa 51 aatacaaatg tgttattcaa aaaggtgtcg gcccccctca gaattttccc 101 cgaacctgat tatgactgtc agtgcatgag ttcaaaaaga gtgtcatgtg 151 aaaccgatca acttctctgt aTATAAACCc ttcagtccac ggcccaaagc 201 AAAGCACACG TACAGCTACA CTTTGTCACT AGCTAAGCTA GCAAGTGCAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00016 Mean Expected Number 0.006 -strand -73 : -79 CATGCAC AC RSP00313 Mean Expected Number 0.001 -strand -51 : -61 CACATGaCACT AC RSP00441 Mean Expected Number 0.006 -strand +27 : +18 gACAAAGTGT AC RSP00447 Mean Expected Number 0.009 +strand -3 : +7 AGCAAAGCAc AC RSP00530 Mean Expected Number 0.002 -strand -61 : -72 TCTTTTTgAACT AC RSP00999 Mean Expected Number 0.006 +strand +26 : +36 TCACTAgCTAA AC RSP01190 Mean Expected Number 0.003 +strand -14 : -5 CCACGGCCCA AC RSP01599 Mean Expected Number 0.009 -strand -161 : -168 TTTCAAAT Totally 8 motifs of 8 different REs have been found Description of REs found 15. Group RE: RY /AC: RSP00016//OS: Glycine max /GENE: beta-conglycinin/RE: RY /TF: unknown 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 506. Group RE: AT-rich F /AC: RSP00530//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich F /TF: unknown 920. Group TF: 3AF3 /AC: RSP00999//OS: Nicotiana tabacum /GENE: rbcS-3A/RE: 3'-III element /TF: 3AF3 1101. Group RE: C-box /Group TF: C factor /AC: RSP01190//OS: Nicotiana tabacum /GENE: Adhl/RE: C-box /TF: C factor 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1144B06.35|22163075..22163625 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +140 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.20 T - 0.17 C - 0.33 1 gaaacctgta gcgcataacg agggcctctc caaacattta catacgcgac 51 gacctgacac gaaccaccgc gcaacggatc ggcacccgtt ccacgcgtct 101 acgcgggcag gaaaactcgc cgattcccaa ctcccaagcg aaccaaaacc 151 ctacatatgt gatgcaTATA AACGagcgcc tccgctgcca cttcacaagc 201 AACTTAACTC GACAGCCAAC AATTTGAAGC TTTGAACAGA TAGCAGATCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00340 Mean Expected Number 0.005 +strand -111 : -102 TCCACGcGTC AC RSP01469 Mean Expected Number 0.008 -strand -39 : -48 TCACATaTGT Totally 2 motifs of 2 different REs have been found Description of REs found 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0493A04.24|complement(22247420..22252457) |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +105 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.14 T - 0.29 C - 0.27 1 agtcgtaatt tccggctaaa aatgcatata gaaggacacg tttcaccttt 51 cacaccggct caaatgtggc agtgaaactt cagttttctc cacaaaaata 101 ataaattaag gaaaaaaatc gtcactacac gtcactcatc cccatctccc 151 aggcttgtcc ggccTATAAA TGcagcctcc ctcccctcta ttctctaatc 201 ACTCAAAACA CTCATCAATG AAATCTGATC AGCGGTAGCT TTTTTTTTTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00566 Mean Expected Number 0.008 -strand -166 : -175 CCTTcTATAT AC RSP00642 Mean Expected Number 0.006 +strand -34 : -27 TAAATGCA AC RSP01035 Mean Expected Number 0.009 -strand -160 : -166 ACGTGTC AC RSP01258 Mean Expected Number 0.005 -strand -67 : -74 TGACGTGT Totally 4 motifs of 4 different REs have been found Description of REs found 542. Group RE: TATA P /AC: RSP00566//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: TATA P /TF: unknown 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 960. Group TF: ABI3; ABI5; AREB1 /AC: RSP01035//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 3 /TF: ABI3; ABI5; AREB1 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0493A04.40|complement(22312712..22313716) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +90 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.16 T - 0.29 C - 0.26 1 atctatatta ctatttttta atttttttat aattatttag gtctcatgca 51 caaaacaaga ggatattacc tcgaaggatg aaataacttt ccccgttaca 101 ctgtCCAATc cgtttattta cacgagaacg tacgtacgcg cgctcgatct 151 cgcgtctcct cccggcctaT ATAAACCcca gtggcgttgc actgagccct 201 AGCTCAAACA CTGTGTACTA CGCAACACAC ACATAGGCAC AGTTAGTGCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00709 Mean Expected Number 0.003 +strand -171 : -163 TAATTATTT AC RSP00933 Mean Expected Number 0.001 +strand -186 : -174 TTTtTAATTTTTT AC RSP00933 Mean Expected Number 0.001 +strand -175 : -163 TTTATAATTaTTT AC RSP01401 Mean Expected Number 0.002 -strand -96 : -106 GACAGTGTaAC AC RSP01604 Mean Expected Number 0.003 +strand +10 : +17 ACTGTGTA Totally 5 motifs of 4 different REs have been found Description of REs found 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 1283. Group TF: TAC1 /AC: RSP01401//OS: Arabidopsis thaliana /GENE: BT2/RE: TAC1 BS /TF: TAC1 1425. Group TF: SPF1 /AC: RSP01604//OS: Ipomoea batatas /GENE: Sporamin; beta-amylase/RE: SP8a /TF: SPF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0690E03.33|complement(22415243..22424674) |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +870 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.13 T - 0.34 C - 0.26 1 cagaatgaga gcaagtttaa cactatagcc aactactggc tccaaatcat 51 ctatagtcaa tttaatagcc cattcatata atagataact attaaaaata 101 tattacatca ttaatacccg gtcccatctc tcatacacac ataatgtctt 151 ggagtccgtg ttgcagccgg cTATAAATCt gcagcccgct ttcttctctc 201 TCTTCTCTTT TTTTTCTTTT ATATCACTGG CTCCCTCCAG CTCGTAGTGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.003 -strand +13 : +4 AAAAAAGAGA AC RSP00635 Mean Expected Number 0.002 +strand -81 : -74 GGTCCCAT AC RSP00859 Mean Expected Number 0.003 +strand -167 : -158 tACTGGCTCC AC RSP00859 Mean Expected Number 0.003 +strand +25 : +34 cACTGGCTCC AC RSP00864 Mean Expected Number 0.005 -strand +3 : -6 AGAGAGAGA AC RSP00891 Mean Expected Number 0.004 +strand -106 : -98 AAAATATAT AC RSP00915 Mean Expected Number 0.009 -strand -150 : -159 GATGATTTGG Totally 7 motifs of 6 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 611. Group RE: NDE Box 3 /AC: RSP00635//OS: Glycine max /GENE: SAUR 15A/RE: NDE Box 3 /TF: unknown 795. Group RE: GACTGGCTCC motif /AC: RSP00859//OS: Zea mays /GENE: H4C7/RE: GACTGGCTCC motif /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0470B03.25|22787901..22793178 |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +120 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.19 T - 0.25 C - 0.30 1 gaagaaaaaa aaatcggcaa aatctgtggc cttgaattct tgaagagcaa 51 aactcaaaat tccaagcaaa gcaccagagc caccttgcca cgtgtaacaa 101 agttgtggag ccatgctggc tctttttttt tgccacgtca catgctgttc 151 atctgagcaa acgtctctaT ATAAACCcgt cccctgcctg ccttgcttgc 201 CACCTATCCC AGCGCCTCTT CCAGGCCACT ACTTCTCTGG GCTCTGGGCC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00002 Mean Expected Number 0.001 -strand -106 : -114 ACACGTGGC AC RSP00113 Mean Expected Number 0.001 -strand -61 : -69 TGACGTGGC AC RSP00175 Mean Expected Number 0.003 -strand -107 : -114 CACGTGGC AC RSP00204 Mean Expected Number 0.004 -strand -105 : -114 tACACGTGGC AC RSP00214 Mean Expected Number 0.006 -strand -61 : -68 TGACGTGG AC RSP00215 Mean Expected Number 0.006 +strand -68 : -61 CCACGTCA AC RSP00219 Mean Expected Number 0.001 -strand -104 : -115 TtACACGTGGCA AC RSP00248 Mean Expected Number 0.007 +strand -69 : -60 GCCACGTCAc AC RSP00445 Mean Expected Number 0.007 -strand -73 : -82 AAAAAAGAGc AC RSP00447 Mean Expected Number 0.004 +strand -136 : -127 AGCAAAGCAc AC RSP00682 Mean Expected Number 0.003 +strand -114 : -105 GCCACGTGtA AC RSP00783 Mean Expected Number 0.000 -strand -105 : -114 TACACGTGGC AC RSP00894 Mean Expected Number 0.004 -strand -163 : -170 AATTCAAG AC RSP00936 Mean Expected Number 0.001 +strand -115 : -104 TGCCACGTGTaA AC RSP00938 Mean Expected Number 0.000 +strand -115 : -104 TGCCACGTGtAA AC RSP01093 Mean Expected Number 0.002 +strand -140 : -130 TCcAAGCAAAG AC RSP01255 Mean Expected Number 0.004 -strand -106 : -113 ACACGTGG AC RSP01280 Mean Expected Number 0.002 -strand -59 : -69 tGTGACGTGGC AC RSP01593 Mean Expected Number 0.000 -strand -105 : -116 TACACGTGGCAa AC RSP01656 Mean Expected Number 0.000 -strand -59 : -70 TgTGACGTGGCA Totally 20 motifs of 20 different REs have been found Description of REs found 2. Group RE: ABRE-3 /AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /TF: unknown 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 212. Group TF: HY5 /AC: RSP00219//OS: Arabidopsis thaliana /GENE: RBCS-1A/RE: G box-1 /TF: HY5 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 738. Group TF: G-box binding TF /AC: RSP00783//OS: Nicotiana tabacum /GENE: OLIGO-GUS/RE: G-box 7 /TF: G-box binding TF 825. Group TF: Dof family /AC: RSP00894//OS: Solanum melongena /GENE: SmCP/RE: ERE 2 /TF: Dof family 865. Group TF: GBF /AC: RSP00936//OS: Lycopersicon esculentum /GENE: RbcS-3A/RE: G box /TF: GBF 867. Group TF: GBF /AC: RSP00938//OS: Arabidopsis thaliana /GENE: RbcS-1A/RE: G box-2 /TF: GBF 1011. Group RE: box 2 /AC: RSP01093//OS: Pisum sativum /GENE: GS2/RE: box 2 /TF: unknown 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 1415. Group TF: GBF /AC: RSP01593//OS: Pisum sativum /GENE: rbcS-3.6/RE: G box /TF: GBF 1474. Group TF: HY5 /AC: RSP01656//OS: Arabidopsis thaliana /GENE: ARF19 (At1g19220)/RE: C/G-box /TF: HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0470B03.26|complement(22791120..22792930) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +551 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.19 T - 0.32 C - 0.18 1 gaatcaaccg ctagcctctt agaaagggaa atcatggcct atgtatgcag 51 tatgtactct aggatattat caagagtaca ctactacaac ttagatattg 101 tttttttttc tctcatcttg catacgcatg catgcagcat ttcgtttcta 151 attggcacga cacgtaTATA CATCgtcgta cgtataccaa aataattaat 201 GCGGTGCGTA TAATTTAGTA GTAGGAGTTT AGAACACGAT GAAAGAATTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00068 Mean Expected Number 0.005 +strand -42 : -33 GACACGTAtA AC RSP00070 Mean Expected Number 0.003 -strand -35 : -42 TACGTGTC AC RSP00108 Mean Expected Number 0.003 +strand -74 : -67 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -67 : -74 CATGCATG AC RSP00709 Mean Expected Number 0.007 -strand -3 : -11 TAATTATTT AC RSP01035 Mean Expected Number 0.009 -strand -36 : -42 ACGTGTC AC RSP01074 Mean Expected Number 0.001 +strand -75 : -66 GCATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand -66 : -75 GCATGCATGC AC RSP01205 Mean Expected Number 0.007 -strand -174 : -183 CCTTTCTAAG AC RSP01288 Mean Expected Number 0.005 -strand -34 : -41 ATACGTGT Totally 10 motifs of 8 different REs have been found Description of REs found 67. Group RE: UV LRE /AC: RSP00068//OS: Arabidopsis thaliana /GENE: CHS/RE: UV LRE /TF: unknown 69. Group TF: TRAB1 /AC: RSP00070//OS: Oryza sativa /GENE: Osem/RE: ABRE motif A /TF: TRAB1 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 960. Group TF: ABI3; ABI5; AREB1 /AC: RSP01035//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 3 /TF: ABI3; ABI5; AREB1 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf 1115. Group RE: EM2 /Group TF: MADS box TFs /AC: RSP01205//OS: Arabidopsis thaliana /GENE: AtCRC/RE: EM2 /TF: MADS box TFs 1185. Group RE: Z-DNA-motif /AC: RSP01288//OS: Arabidopsis thaliana /GENE: cab1/RE: Z-DNA-motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0013B04.19|complement(23043285..23048836) |SUPPORT| 9 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +251 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.14 T - 0.29 C - 0.33 1 aaacattagc ccatggaaac aaacagggcc aggaatcttc taatctccct 51 ttcatgtgtc cctccttttt ttctccctat ccccaaagat ttcacatttt 101 ctaatgagca tcatgccgtc catgagctct gttttttatc ctaacacccc 151 tctgcagccg tgctcaccct cTATAAATAc cccatacagg tgtcttccaa 201 TAGCACCACC ATTTGGAAGA ATCCTCCCCA AGATTGCTCG ATCCCCTCGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00331 Mean Expected Number 0.005 -strand -181 : -189 GTTTCCATG AC RSP01296 Mean Expected Number 0.002 +strand -30 : -22 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -30 : -21 CTATAAATAC Totally 3 motifs of 3 different REs have been found Description of REs found 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0013B04.34|23089837..23091783 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +132 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.23 T - 0.25 C - 0.27 1 acggctcaag gcggcactcc atcaccggac accggggtcc agactactcg 51 tttccgttgg agaaataacc acctttatcc atgttgctta tccgtgaatt 101 gcaacagcat tgATTGTtcg cgtttaattc gcctcggcca tgtaacctcc 151 gacctgatcc tcttggacac TATAAATAga ggccagttca ggcaatgcaa 201 GAGCAGAGAA GCAGAGTACA GCAGGCAGCT CTTCTTCTCT TTGCGAAGGT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00880 Mean Expected Number 0.006 -strand -142 : -151 CAACGGaAAC AC RSP01144 Mean Expected Number 0.000 +strand -138 : -125 AAATAACCACCTTT AC RSP01221 Mean Expected Number 0.005 +strand -135 : -128 TAACCACC AC RSP01223 Mean Expected Number 0.001 +strand -147 : -139 CCGTTGGAG AC RSP01296 Mean Expected Number 0.001 +strand -31 : -23 CTATAAATA AC RSP01301 Mean Expected Number 0.008 +strand -31 : -22 CTATAAATAg AC RSP01708 Mean Expected Number 0.004 +strand -31 : -22 CTATAAATAG AC RSP01708 Mean Expected Number 0.004 -strand -22 : -31 CTATTTATAG Totally 8 motifs of 7 different REs have been found Description of REs found 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 1062. Group RE: GARE /Group TF: MYBGA (GAMyb) /AC: RSP01144//OS: Oryza sativa /GENE: alpha-Amy8/RE: GARE /TF: MYBGA (GAMyb) 1128. Group RE: GARE /AC: RSP01221//OS: Oryza sativa /GENE: Amy3E (Amy8)/RE: GARE /TF: unknown 1129. Group TF: C-myb /AC: RSP01223//OS: Oryza sativa /GENE: Amy3E (Amy8)/RE: C-myb motif /TF: C-myb 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0451G12.21|complement(23166344..23167571) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.24 T - 0.20 C - 0.35 1 gatgaaaacg gccaccggcg cgtggcgcat gcactcgcat tgacccaacc 51 cgagccgttt cgcgagtgcg agccggacac atcgcccctg gttcgcttcc 101 cgtggaagcg gttaaaagat gccgcaccac actacgtgcg ccacgtacat 151 catcccgtgc catgtccaTA TAAACGcttc acccatcgag cgcttggctc 201 ACCACGGAAA CACTCATTCT CGGTGTCTCT CACTCGCTCT GTACGTACGT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00043 Mean Expected Number 0.005 -strand -54 : -61 TACGTGGC AC RSP00051 Mean Expected Number 0.000 +strand -61 : -52 GCCACGTACA AC RSP00052 Mean Expected Number 0.005 -strand -53 : -63 GTACGTGGCGC AC RSP00065 Mean Expected Number 0.002 -strand -55 : -63 ACGTGGCGC AC RSP00075 Mean Expected Number 0.001 -strand -53 : -62 GTACGTGGCG AC RSP01020 Mean Expected Number 0.005 +strand -199 : -193 ATGAAAA AC RSP01276 Mean Expected Number 0.008 -strand -53 : -60 GTACGTGG AC RSP01511 Mean Expected Number 0.006 -strand -76 : -83 GCGGCATC Totally 8 motifs of 8 different REs have been found Description of REs found 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 50. Group RE: A3 /AC: RSP00051//OS: Hordeum vulgare /GENE: HVA22/RE: A3 /TF: unknown 51. Group RE: ABRE /AC: RSP00052//OS: Oryza sativa; /GENE: Rab-16A/RE: ABRE /TF: unknown 64. Group TF: EmBP-1 /AC: RSP00065//OS: Triticum aestivum /GENE: Em/RE: Em1a /TF: EmBP-1 74. Group TF: TAF-1 /AC: RSP00075//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: Iwt /TF: TAF-1 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1175. Group RE: Box III /AC: RSP01276//OS: Petroselinum crispum /GENE: CHS/RE: Box III /TF: unknown 1365. Group RE: OLS /AC: RSP01511//OS: Triticum aestivum /GENE: H1 (TH315)/RE: OLS /TF: unknown ||Identical REs AC: RSP01512 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1111_E05.19|complement(23246564..23249204) |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +126 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.24 T - 0.16 C - 0.31 1 ctgggctggt gcgaccaact ggttcaaaac tccatcgcac cactgactcg 51 tccaaaatgc aatcacctgc acgaacgaac gcacgcgcga tgcttccgat 101 gatcgaagca gccagcaaag gcgagaccgc gagaccttct catgttggaa 151 acgatggcgt cctcgcgTAT AAATTcatcg cccgtgcact gcagcgaact 201 CACATCGAGA TCAACGATAG AGCCAAGCAC AAACACGAGC TAGACGACGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.007 +strand -33 : -27 TATAAAT AC RSP01250 Mean Expected Number 0.006 +strand -147 : -138 AAAATgCAAT AC RSP01692 Mean Expected Number 0.003 -strand -94 : -101 TTCGATCA Totally 3 motifs of 3 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C 1509. Group RE: CARE J /AC: RSP01692//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE J /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1111_E05.24|complement(23257631..23259977) |SUPPORT| 4 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +182 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.19 T - 0.26 C - 0.24 1 aacttgtgaa aattttcttc gatcacccgt tccattccta ggagcagaaa 51 tggtggtgca actgacgcat gcaaacgaca aattttatag tgatcgcttc 101 aactgcaact gtataagcta cgtacaaatt aaaagccgtg tacgttcttt 151 ctttaatcct ccacTATAAA TAcgtggccc gagcgcgtca caaagctatc 201 AATCAGATCG AGCAAGACGA ACAGACCAGA CGAGAGATTG CCTTTTTAGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00043 Mean Expected Number 0.002 +strand -30 : -23 TACGTGGC AC RSP00051 Mean Expected Number 0.007 +strand -84 : -75 GCtACGTACA AC RSP00064 Mean Expected Number 0.004 +strand -32 : -23 AaTACGTGGC AC RSP00819 Mean Expected Number 0.003 -strand -23 : -32 GCCACGTaTT AC RSP00880 Mean Expected Number 0.008 +strand -101 : -92 CAACtGCAAC AC RSP01034 Mean Expected Number 0.008 +strand -29 : -23 ACGTGGC AC RSP01296 Mean Expected Number 0.003 +strand -37 : -29 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -37 : -28 CTATAAATAC AC RSP01692 Mean Expected Number 0.004 +strand -183 : -176 TTCGATCA AC RSP01714 Mean Expected Number 0.001 -strand -22 : -33 GGcCACGTATTT Totally 10 motifs of 10 different REs have been found Description of REs found 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 50. Group RE: A3 /AC: RSP00051//OS: Hordeum vulgare /GENE: HVA22/RE: A3 /TF: unknown 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 765. Group TF: ACE-binding TF /AC: RSP00819//OS: Arabidopsis thaliana /GENE: F3H/RE: ACE-core (AtF3H) /TF: ACE-binding TF 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1509. Group RE: CARE J /AC: RSP01692//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE J /TF: unknown 1522. Group TF: STF1/HY5 /AC: RSP01714//OS: Arabidopsis thaliana /GENE: REH1/PIN3 (At1g70940)/RE: G/A-box /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0419H09.28|complement(23724078..23725312) |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +30 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.19 G - 0.19 T - 0.14 C - 0.48 1 atggccccac cccacacact ctccacaccc gggcccaccc ccacccgctt 51 ccccagaaat attgctacgc ctcctcacga cacctcctca aaagtcgcgc 101 ccccgctccg gcccactgga ccaagctcac cgcgctcggc ccatggctgg 151 acccctccct cccggctaTA TAAACCtctc caccaccccg cccctaccac 201 CACGGTGTGG CGAAGGTGTC ACTGACAGCC ATGGCCCACA AGCGCGGCCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.006 -strand -27 : -32 TTTATA AC RSP00095 Mean Expected Number 0.008 -strand -163 : -171 GTGGGCCCG AC RSP00146 Mean Expected Number 0.001 -strand -28 : -34 TTATATA AC RSP00147 Mean Expected Number 0.006 +strand -32 : -27 TATAAA Totally 4 motifs of 4 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0605H02.22|complement(<23959246..23965172) |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +3844 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.31 C - 0.22 1 aagaatagta agtctggata atcttctacg taaacactct aacgagatct 51 tacacctgaa ccacctcaaa aaccataagt tagacctatt tttgggtact 101 gtaacttcct cgagattaga ttagacgagg ttatcttgaa acaactcatg 151 ctgttaccag tggctggcTA TAAAACgctc gtcggtgtat gttattacct 201 CGCCTTACTC ACGGTGATTA GTTTAACCCC ATCCTTTGGT TGGGTCTCAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00746 Mean Expected Number 0.001 -strand +32 : +21 ATGGGGTTAAAc AC RSP01209 Mean Expected Number 0.007 +strand -115 : -106 CTATTTTTGG AC RSP01347 Mean Expected Number 0.000 +strand +25 : +35 AACCCCATCCT Totally 3 motifs of 3 different REs have been found Description of REs found 708. Group TF: GT-1 /AC: RSP00746//OS: Nicotiana plumbaginifolia /GENE: Cab-E/RE: box 6 /TF: GT-1 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs 1230. Group RE: IMH2 /AC: RSP01347//OS: Cucumis sativus /GENE: ICL/RE: IMH2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0686H11.17|complement(24090709..24091700) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +164 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.14 T - 0.20 C - 0.36 1 gcagtaaaga ttgccatcgg acgcagtaaa acgtgtcact accccactgt 51 tacaaaaaaa aaaaacatca ccatttgctg tatttttaac gttaaccaca 101 ccaccacact agcgagtagc gatagaccgg gaggccactc caccccatcc 151 ccacactcta gaagcgtcTA TAAATAcctc gactcctccc actgtatcca 201 CTACCATCTC CCGTGTCCTC CTCCCACCTC GCTCCCCCGT AAAACCCGAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00565 Mean Expected Number 0.004 +strand -121 : -115 GTATTTT AC RSP01035 Mean Expected Number 0.008 +strand -170 : -164 ACGTGTC AC RSP01296 Mean Expected Number 0.002 +strand -33 : -25 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -33 : -24 CTATAAATAC Totally 4 motifs of 4 different REs have been found Description of REs found 541. Group RE: AT-rich G /AC: RSP00565//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich G /TF: unknown 960. Group TF: ABI3; ABI5; AREB1 /AC: RSP01035//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 3 /TF: ABI3; ABI5; AREB1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: B1142B04.37|24287931..24289559 |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +75 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.17 G - 0.28 T - 0.20 C - 0.34 1 acaggcaaca gcgcggcgcc ggcgaacgtc acgcccaaga ttatattccc 51 cctctcgcgc tcgcgcgcgc cgcgacgtcg tcggagccaa cattattttt 101 ctgtttcctg tcaccgtcgc cgttgatctc aagcgagatt tgaggtttgg 151 ccacgacgac gcctgccTAT AAATAccagg tggtggtcac cgcccggcgg 201 CGTCGATCGA TCCGTCGCAG TCGTCTCCGG CGAGAAATCG GCTGCGCCCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.009 -strand -28 : -33 TTTATA AC RSP00147 Mean Expected Number 0.009 +strand -33 : -28 TATAAA AC RSP00509 Mean Expected Number 0.000 +strand -33 : -22 TATAAATACCAG AC RSP00695 Mean Expected Number 0.002 +strand -33 : -27 TATAAAT AC RSP00759 Mean Expected Number 0.002 +strand -161 : -155 ATTATAT AC RSP00878 Mean Expected Number 0.006 +strand -25 : -18 CCAGGTGG AC RSP00880 Mean Expected Number 0.010 -strand -76 : -85 CAACGGCgAC AC RSP00996 Mean Expected Number 0.002 +strand -79 : -70 GTTGATCTCA AC RSP01103 Mean Expected Number 0.002 -strand -53 : -60 AAACCTCA AC RSP01296 Mean Expected Number 0.000 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -34 : -25 CTATAAATAC Totally 11 motifs of 11 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 721. Group RE: submotif D /AC: RSP00759//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif D /TF: unknown 814. Group TF: RPCF-1 /AC: RSP00878//OS: Arabidopsis thaliana /GENE: PCNA/RE: Site I /TF: RPCF-1 816. Group TF: Dof family /AC: RSP00880//OS: Hordeum vulgare /GENE: Al21/RE: M1 /TF: Dof family 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) 1021. Group RE: AC1 /AC: RSP01103//OS: Spinacia oleracea /GENE: rps22/RE: AC1 /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1345_D02.37|24581889..24582465 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +63 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.16 T - 0.15 C - 0.35 1 aaaaaaaaaa gaaaaagaaa aacacggcga atcccgtgaa atcttcgctt 51 caattcgctc ccaagcacac acgccccggc ggcggcgccc gtagcatctc 101 tgatctctct cagcctttca aaaaccatac gcgcgcacaa acgcgccatc 151 tctccatctc gccggcgtcg cTATAAAACg cggcgatcac gcttgcatct 201 CACTCACACA ACAAACCACC CCCAAGATCA AGAACAACAA CAACAACAAC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.007 -strand -16 : -22 CGCCGCG AC RSP00613 Mean Expected Number 0.009 +strand +27 : +34 ATCAAGAA Totally 2 motifs of 2 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 589. Group RE: UN Z1 /AC: RSP00613//OS: Lycopersicon esculentum /GENE: rbcS2/RE: UN Z1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1345_D02.47|24608951..24610330 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +826 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.20 T - 0.27 C - 0.24 1 ctagctagca aaaaggccga tcagtttttg attagtgaat gggagcagta 51 tttttgatcc ggtcacgcag ggccacaaat taaagctgga ttaattgctt 101 ttaattaatc gcagtagttc atctcgaaaa taATTGAatt agttgggacc 151 attttggcct cgaaacccct cTATAAATAg cccctccacc tcaacacatc 201 GCTTCACACA CGAGATCTCA TCGATCAGTC ACAGTGACGC AGTGAGCACT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand -200 : -193 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -193 : -200 CTAGCTAG AC RSP00681 Mean Expected Number 0.002 +strand -99 : -91 TAATTAATC AC RSP00698 Mean Expected Number 0.003 +strand -100 : -90 TtAATTAATCG AC RSP00847 Mean Expected Number 0.008 +strand -15 : -6 CCACCTCAaC AC RSP01296 Mean Expected Number 0.003 +strand -30 : -22 CTATAAATA AC RSP01708 Mean Expected Number 0.008 +strand -30 : -21 CTATAAATAG AC RSP01708 Mean Expected Number 0.008 -strand -21 : -30 CTATTTATAG Totally 8 motifs of 6 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1134_H03.9-1|24693386..24701508 |SUPPORT| 9 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +255 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.13 T - 0.27 C - 0.31 1 ttctttaatt aattaattaa ttaacatata tatccctttt tactgggctt 51 ttgcagccaa ccctgctctc ccaaatcacg gtaaaaaggt cgtttagaat 101 tccaaacacg gtgtaaaaaa gcgcagttga atcaTCAATt ctgtgatggc 151 aaaaccacct acctggcgcc TATAAACGca aaaaacccaa taaatctcgc 201 CCTCGTTGCC TCCCCTCCCT GCCTACCCCC ATCTCCACCT CCGCCTCCAC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00961 Mean Expected Number 0.005 -strand -146 : -153 TGCAAAAG Totally 1 motifs of 1 different REs have been found Description of REs found 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1770_H02.9|complement(26062115..26065050) |SUPPORT| 9 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +143 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.16 T - 0.37 C - 0.18 1 tcgaatattt ttttctagtg ccgagcattt ctagctccat aaattcatag 51 agctggatct ataattatat atataacatt tgaatcaatc gttttgtttt 101 cattttaggt gaaatataaa attttgaatc actataattt aacataggaa 151 tttcaaatac agtgTATAAA CAtgtggctg actttctttt ttaaaatttt 201 AATCCATCTC AAACACTGGC GCGTCGGCGG TCAGTGGCCC GTCCACTCGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00683 Mean Expected Number 0.003 -strand +51 : +42 GCCgAGTGGA AC RSP00698 Mean Expected Number 0.005 +strand -120 : -110 TGAATcAATCG AC RSP00790 Mean Expected Number 0.001 -strand -153 : -163 aTGAATTTATG Totally 3 motifs of 3 different REs have been found Description of REs found 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 743. Group RE: A segment /AC: RSP00790//OS: Flaveria trinervia /GENE: ppcA1/RE: A segment /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1770_H02.15|complement(26086610..26090401) |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +132 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.16 T - 0.27 C - 0.24 1 aaacagagca agcacagcta gtagctagcc aatattcaga taagagagtg 51 gagtcaggaa ctcattagaa gagacatctt taatttgctc atggccattg 101 ggacCCAATc acccaacaca tttgataatt gatactccat tttgattcct 151 cttcttcccc agctctagct ataTATAAAC Cactccaatg gcagcacaca 201 AATTCATGAA TTCCCAGTTC AGAGTTTCAG GTACTCTCAA TCTGAAACAT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01469 Mean Expected Number 0.010 -strand -76 : -85 TCAaATGTGT AC RSP01602 Mean Expected Number 0.007 +strand +35 : +42 TCTCAATC Totally 2 motifs of 2 different REs have been found Description of REs found 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) 1423. Group RE: Inr /AC: RSP01602//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0702E04.24|complement(26308830..26311693) |SUPPORT| 3 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +90 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.25 G - 0.18 T - 0.20 C - 0.37 1 gcagtaaagt taaaaaaaga gaaaaaaatc tagttgagga ggaaatgcat 51 gagcaagttt accattacca ccccggctgg gctctgggct gtcgtccgcc 101 tcagcgtctt aaatgcaaca tctaactctc accaccctcc tctTCAATgc 151 ccccgtctcc ctctcgccTA TAAACCacgc cgcccgccac cgccgctcgc 201 CATCGCCACC GTCGTTCACA CCACACCACC TGCTGCACAC AGCTCGATCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.003 +strand -188 : -179 AAAAAAGAGA AC RSP00629 Mean Expected Number 0.004 +strand -177 : -170 AAAAATCT AC RSP00642 Mean Expected Number 0.003 +strand -91 : -84 TAAATGCA AC RSP00888 Mean Expected Number 0.001 +strand -177 : -169 AAAAATCTA AC RSP01470 Mean Expected Number 0.006 -strand -149 : -158 TCATGCATtT Totally 5 motifs of 5 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 820. Group TF: CCA1 /AC: RSP00888//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: CCA1 motif (2) /TF: CCA1 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0702C09.33|complement(26480623..26483466) |SUPPORT| 5 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +172 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.39 G - 0.20 T - 0.20 C - 0.21 1 acatattcag agtagtggag agagggacag atctagaggt agaaaaagaa 51 aattcatata aatgatatat cagagtgaaa aagaaatatc aagcacaaga 101 aaaaaaagca aaggttagat atgcatctcc ccctactgta caccaccaaa 151 agtggagggt ctccaactaT ATAAACActg agccatggcc aaggccaaac 201 CACACATGCA GTTGTAGTAG CACTTAAGCC TTCCTCTCTA GCTAGCATCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00157 Mean Expected Number 0.002 +strand -149 : -138 ATTcATATAAAT AC RSP00157 Mean Expected Number 0.002 -strand -138 : -149 ATTTATATgAAT AC RSP00270 Mean Expected Number 0.005 -strand -45 : -55 TcCACTTTTGG AC RSP00503 Mean Expected Number 0.003 +strand +38 : +45 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +45 : +38 CTAGCTAG AC RSP00863 Mean Expected Number 0.000 -strand +39 : +31 AGAGAGGAA AC RSP01643 Mean Expected Number 0.000 +strand -158 : -146 aAAAAGAAAATTC Totally 7 motifs of 5 different REs have been found Description of REs found 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 262. Group TF: OBP1 /AC: RSP00270//OS: Arabidopsis thaliana /GENE: GST6/RE: OBP1 BS /TF: OBP1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 1463. Group TF: WRAF1; WRAF2 /AC: RSP01643//OS: Nicotiana tabacum /GENE: tpoxN1/RE: VWRE (np6a-1) /TF: WRAF1; WRAF2 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OSJNBa0033D24.26|complement(26524008..26524575) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +124 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.20 T - 0.32 C - 0.19 1 aatttaattt gattaattca gtgcttcctt cccgttacat tacactgcat 51 tacattaaat tacattacat tacatggttg ggaaaaaata attaaggagg 101 aagaagaaat taaagggggg catgcATTGA tgcagatcac tttcagaggg 151 tttggccggc TATAAATAta tatgcttagc taggctaaca ctcaagcctc 201 TCTTTGAGAG GCAGCTTAGC TGCTTGCTGC TGCTGCCTGC ATTCTTCTTC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00698 Mean Expected Number 0.004 -strand -181 : -191 TGAATTAATCa AC RSP00709 Mean Expected Number 0.005 -strand -107 : -115 TAATTATTT AC RSP01296 Mean Expected Number 0.003 +strand -41 : -33 CTATAAATA Totally 3 motifs of 3 different REs have been found Description of REs found 664. Group RE: Box III /AC: RSP00698//OS: Brassica oleracea /GENE: SLG13/RE: Box III /TF: unknown 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0666G10.110|26700343..26701318 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +236 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.16 T - 0.35 C - 0.25 1 ttgttgtcaa agtccaaata acaatgcttc tctaattggt atatgtcgag 51 ccttttgctt tttatctatg cctccaaagt ttccttgctt aatctgaagt 101 tttggactgc ttaatgacag gttgcatgca cactaatccc acctctttgt 151 tgagactttc tctcctcTAT AAATGaactc atgtgccctt aggacaaggc 201 ACATGTCTCT GAACCTCCTG AACCCTCTTG CTGTCTCATC CATGCAAAGT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00243 Mean Expected Number 0.004 +strand -18 : -11 GTGCCCTT AC RSP00301 Mean Expected Number 0.007 +strand +43 : +49 TGCAAAG AC RSP00304 Mean Expected Number 0.004 +strand -86 : -79 TGACAGGT Totally 3 motifs of 3 different REs have been found Description of REs found 236. Group TF: MNF1; MNB1a; MNB1b /AC: RSP00243//OS: Zea mays /GENE: PEPC/RE: MNF1 BS core /TF: MNF1; MNB1a; MNB1b 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0623F08.31|complement(27050890..27052505) |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +152 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.27 T - 0.11 C - 0.40 1 gaagcgacaa cgcgtcctgg gccgtcggat ccgcaccggc gcgcggatta 51 atgcggcggg gcccggtaca ggtcaccacg ggtccccacc acgacccggt 101 tggggcggtg gccccgggcc acatcgaccg cacaagggac cccaccgcca 151 agtgagacca cccccaccac ttGATAAATC caactcaccc cattcgcagc 201 AGCGAAGCGA AGCGAGTGAA CACACACCTC TCCCCCCACC CTTTCCCGCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00015 Mean Expected Number 0.002 +strand +42 : +49 TTTCCCGC AC RSP00253 Mean Expected Number 0.002 -strand -152 : -159 AATCCGCG AC RSP00357 Mean Expected Number 0.008 +strand -20 : -13 CAACTCAC AC RSP01185 Mean Expected Number 0.010 +strand -21 : -10 CCAACTcACCCC AC RSP01497 Mean Expected Number 0.008 +strand -180 : -171 GCCGTCGGAT Totally 5 motifs of 5 different REs have been found Description of REs found 14. Group TF: E2F1 /AC: RSP00015//OS: Arabidopsis thaliana /GENE: AtCDC6/RE: E2F1-BE /TF: E2F1 ||Identical REs AC: RSP00165 RSP00298 246. Group RE: Oct (r) /AC: RSP00253//OS: Triticum aestivum /GENE: H3/RE: Oct (r) /TF: unknown ||Identical REs AC: RSP01503 RSP01504 342. Group RE: CARE1 /AC: RSP00357//OS: Oryza sativa /GENE: Rep-1/RE: CARE1 /TF: unknown 1097. Group RE: box 2 /AC: RSP01185//OS: Petunia hybrida /GENE: chsA/RE: box 2 /TF: unknown 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1323_A06.22|27118836..27119487 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.26 T - 0.14 C - 0.36 1 tctccgaccc cggccgagac gcacggcggg gaagaggctc acagtccaag 51 agcgtgacgc atgttcggta ccacgcgcac aaactgccgt gctcggcttc 101 tccatcgatc accggcatag gtgagccatg caaagctcgc cgggcgcccc 151 caagctccgg ccacccccTA TAAAACccgc cgctcctcac cgtcaccggc 201 AAGCACAGCA AAGCAGCAGC AGCAAAGGTA AGGTAATATT TGCAGCATCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00164 Mean Expected Number 0.009 +strand +34 : +39 TAATAT AC RSP00206 Mean Expected Number 0.000 +strand +28 : +39 GTaAGGTAATAT AC RSP00447 Mean Expected Number 0.007 +strand +7 : +16 AGCAAAGCAg AC RSP00871 Mean Expected Number 0.002 +strand -81 : -72 GGTGAGcCAT Totally 4 motifs of 4 different REs have been found Description of REs found 159. Group RE: TATA3 /AC: RSP00164//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA3 /TF: unknown ||Identical REs AC: RSP01047 199. Group TF: GT-1 /AC: RSP00206//OS: Pisum sativum /GENE: rbcS-3A/RE: BOX II* /TF: GT-1 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 807. Group RE: GLM1 /AC: RSP00871//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0439B07.22|complement(27579704..27584965) |SUPPORT| 9 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +295 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.14 T - 0.26 C - 0.31 1 cgatcttgac ttgactcgca cctgcagctg ccacgtcaga gccacgtcgg 51 attccaacac gtattccggc gtgggcatcg gctctttcta gagcaaaccc 101 caaatcaaat cttgcacgaa cacccctcca acttccccac gtttacaaat 151 ccaaccctca cccTATAAAT Aataaatagc gaattcttac tctttttttt 201 TATTAATATA TAATAAAAGA AGATCGAAGC GAAGCGCACC TCTCTCCTCT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00022 Mean Expected Number 0.003 +strand +10 : +18 ATAATAAAA AC RSP00024 Mean Expected Number 0.009 -strand -27 : -34 TATTATTT AC RSP00113 Mean Expected Number 0.001 -strand -163 : -171 TGACGTGGC AC RSP00214 Mean Expected Number 0.007 -strand -163 : -170 TGACGTGG AC RSP00215 Mean Expected Number 0.007 +strand -170 : -163 CCACGTCA AC RSP00247 Mean Expected Number 0.005 +strand -171 : -162 GCCACGTcAG AC RSP00248 Mean Expected Number 0.005 +strand -171 : -162 GCCACGTCAG AC RSP00248 Mean Expected Number 0.005 +strand -160 : -151 GCCACGTCgG AC RSP00445 Mean Expected Number 0.009 -strand -3 : -12 AAAAAAGAGt AC RSP00986 Mean Expected Number 0.003 +strand -159 : -152 CCACGTCG AC RSP01160 Mean Expected Number 0.000 -strand -149 : -160 ATCcGACGTGGC AC RSP01288 Mean Expected Number 0.005 -strand -137 : -144 ATACGTGT AC RSP01296 Mean Expected Number 0.003 +strand -38 : -30 CTATAAATA AC RSP01656 Mean Expected Number 0.000 -strand -161 : -172 TCTGACGTGGCA AC RSP01702 Mean Expected Number 0.007 +strand -145 : -136 AACACGTATT Totally 15 motifs of 14 different REs have been found Description of REs found 21. Group TF: PCF1 /AC: RSP00022//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX1 /TF: PCF1 23. Group TF: PCF1 /AC: RSP00024//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX3 /TF: PCF1 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 1073. Group RE: G-box /Group TF: CG-1 /AC: RSP01160//OS: Nicotiana plumbaginifolia /GENE: CAB/RE: G-box /TF: CG-1 1185. Group RE: Z-DNA-motif /AC: RSP01288//OS: Arabidopsis thaliana /GENE: cab1/RE: Z-DNA-motif /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1474. Group TF: HY5 /AC: RSP01656//OS: Arabidopsis thaliana /GENE: ARF19 (At1g19220)/RE: C/G-box /TF: HY5 1511. Group RE: ACGT1 /AC: RSP01702//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: OJ1150_A11.29|27670983..27677282 |SUPPORT| 7 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +224 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.33 C - 0.24 1 gcacagatga tccagtaata ctctgacacg cctagcagga tgttaggtga 51 tcgtctgatc aagcactagt gatcgataat cctgctcctt ttttattact 101 tattttttga ccgaattggt ccagcttatA TTGGaagcaa caagagatcg 151 atttgcctat ctaattgcct aTATATATCt gcacatgagc ctccctcttg 201 CGTGCCTCAC TCACAGTCAC AGGTGCTTGC TTAGCTTAGC TTAGCTTTGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00320 Mean Expected Number 0.002 -strand -120 : -130 GATtATCGATC AC RSP01237 Mean Expected Number 0.007 +strand -32 : -23 CTaTATATAT Totally 2 motifs of 2 different REs have been found Description of REs found 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0562A06.41|27823970..27829291 |SUPPORT|12 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.18 T - 0.31 C - 0.16 1 gatggacaaa gtacacatgt atagataaaa tgatcaaacg agatggatga 51 gaaaaacagg taattaacta ctcctactat ttgtatttat ttattactaa 101 atagatacta tttctaaatg tacagcacct gtggatcata gtacaccatg 151 tacacgagta taaaataaaa TATAAATAgg gacatccagg tcatgtcatt 201 CATTTCTAGC TAGTTAGTAT CTCATCTCCT TTTTGCTGAG GCTGAGGGAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00460 Mean Expected Number 0.005 +strand -11 : -2 GtCATGTCAT AC RSP00503 Mean Expected Number 0.002 +strand +6 : +13 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand +13 : +6 CTAGCTAG Totally 3 motifs of 2 different REs have been found Description of REs found 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0543D10.41|27998873..28000699 |SUPPORT| 1 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +29 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.29 T - 0.20 C - 0.17 1 gggaagggat gtagtaccta gctactcttg taccagctag attaagtata 51 aaccaaaaac aacgggagta gtagtagtaa gaatgtaaaa cggttccaac 101 ataacgcaac aacggaacgg ttggatattc ggttgggagg agaagggaga 151 ttccgtttga gtaggtTATA AATAgcaagg aatacatacg tacgttccaa 201 ATCATCACAA AGCAAGCAAT TAAGCTGGCA TGGGCGGCGG CGGCGGGGAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00914 Mean Expected Number 0.001 -strand +6 : -4 GATGATTTGG AC RSP00915 Mean Expected Number 0.001 -strand +6 : -4 GATGATTTGG AC RSP01711 Mean Expected Number 0.007 +strand -164 : -155 CTAGATTAAG Totally 3 motifs of 3 different REs have been found Description of REs found 845. Group RE: B2 /Group TF: Opaque-2 /AC: RSP00914//OS: Zea mays /GENE: b-32/RE: B2 /TF: Opaque-2 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 1519. Group TF: RIN /AC: RSP01711//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Others /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 8 ( 2 contigs)|GENE: P0705A05.135|28101048..28102681 |SUPPORT| 2 exon(s)|Contig: NT_1072391.txt | -200:+51 from mRNA start|,5"-UTR: +83 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.22 T - 0.26 C - 0.23 1 cggcgcatcg atcgatctgt gcatgcacaa taatacaatg ctgttacagc 51 agctagccta gctagttaag ttacaccgac aagtgcaggc acgtacggta 101 catttggttt gctgcatcga tggaGCAATc atgcatgtat gtatgcagtg 151 ctcccggccg gcTATAAATA cccatatata tccccaggca gcaagcatat 201 GTAGTATGCA GATAGCTAGC AGCAAATTAA TTATATATAT ATAATCCTCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -71 : -64 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -64 : -71 CATGCATG AC RSP00503 Mean Expected Number 0.003 +strand -143 : -136 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -136 : -143 CTAGCTAG AC RSP01296 Mean Expected Number 0.002 +strand -39 : -31 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -39 : -30 CTATAAATAC AC RSP01470 Mean Expected Number 0.007 +strand -72 : -63 TCATGCATGT Totally 7 motifs of 5 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBa0069P02.20|complement(546275..549785) |SUPPORT|12 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +155 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.24 G - 0.16 T - 0.28 C - 0.31 1 gtggttttgc tttgcttggt cgtctccaaa ttgaccatgg caatccaatc 51 ctattcttac tcgggtcggg ggtcagagcg caccgcatat cgcatcattt 101 ttttcgggca atCCAATcgt ataggtttcc actacatact ttcccatttt 151 tttcttacac tttggttcTA TAAAACgccg cacatgacgt cgaaagtcac 201 CCCGCTATCG CAGCAATCCA AAATCCCCAA CCCAACCCAA CCCAACCCAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00441 Mean Expected Number 0.008 -strand -35 : -44 AcCAAAGTGT AC RSP00447 Mean Expected Number 0.007 -strand -185 : -194 AGCAAAGCAA AC RSP00467 Mean Expected Number 0.003 -strand -164 : -173 TGGTCAATTt AC RSP01091 Mean Expected Number 0.003 -strand -30 : -40 ATAGAAcCAAA AC RSP01275 Mean Expected Number 0.002 -strand -8 : -17 TCgACGTCAT AC RSP01621 Mean Expected Number 0.008 +strand -45 : -36 TACACTTTgG Totally 6 motifs of 6 different REs have been found Description of REs found 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 445. Group RE: ERE1 /AC: RSP00467//OS: Dianthus caryophyylus /GENE: hcbt2/RE: ERE1 /TF: unknown 1009. Group RE: box 1 /AC: RSP01091//OS: Pisum sativum /GENE: GS2/RE: box 1 /TF: unknown 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown 1441. Group TF: GmDof4; GmDof22 /AC: RSP01621//OS: Glycine max /GENE: Synthetic OLIGO/RE: E4 /TF: GmDof4; GmDof22 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OJ1451_A02.24|complement(723187..727947) |SUPPORT| 3 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +43 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.23 T - 0.22 C - 0.22 1 aatcttctgg gcatcatgaa atcggattag ataaaaagta atctgtacta 51 gaacttacca aaattttgca gctaggggca tgtagagcaa gcaaacgcct 101 cggagacgga tgaacaacaa gcccggctca tcgttcgcgt gcccttgtcg 151 ctcgcggcga cgacacTATA AATActtgca cgtagccagt gacgaatccc 201 AGAACGAAAA TAGAGAAAAA TTAATTTGGG AGTACTAATT AAGATGTCGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.007 -strand -42 : -48 CGCCGCG AC RSP00189 Mean Expected Number 0.003 +strand -24 : -15 TgCACGTAGC AC RSP00243 Mean Expected Number 0.001 +strand -62 : -55 GTGCCCTT AC RSP01296 Mean Expected Number 0.002 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -35 : -26 CTATAAATAC Totally 5 motifs of 5 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 236. Group TF: MNF1; MNB1a; MNB1b /AC: RSP00243//OS: Zea mays /GENE: PEPC/RE: MNF1 BS core /TF: MNF1; MNB1a; MNB1b 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBb0066C12.38-1|complement(1342974..1346322) |SUPPORT|10 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +53 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.16 T - 0.30 C - 0.25 1 aaaacgtata aggtgtaaaa taaaacatat tttatgttca cgttcataat 51 taaaagttac tatattatga aaatgatata tggtgtgaaa ctgtgaaatg 101 agacatattt tcgtgtttag ttttagtctg gcggcaaacc gccgtgccgg 151 ctcagtcgct gtaaacgccT ATAAAACctc caccatatca cacagcagct 201 CACTTGTCTC GCTTCCTCCT CCGACTCGCC TCTTCCCACC AACTCCTTCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.004 +strand -115 : -105 TGAAAcTGTGA AC RSP00166 Mean Expected Number 0.002 -strand -63 : -70 TTTGCCGC AC RSP00438 Mean Expected Number 0.010 +strand -71 : -66 GGCGGC AC RSP00807 Mean Expected Number 0.010 -strand -66 : -71 GCCGCC AC RSP00943 Mean Expected Number 0.002 -strand -100 : -110 TCATTTCACAg AC RSP01104 Mean Expected Number 0.007 +strand -27 : -20 AAACCTCC AC RSP01596 Mean Expected Number 0.002 +strand -110 : -100 cTGTGAAATGA Totally 7 motifs of 7 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 160. Group TF: E2F /AC: RSP00166//OS: Nicotiana tabacum /GENE: RNP2/RE: E2Fb /TF: E2F 418. Group RE: PR-box /AC: RSP00438//OS: Arabidopsis thaliana /GENE: PR-1/RE: PR-box /TF: unknown 760. Group RE: GCC box /Group TF: Pti4 /AC: RSP00807//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: GCC box /TF: Pti4 ||Identical REs AC: RSP00809 RSP00811 RSP00814 RSP00921 RSP01328 872. Group TF: GBF /AC: RSP00943//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box III /TF: GBF 1022. Group RE: AC2 /AC: RSP01104//OS: Spinacia oleracea /GENE: rps22/RE: AC2 /TF: unknown 1417. Group RE: Box III /AC: RSP01596//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBb0066C12.38-2|complement(1343559..1346321) |SUPPORT| 9 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +52 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.16 T - 0.30 C - 0.25 1 aaacgtataa ggtgtaaaat aaaacatatt ttatgttcac gttcataatt 51 aaaagttact atattatgaa aatgatatat ggtgtgaaac tgtgaaatga 101 gacatatttt cgtgtttagt tttagtctgg cggcaaaccg ccgtgccggc 151 tcagtcgctg taaacgccTA TAAAACctcc accatatcac acagcagctc 201 ACTTGTCTCG CTTCCTCCTC CGACTCGCCT CTTCCCACCA ACTCCTTCCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.004 +strand -116 : -106 TGAAAcTGTGA AC RSP00166 Mean Expected Number 0.002 -strand -64 : -71 TTTGCCGC AC RSP00943 Mean Expected Number 0.002 -strand -101 : -111 TCATTTCACAg AC RSP01104 Mean Expected Number 0.007 +strand -28 : -21 AAACCTCC AC RSP01596 Mean Expected Number 0.002 +strand -111 : -101 cTGTGAAATGA Totally 5 motifs of 5 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 160. Group TF: E2F /AC: RSP00166//OS: Nicotiana tabacum /GENE: RNP2/RE: E2Fb /TF: E2F 872. Group TF: GBF /AC: RSP00943//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box III /TF: GBF 1022. Group RE: AC2 /AC: RSP01104//OS: Spinacia oleracea /GENE: rps22/RE: AC2 /TF: unknown 1417. Group RE: Box III /AC: RSP01596//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0523B07.38-1|complement(1491582..1497074) |SUPPORT|11 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +268 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.12 T - 0.31 C - 0.28 1 taactacact ttctctacac ttttatatct ctacactttt ataggactat 51 atcctattcg gagtaatata tactcagcct attacaatta ttagaaatag 101 aactatatta ttctattaag gctaatatat ggatccgact cctacttcta 151 acgtagattt tcggccttTA TAAACCagca tcacccctcc cctaatcctc 201 GACCTCACCA TCGTCGGCCG GACCTCCACG GACCGCATAC GCGCGACACG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00085 Mean Expected Number 0.002 +strand -119 : -104 TTACaATTATTAGAAA AC RSP00085 Mean Expected Number 0.002 -strand -104 : -119 TTTCTAATAATtGTAA AC RSP00354 Mean Expected Number 0.002 +strand -52 : -45 TAACGTAG AC RSP00395 Mean Expected Number 0.007 +strand -52 : -43 TaACGTAGAT AC RSP00953 Mean Expected Number 0.004 +strand -116 : -108 CAATTATTA AC RSP01437 Mean Expected Number 0.004 -strand -143 : -151 AATAGGATA Totally 6 motifs of 5 different REs have been found Description of REs found 83. Group TF: AGL3 /AC: RSP00085//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AGL3-BE /TF: AGL3 339. Group RE: GARE1 /AC: RSP00354//OS: Oryza sativa /GENE: Rep-1/RE: GARE1 /TF: unknown 378. Group TF: Opaque-1 /AC: RSP00395//OS: Zea mays /GENE: gamma-27kDa zein/RE: O2-like-box /TF: Opaque-1 880. Group TF: ATHB6 /AC: RSP00953//OS: Arabidopsis thaliana /GENE: ATHB6/RE: ATHB6 BS /TF: ATHB6 1310. Group RE: GATA /Group TF: R-GATA /AC: RSP01437//OS: Oryza sativa /GENE: RSs1/RE: GATA /TF: R-GATA ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0523B07.46|complement(1532778..1535770) |SUPPORT| 7 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +65 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.18 G - 0.20 T - 0.28 C - 0.33 1 ttggcaatcc cttaaaaatg atttacagaa attacctcac attgtttttg 51 aaaagaaaga atgtacagca tcggtttggg ctgagggagt cgttgccatc 101 ttgggccgcg cgcaaacagc ccataccttg gcccattagg gttttgctcc 151 ctaggtttcg tctcccccct aTATAAATGc ttctcctgcg ccgtcgtttc 201 CCTCTTCCAT CCTTCGCTCG CTCCGCCGCC GCCGCCGCCG CCTCCTCCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00146 Mean Expected Number 0.006 -strand -25 : -31 TTATATA AC RSP00206 Mean Expected Number 0.001 -strand -161 : -172 GTGAGGTAATtT AC RSP00279 Mean Expected Number 0.001 +strand -65 : -57 TTAGGGTTT AC RSP00369 Mean Expected Number 0.001 -strand -57 : -65 AAACCCTAA AC RSP00695 Mean Expected Number 0.006 +strand -29 : -23 TATAAAT AC RSP01303 Mean Expected Number 0.001 -strand -56 : -65 aAAACCCTAA Totally 6 motifs of 6 different REs have been found Description of REs found 142. Group RE: TATA1 /AC: RSP00146//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA1 /TF: unknown 199. Group TF: GT-1 /AC: RSP00206//OS: Pisum sativum /GENE: rbcS-3A/RE: BOX II* /TF: GT-1 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: B1008E06.43|2339873..2343178 |SUPPORT| 3 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +2305 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.15 G - 0.21 T - 0.21 C - 0.43 1 aactgacgtc agccgctgag ccgaaccgac atgctcagcc aatcacgagc 51 ggaagccggc gccgtgtccc tcttcctcac gcgcgccgcc gccggcgccg 101 ttttcttctc ccctaagcag ccgtcgccgt gccttcctcg tcctcctccg 151 gaccgacctc cgccgccTAT AAATAgccgg ccatccctct tcttttcccc 201 ACAAACCGAG CTCTCTTCTC TCTCTCCATC CATGGCCGAT CGTCGACGCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00004 Mean Expected Number 0.005 -strand -28 : -33 TTTATA AC RSP00147 Mean Expected Number 0.005 +strand -33 : -28 TATAAA AC RSP00695 Mean Expected Number 0.001 +strand -33 : -27 TATAAAT AC RSP00864 Mean Expected Number 0.003 -strand +25 : +17 AGAGAGAGA AC RSP00865 Mean Expected Number 0.007 -strand +27 : +19 GGAGAGAGA AC RSP01296 Mean Expected Number 0.000 +strand -34 : -26 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -34 : -25 CTATAAATAg AC RSP01708 Mean Expected Number 0.000 +strand -34 : -25 CTATAAATAG AC RSP01708 Mean Expected Number 0.000 -strand -25 : -34 CTATTTATAG Totally 9 motifs of 8 different REs have been found Description of REs found 4. Group RE: Motif g /AC: RSP00004//OS: Pisum sativum /GENE: PSPAL2/RE: Motif g /TF: unknown 143. Group RE: TATA2 /AC: RSP00147//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: TATA2 /TF: unknown 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0012A04.46|complement(2537170..2538608) |SUPPORT| 3 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +141 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.22 G - 0.19 T - 0.38 C - 0.21 1 ctggcttctg catgtagacg tgttcactca cacaaaacaa attaaaaatt 51 gtgagtgttt atgctgtttg atgattggtt gtttgttctg ttttggacat 101 gcttgttaat tagtttctct ctctagactc ttccttcctt gatctttcct 151 ctctcttctt tgcctgccta TATAAATGct ggtactaata tcttgctgct 201 CATAGCAGGG GAGTGGCTCA GCTTATAGCT TAAACCATCA GAGCTGCAAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00301 Mean Expected Number 0.007 +strand +45 : +51 TGCAAAG AC RSP00863 Mean Expected Number 0.004 -strand -47 : -55 AGAGAGGAA AC RSP00864 Mean Expected Number 0.004 -strand -77 : -85 AGAGAGAGA Totally 3 motifs of 3 different REs have been found Description of REs found 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0515A04.30|2595952..2596800 |SUPPORT| 2 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.18 T - 0.30 C - 0.25 1 cacagagtca aactctactc ctttcatcat tgtctcttgt gtcacatgga 51 tatacacttt cgatggaaat tccaacattg cggtcgcatg atcttgtcgt 101 ccatcttatc gtccactccc ttttccaaat tttgcatgtg atacactgga 151 ttggaatctg ttgctccaTA TAAATAagtg actctgagag tagcaaagcc 201 AAAGCAACTT CACACACACA GTGTACTGAT CAACACTTCT GGAAGTGGAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00114 Mean Expected Number 0.008 +strand -108 : -99 CTTGTCGTCc AC RSP00447 Mean Expected Number 0.004 +strand -9 : +1 AGCAAAGCcA AC RSP00872 Mean Expected Number 0.007 +strand -163 : -154 TGTGTcACAT AC RSP01621 Mean Expected Number 0.009 +strand -148 : -139 TACACTTTcG Totally 4 motifs of 4 different REs have been found Description of REs found 112. Group RE: B2 /AC: RSP00114//OS: Glycine max /GENE: GmAux28/RE: B2 /TF: unknown 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown 1441. Group TF: GmDof4; GmDof22 /AC: RSP01621//OS: Glycine max /GENE: Synthetic OLIGO/RE: E4 /TF: GmDof4; GmDof22 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBb0012I09.11|2752272..2752930 |SUPPORT| 1 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +37 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.37 G - 0.22 T - 0.17 C - 0.25 1 aaaatcaaaa aagaaaaaag aaaatctaaa aaaaaaagaa aaagcaaaaa 51 aagaaaaggc cgtagcaatc gcgcaaaacc aaacgtgttc gcgttcggta 101 tctcgacctt tctccaaatc cgatgcttaa tcctcatacg gtatactccg 151 taggtcggtc gacctgaccT ATAAATCcgc agccgccacg cgaaccaaaa 201 ACCGGATCGG ATCGGACCGC GTCTTACCAG ATTGGCGATG GCGGCGGCGG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00557 Mean Expected Number 0.000 -strand -152 : -167 TTTTGCTTTTTCTTTt AC RSP00716 Mean Expected Number 0.009 +strand -127 : -119 CAAAACCAA Totally 2 motifs of 2 different REs have been found Description of REs found 533. Group RE: UN U2 /AC: RSP00557//OS: Lycopersicon esculentum /GENE: rbcS3C/RE: UN U2 /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBb0012I09.21|complement(2785387..2787421) |SUPPORT| 3 exon(s)|Contig: NT_1070791.txt | -200:+51 from mRNA start|,5"-UTR: +93 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.35 G - 0.17 T - 0.29 C - 0.19 1 ttttctcttg attcattgtt aaatatactt atatgtatac atatagtttt 51 acatatttca caaaagtttt tgaataagac gaacgttaaa tatgtgttaa 101 aaagttaacg gtatcaacta tttagaaaca aagggagtgt gtgcttggct 151 gtgagatctc gcccTATAAA TAcccacccc ccactgcaca gggagagagc 201 AAACCACGAG CAACGAACTC ACCTGCAAAT TAAGCCAGGT AATAAAACTT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.006 +strand -37 : -29 CTATAAATA AC RSP01301 Mean Expected Number 0.001 +strand -37 : -28 CTATAAATAC Totally 2 motifs of 2 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBb0024J13.25|complement(235634..237993) |SUPPORT| 5 exon(s)|Contig: NT_1070811.txt | -200:+51 from mRNA start|,5"-UTR: +61 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.30 G - 0.21 T - 0.23 C - 0.26 1 taaaacctgg taactgaaca caggatggaa actctgaata atgaacggtt 51 gcatgcagag tactacctgc ttggaggcaa taatgtaagc gtgtaaggct 101 cactgtgggc tcctcctctg cttgatcccc ctttccttcc ggcctcctcc 151 tctgcttgat catcccTATA AATAcaaagg gcgtgcacat ggaaaagtat 201 CACGTAAGCA CACAAAGACA CTAGTAGAAA ACACCTGACG AACGACTCTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01073 Mean Expected Number 0.001 -strand -43 : -51 CAAGCAGAG AC RSP01073 Mean Expected Number 0.001 -strand -77 : -85 CAAGCAGAG AC RSP01296 Mean Expected Number 0.002 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.000 +strand -35 : -26 CTATAAATAC Totally 4 motifs of 3 different REs have been found Description of REs found 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0692F07.7|264844..266227 |SUPPORT| 1 exon(s)|Contig: NT_1070811.txt | -200:+51 from mRNA start|,5"-UTR: +7 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.29 G - 0.25 T - 0.20 C - 0.27 1 tggagtatta cacaggcaat tatttaagca aacaacagct catatttcct 51 gcaccgtgga aaacacgtta ggatccagat cgcgttgact caacagcaca 101 ctacattcac acagccagta gagacttgga gggcgctgca cgcttactta 151 cagtctaatg ccaacTATAA ATCacaacac ggtgtgatct actctcgatc 201 GACTCCCATG GCGAGGGGGA GGCGGCGGCG CCGTCGCCAG CGCAGGAAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00057 Mean Expected Number 0.009 -strand -71 : -80 TCCAaGTCTC AC RSP00158 Mean Expected Number 0.002 -strand -167 : -177 TgTTTGCTTAA AC RSP00655 Mean Expected Number 0.009 +strand -180 : -174 TATTTAA AC RSP01190 Mean Expected Number 0.004 -strand -142 : -151 CCACGGTGCA Totally 4 motifs of 4 different REs have been found Description of REs found 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 153. Group RE: D3 /AC: RSP00158//OS: Glycine max /GENE: GmAux28/RE: D3 /TF: unknown 629. Group RE: TATA box /AC: RSP00655//OS: Oryza sativa /GENE: PAL/RE: TATA box /TF: unknown 1101. Group RE: C-box /Group TF: C factor /AC: RSP01190//OS: Nicotiana tabacum /GENE: Adhl/RE: C-box /TF: C factor ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: B1040D06.26|complement(164583..165227) |SUPPORT| 1 exon(s)|Contig: NT_1070831.txt | -200:+51 from mRNA start|,5"-UTR: +235 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.28 G - 0.22 T - 0.27 C - 0.24 1 agtttaaatg aacttagaat aaataaaact caattaggcc cataaggatg 51 ggccgtatgt ctttcacaac ttggcctgtt aagtgcacat ggcccatgtg 101 gcccaagtcg gcttaggtgc actgagagcc atcggattcg ATTGAacggt 151 tagtattgtt cgtgatttaT ATAAAACatt cccatgttga aaccctaacc 201 CTAAATTCAT TCTCCTCCAT CTCCCACCGC GAGTAGCAAC AGCGGCGGTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00153 Mean Expected Number 0.004 +strand -107 : -98 CCAtGTGGCC AC RSP00157 Mean Expected Number 0.001 +strand -36 : -25 ATTTATATAAAa AC RSP00157 Mean Expected Number 0.001 -strand -25 : -36 tTTTATATAAAT AC RSP00279 Mean Expected Number 0.001 -strand -3 : -11 TTAGGGTTT AC RSP00369 Mean Expected Number 0.001 +strand -11 : -3 AAACCCTAA AC RSP00297 Mean Expected Number 0.000 +strand -110 : -3 GGCCCA-- ** bp --ACCCTAA AC RSP00297 Mean Expected Number 0.000 +strand -110 : +3 GGCCCA-- ** bp --ACCCTAA AC RSP00297 Mean Expected Number 0.000 +strand -101 : +3 GGCCCA-- ** bp --ACCCTAA AC RSP01303 Mean Expected Number 0.003 +strand -12 : -3 gAAACCCTAA AC RSP01497 Mean Expected Number 0.005 +strand -73 : -64 GCCaTCGGAT Totally 10 motifs of 7 different REs have been found Description of REs found 149. Group RE: Box II /AC: RSP00153//OS: Petroselinum crispum /GENE: CHS/RE: Box II /TF: CPRF-1; CPRF-2; CPRF-3; ||Identical REs AC: RSP00154 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 925. Group TF: At-TCP20 /AC: RSP00297//OS: Arabidopsis thaliana /GENE: PCNA/RE: Box II/telo-box (motifs 2 & 3) /TF: At-TCP20 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OJ1352_A10.23|complement(2031495..2034621) |SUPPORT| 4 exon(s)|Contig: NT_1070761.txt | -200:+51 from mRNA start|,5"-UTR: +206 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.21 G - 0.18 T - 0.31 C - 0.31 1 tacgagcgca caaggaaaat aaaagaagtt ttctcaccaa ctggggtgtg 51 tgatggccct tccatcaaat gggccctacc atattttttt tttccttttc 101 caaccgtctt gaaccactct cgctctcggt ctgtgtctct cttgccatat 151 tcgtgttgtt ttcctcTATA AATAcagcca cggtgcgtgc ctcgtctcct 201 TGCATCCGCT GCACCCACCA CTCAAAAACC TGCAGCTTGC TCCCTAGCTT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01044 Mean Expected Number 0.001 +strand -169 : -158 TCTCACCAACtG AC RSP01296 Mean Expected Number 0.001 +strand -35 : -27 CTATAAATA AC RSP01301 Mean Expected Number 0.008 +strand -35 : -26 CTATAAATAC Totally 3 motifs of 3 different REs have been found Description of REs found 968. Group RE: box L /AC: RSP01044//OS: Petroselinum crispum /GENE: CCoAOMT/RE: box L /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0711F01.41|complement(323794..329516) |SUPPORT| 2 exon(s)|Contig: NT_1070821.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.27 C - 0.20 1 taaagatgga aacggttttt ctgattgtac tacgacgtca aacatttaga 51 ctccttttaa aatgaactac agtgtcaaat ataacgggac agagggagta 101 ttatattatg gaacggaggg agtaataata agctacagta gtaaaaaaaa 151 ttcttgaccc cTATAAATAg tgcagctact ctcacttccc ctagctaggt 201 AGTGCAACAC ACACCTCTAG CTTCTAGCTA GCTTGCTTCT CCGAGCATGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand -10 : -3 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 +strand +24 : +31 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand +31 : +24 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -3 : -10 CTAGCTAG AC RSP00868 Mean Expected Number 0.003 +strand -102 : -91 TATTATATTATg AC RSP01296 Mean Expected Number 0.004 +strand -40 : -32 CTATAAATA Totally 6 motifs of 3 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0711F01.51|359672..365413 |SUPPORT|18 exon(s)|Contig: NT_1070821.txt | -200:+51 from mRNA start|,5"-UTR: +989 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.20 T - 0.21 C - 0.27 1 tagctttcaa aataacttag ttagttctcc aaacaggaca gtagtatacg 51 agtataggga ccgtacgtgc aatttaatcg atagcataga cagtccctag 101 tccctaagca ccgacggaga aagcggattt ggcgggagcc gagccgagcc 151 gagaaatcga cggcataTAT AAACCgcgac aagttaaacc aaacccaatc 201 AATCGGTTTA ACTCAAAATC CCAACTCCGA ACGCCTCTTC TTCTCCTCAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00072 Mean Expected Number 0.007 +strand -138 : -132 GTACGTG AC RSP00808 Mean Expected Number 0.006 +strand -181 : -175 GTTAGTT AC RSP00837 Mean Expected Number 0.006 +strand -47 : -38 AaATCGACGG AC RSP00877 Mean Expected Number 0.000 -strand -65 : -73 CCCGCCAAA AC RSP00988 Mean Expected Number 0.000 -strand -63 : -74 CTCCCGCCAAAt Totally 5 motifs of 5 different REs have been found Description of REs found 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 761. Group TF: Pti4 /AC: RSP00808//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: Myb1 /TF: Pti4 ||Identical REs AC: RSP00810 RSP00812 RSP00813 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown 813. Group TF: AtE2F /AC: RSP00877//OS: Arabidopsis thaliana /GENE: MCM3/RE: Site 2 E2F (D2) /TF: AtE2F 909. Group TF: E2F/DP /AC: RSP00988//OS: Zea mays /GENE: RBR3/RE: E2F/DP I /TF: E2F/DP ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0564H06.14|complement(746664..756909) |SUPPORT| 8 exon(s)|Contig: NT_1070821.txt | -200:+51 from mRNA start|,5"-UTR: +33 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.33 G - 0.18 T - 0.29 C - 0.21 1 gatacgaaaa ttaattggaa ttttggattt ggatgggagg aaatatcagt 51 tgcaccatcg ccgaagagat taattccacc aaaaccatat gtgtacgact 101 ctgcacgttt ctttccccta acaaatacat gtacacacaa caaactcttt 151 tggaaactac tccatataTA TAAATAggct atgttcattc taatgcccaa 201 GTGATGGAAG AGAGTATGAC GAAGCCCACG ACGATGGCCA TTTTTCTTTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00157 Mean Expected Number 0.005 +strand -37 : -26 ATaTATATAAAT AC RSP00157 Mean Expected Number 0.005 -strand -26 : -37 ATTTATATAtAT AC RSP00860 Mean Expected Number 0.002 -strand +51 : +43 AGAAAGAAA Totally 3 motifs of 2 different REs have been found Description of REs found 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OSJNBa0048A13.10|complement(1735030..1735770) |SUPPORT| 1 exon(s)|Contig: NT_1070821.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.32 G - 0.22 T - 0.14 C - 0.31 1 gccgacgcgg ctaaactaaa ctaaccgaaa cccaaaaccg ccttcgctaa 51 gtaaaggcgc ctccagagca gaccggacta ttccaatccg gaccaaactg 101 cccccaacct tcttgccgga aaagaaaggc aaaccgcgtc ggaatcggaa 151 acggcaaacc cccgcctcTA TAAATCcacg ctcgtcaacg cgaatcgttt 201 CAGAGCTCTC GAGGAGGAGG AGGAAGGAAT CATCAAGGCA ACCGATCAAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00695 Mean Expected Number 0.007 +strand -32 : -26 TATAAAT AC RSP01301 Mean Expected Number 0.008 +strand -33 : -24 CTATAAATcC AC RSP01761 Mean Expected Number 0.000 +strand -98 : -87 CCcAACCTTCTT Totally 3 motifs of 3 different REs have been found Description of REs found 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1566. Group TF: NSP1 /AC: RSP01761//OS: Arabidopsis thaliana /GENE: ANAC13 (At1g32870)/RE: MRE (ANAC13) /TF: NSP1 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OJ1005_D12.40-1|complement(3385740..3388413) |SUPPORT| 2 exon(s)|Contig: NT_1070841.txt | -200:+51 from mRNA start|,5"-UTR: +71 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.34 G - 0.13 T - 0.38 C - 0.15 1 attacgtatt ctattcatag ttaaatttgt tattttttat atacttgtat 51 aaattgaatt tgaatttaca tgtttgtaaa gtgacatatc acataggaat 101 ATTGAtctat catactaatt tttttaaaaa aaatttaata acttttaaaa 151 tgacatgTAT AAATGaggga tatccccagg gaatgaattg agttttccat 201 ATAAACCGCC GTGTCGCCGT GCACACTCAT CATCCTCGCA ATATCTCATT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00460 Mean Expected Number 0.004 -strand -42 : -51 tACATGTCAT AC RSP00495 Mean Expected Number 0.009 +strand -126 : -119 TGTAAAGT AC RSP00869 Mean Expected Number 0.001 +strand -126 : -118 TGTAAAGTG AC RSP01598 Mean Expected Number 0.008 -strand -46 : -53 TGTCATTT Totally 4 motifs of 4 different REs have been found Description of REs found 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 471. Group RE: P-box 2 /AC: RSP00495//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 2 /TF: unknown ||Identical REs AC: RSP00686 805. Group RE: EM1 /AC: RSP00869//OS: Triticum aestivum /GENE: LMWG-1D1/RE: EM1 /TF: unknown 1419. Group RE: Inr /AC: RSP01598//OS: Spinacia oleracea /GENE: RPL21/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0676H02.5|complement(3410631..3411506) |SUPPORT| 1 exon(s)|Contig: NT_1070841.txt | -200:+51 from mRNA start|,5"-UTR: +295 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.23 C - 0.28 1 tttctataaa tagaaaaata attaaaatta gaaagagaga gaaatcaatg 51 attttagcct gccccaaacg tgcggcccat taggcggccc aatctgcaat 101 ggcCCAATgc cggagaagcc ggggccgtcc gatctaatgg atggtcccga 151 tggatccccg acctaTATAA ATAccggata gcaaaaacct aaccctaatc 201 AATCCATTTC CACCGAAACC GATCCCCTTT CTCTCTCTCC CTCTCTCAAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00085 Mean Expected Number 0.001 +strand -200 : -185 TTTCTATAAATAGAAA AC RSP00085 Mean Expected Number 0.001 -strand -185 : -200 TTTCTATTTATAGAAA AC RSP00115 Mean Expected Number 0.006 +strand -163 : -153 AgAGAAATCAA AC RSP00416 Mean Expected Number 0.007 -strand -58 : -64 CATCCAT AC RSP00509 Mean Expected Number 0.001 +strand -35 : -24 TATAAATACCgG AC RSP00653 Mean Expected Number 0.001 -strand -158 : -168 TTCTCTCTCtT AC RSP00709 Mean Expected Number 0.003 -strand -177 : -185 TAATTATTT AC RSP00861 Mean Expected Number 0.001 +strand -171 : -163 AGAAAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -167 : -159 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand +38 : +30 AGAGAGAGA AC RSP00865 Mean Expected Number 0.001 -strand +40 : +32 GGAGAGAGA AC RSP00297 Mean Expected Number 0.000 +strand -127 : -3 GGCCCA-- ** bp --ACCCTAA AC RSP00297 Mean Expected Number 0.000 +strand -115 : -3 GGCCCA-- ** bp --ACCCTAA AC RSP01283 Mean Expected Number 0.000 -strand +45 : +29 GAGAGgGAGAGAGAGAA AC RSP01296 Mean Expected Number 0.002 +strand -197 : -189 CTATAAATA AC RSP01497 Mean Expected Number 0.003 +strand -77 : -68 GCCGTCcGAT AC RSP01505 Mean Expected Number 0.001 -strand -67 : -75 GATCGGACG AC RSP01708 Mean Expected Number 0.005 +strand -197 : -188 CTATAAATAG AC RSP01708 Mean Expected Number 0.005 -strand -188 : -197 CTATTTATAG Totally 19 motifs of 15 different REs have been found Description of REs found 83. Group TF: AGL3 /AC: RSP00085//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AGL3-BE /TF: AGL3 113. Group TF: ATBP-1 /AC: RSP00115//OS: Pisum sativum /GENE: GS2/RE: BOX 1 /TF: ATBP-1 398. Group RE: Box-1 /AC: RSP00416//OS: Hordeum vulgare /GENE: EPB-1/RE: Box-1 /TF: unknown 485. Group RE: TATA box /AC: RSP00509//OS: Avena fatua /GENE: alpha-Amy2/A/RE: TATA box /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 925. Group TF: At-TCP20 /AC: RSP00297//OS: Arabidopsis thaliana /GENE: PCNA/RE: Box II/telo-box (motifs 2 & 3) /TF: At-TCP20 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: P0676H02.28|3480563..3481780 |SUPPORT| 2 exon(s)|Contig: NT_1070841.txt | -200:+51 from mRNA start|,5"-UTR: +109 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.27 G - 0.19 T - 0.32 C - 0.22 1 agctttgagt tgcaccaaag gcattccaat tacttttttt tttcacatct 51 gagcaaattt atagtggttt ttagaaagaa tccgatcgga aaaggggatt 101 gacaattcga cATTGGccaa ctctttatct gtactttgtc acttgactta 151 ttctctggcc gtgcgTATAA ATAgaccctg cctacaacct ccgggcaaat 201 GTGCAGCAGC AACAGTATAG CTGAGATTGG TCATCTGACA TCCTTATCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00254 Mean Expected Number 0.009 -strand -106 : -112 CCTTTTC Totally 1 motifs of 1 different REs have been found Description of REs found 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 ------------------------------------------------------------ > O.sativa (japonica), Chr 9 (11 contigs)|GENE: OJ1509_C06.19|3704588..3705563 |SUPPORT| 3 exon(s)|Contig: NT_1070841.txt | -200:+51 from mRNA start|,5"-UTR: +101 bp |Taxon: Monocot |Promoter: TATA Nucleotide Frequencies: A - 0.20 G - 0.23 T - 0.32 C - 0.24 1 aattatgatc gattctcgtg tcaatgtgtg ttttttgtgg atcttcttgg 51 tttggagttc cctagcgtgc gtccgtattg gaagatatct caggtttgcg 101 ccctgtacat gcagcggcga cgttggaaac acggcccgcc ATTGCgtgtt 151 ttcctacgca acctttgtcT ATAAAACggc cggtgcaaac tgaaccctgc 201 AAGTCAGCTT CAGTTCGCTG CATCTCTCCT GCAAGAATTA ATATATCTTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00405 Mean Expected Number 0.007 +strand -150 : -143 TTTGGAGT AC RSP00867 Mean Expected Number 0.005 +strand -104 : -97 TGCGCCCT Totally 2 motifs of 2 different REs have been found Description of REs found 387. Group RE: adjb /AC: RSP00405//OS: Nicotiana tabacum /GENE: RNP2/RE: adjb /TF: unknown 803. Group RE: GCC-box /AC: RSP00867//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: GCC-box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.2|8020..9237 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +580 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.21 T - 0.31 C - 0.23 1 aggaaaaagt caaactttaa ctttcttaaa agtaggccga atctaattcg 51 taacccttaa ccagaaaacc ggataggacg gattcttaaa agtttggcgt 101 ttatgtggca ttagaattaa aaatatatgt ggagctcaca tgatcatctc 151 tctaatcctt cttcctcctc tctctctctt atctctctct tttcttttcc 201 CCTTCGGCCC TGGAGGCGGT GGGTAGGACG TTGACAGGTG CTGGAGCGGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.006 +strand +32 : +39 TGACAGGT AC RSP00379 Mean Expected Number 0.002 +strand -131 : -122 CGGATAGGaC AC RSP00864 Mean Expected Number 0.002 -strand -11 : -19 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -22 : -30 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand -24 : -32 AGAGAGAGA AC RSP00891 Mean Expected Number 0.002 +strand -81 : -73 AAAATATAT Totally 6 motifs of 4 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 364. Group RE: LS7 /AC: RSP00379//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS7 /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.3|9522..12487 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +54 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.16 T - 0.36 C - 0.27 1 ctctttttct cctttccttc ttggagtatc tttatctttt tccttgtact 51 atggaggagt actattttct ttcttttttt ctcactcaac tgctcctttt 101 tttctttaga agaaaaaaga aaagaaaagg aaaaggaaaa gttctgggac 151 tcactcctac ttgtgggtgg tcgtgctgta ctccagtccc cgcttcactc 201 CACTCGCCGT CACCCCCCAC CTTGACCTCC GCTTCGAATT CGAATTCGAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00254 Mean Expected Number 0.002 -strand -65 : -71 CCTTTTC AC RSP00254 Mean Expected Number 0.002 -strand -71 : -77 CCTTTTC AC RSP00444 Mean Expected Number 0.001 -strand -122 : -135 AAAAAAGAAAGAAA AC RSP00445 Mean Expected Number 0.001 +strand -88 : -79 AAAAAAGAaA AC RSP01006 Mean Expected Number 0.003 -strand -30 : -36 ACCACCC Totally 5 motifs of 4 different REs have been found Description of REs found 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 424. Group TF: Dof1 /AC: RSP00444//OS: Zea mays /GENE: cyPPDK1/RE: box d /TF: Dof1 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 931. Group TF: PtMYB1; PtMYB4 /AC: RSP01006//OS: Pinus sylvestris /GENE: PsGS1b/RE: GS1b AC box 1 (AC-II) /TF: PtMYB1; PtMYB4 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.4|13200..16946 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +201 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.24 T - 0.31 C - 0.25 1 gagagtttct ctttcttttt cttttctctc tttgtttttg agctggagga 51 ttcttctctc ttcttaagct catcagggcc agctaagcca gcacaagcaa 101 aaggactctg tattttctgt gttgtctcct ctagtcctct cctcccttct 151 gttccagtca ggacatacaa agcaaagatc cctccctctg ctgtgcaggc 201 TGCAGCAGGC GAGGAGAGGC AACCAGAGGG AGGGTAGGTT GGTTTGGAAG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00035 Mean Expected Number 0.005 +strand -103 : -97 CAAAAGG AC RSP00079 Mean Expected Number 0.007 -strand +42 : +33 CCaACCTACC AC RSP00230 Mean Expected Number 0.010 -strand +40 : +31 AACCTAcCCT AC RSP00653 Mean Expected Number 0.006 +strand -147 : -137 TTCTCTCTtCT AC RSP00861 Mean Expected Number 0.004 -strand -185 : -193 AGAAAGAGA Totally 5 motifs of 5 different REs have been found Description of REs found 34. Group RE: D1 /Group TF: Dof family /AC: RSP00035//OS: Hordeum vulgare /GENE: Al21/RE: D1 /TF: Dof family 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 223. Group TF: PcMYB1 /AC: RSP00230//OS: Petroselinum crispum /GENE: CHS-1/RE: MRECHS /TF: PcMYB1 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.5|19642..23696 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +392 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.17 T - 0.30 C - 0.20 1 caaacttaat cttcaccatc atcaatttta aagtttaaac accatgttta 51 gggtttaggg ataagattca aaatcaatat ccagcaagct atatatagca 101 gagttggact cttattttaa tctgaggcat gataatattt ttatacagcg 151 taaatggatg gccatattca tttatccgat tgatatctaa ttttatccct 201 CACAAGTCAC AGGGAGGAGT CGAAAAGAGT CAATACCAGC CGCGCCACCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00125 Mean Expected Number 0.003 +strand -67 : -56 AATATTTTTATa AC RSP00135 Mean Expected Number 0.002 +strand -67 : -56 AATATTTTTATa AC RSP00279 Mean Expected Number 0.001 +strand -153 : -145 TTAGGGTTT AC RSP00369 Mean Expected Number 0.001 -strand -145 : -153 AAACCCTAA AC RSP00593 Mean Expected Number 0.003 -strand -132 : -140 GAATCTTAT AC RSP01303 Mean Expected Number 0.002 -strand -144 : -153 TAAACCCTAA AC RSP01304 Mean Expected Number 0.002 -strand -144 : -153 TaAACCCTAA Totally 7 motifs of 7 different REs have been found Description of REs found 123. Group RE: AT-1 (3) /AC: RSP00125//OS: Nicotiana plumbaginifolia /GENE: cab-E/RE: AT-1 (3) /TF: unknown ||Identical REs AC: RSP00133 RSP00788 131. Group RE: AT-1 (4) /AC: RSP00135//OS: Nicotiana plumbaginifolia /GENE: cab-E/RE: AT-1 (4) /TF: unknown 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 569. Group RE: GATA/2 B /AC: RSP00593//OS: Lycopersicon esculentum /GENE: rbcS1/RE: GATA/2 B /TF: unknown 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown 1197. Group RE: Telo box /AC: RSP01304//OS: Lycopersicon esculentum /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.6|23943..25446 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.23 T - 0.22 C - 0.29 1 gagtacataa atatacatga cgatatgatc ctgtaagata ttctattcca 51 ttatccaaaa aaaatgaaat ccctgccgtc cgatgcgatg ggcgatggta 101 aaaccctagc tcgaagccaa gcacagcctg ggccgggccc ggcccagccc 151 aacaagtagt ccgctgttat aaagggaagg taggcatctc cccccgcgcg 201 CCGCGACTCG TTAGGCTACT CCACCCACTC TTGTTTAGGG TTTCCCTCAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00260 Mean Expected Number 0.008 +strand +34 : +40 TTTAGGG AC RSP00279 Mean Expected Number 0.000 +strand +35 : +43 TTAGGGTTT AC RSP00369 Mean Expected Number 0.000 -strand +43 : +35 AAACCCTAA AC RSP01303 Mean Expected Number 0.001 -strand +44 : +35 gAAACCCTAA AC RSP01497 Mean Expected Number 0.006 +strand -126 : -117 GCCGTCcGAT Totally 5 motifs of 5 different REs have been found Description of REs found 253. Group RE: RTBP1 BS /AC: RSP00260//OS: Oryza sativa /GENE: Synthetic OLIGO/RE: RTBP1 BS /TF: unknown 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.7|26618..31255 |SUPPORT|14 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +124 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.33 T - 0.21 C - 0.14 1 gagaattaat atgtcatctt atgattataa ttatatgcca atccaacatt 51 cgtgtaaata taaatatatt tccatgccgt aaaaaagttt gaaagggcta 101 aagaaaaaga ggagagagag agagagagag gggggggggg gggcggggtg 151 gtgtggaatt gatgataggc caaaggtggt gaggaagaat ctgggtcgtc 201 CAGGCAAGAT CCCACGGGCG ATGCGAACGA GCACCGGATC CGCTGCGGCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00337 Mean Expected Number 0.006 -strand -134 : -142 ATATTTATA AC RSP00572 Mean Expected Number 0.003 +strand -192 : -185 ATATGTCA AC RSP00864 Mean Expected Number 0.010 +strand -88 : -80 AGAGAGAGA AC RSP00864 Mean Expected Number 0.010 +strand -86 : -78 AGAGAGAGA AC RSP00864 Mean Expected Number 0.010 +strand -84 : -76 AGAGAGAGA AC RSP00864 Mean Expected Number 0.010 +strand -82 : -74 AGAGAGAGA AC RSP00864 Mean Expected Number 0.010 +strand -80 : -72 AGAGAGAGA AC RSP00865 Mean Expected Number 0.010 +strand -90 : -82 GGAGAGAGA AC RSP01046 Mean Expected Number 0.000 +strand -162 : -154 CAATCCAAC AC RSP01150 Mean Expected Number 0.002 -strand -169 : -179 AATTATAATCA AC RSP01202 Mean Expected Number 0.004 +strand -31 : -24 CCAAAGGT AC RSP01283 Mean Expected Number 0.000 +strand -89 : -73 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -87 : -71 GAGAGAGAGAGAGAGAg Totally 13 motifs of 8 different REs have been found Description of REs found 323. Group TF: SEF1 /AC: RSP00337//OS: Glycine max /GENE: beta-conglicinin (7S globulin) alpha' and beta subunits genes/RE: SEF1 BS /TF: SEF1 548. Group RE: 3'/AT-rich J1 /AC: RSP00572//OS: Lycopersicon esculentum /GENE: rbcS1/RE: 3'/AT-rich J1 /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 970. Group RE: NON /AC: RSP01046//OS: Nicotiana tabacum /GENE: histone genes (oligo)/RE: NON /TF: unknown 1066. Group RE: C-DP BS2 /AC: RSP01150//OS: Cucumis sativus/GENE: POR/RE: C-DP BS2 /TF: unknown 1113. Group TF: NIT2 /AC: RSP01202//OS: Chlorella vulgaris /GENE: NR/RE: NIT2 BS III /TF: NIT2 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.22|69617..75151 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +81 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.22 T - 0.27 C - 0.29 1 gttcccgtta tatatggtat ttcggtttaa ggataaattt ggtaaactta 51 atccaacaac gaatagtggg cgtaggctta ggcctgggcc tggtcctggt 101 cctggtacgg cccaacaaca cgagaaacaa gtccctttcc cttgccctct 151 tgttgagaga tttgggattt gagaagctgc tgctgctcac ctcccctctc 201 CTCCCCACAA TCGAATCGAA TCGAATCCTC CTCCTCCAGG CTCCAAGCCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00332 Mean Expected Number 0.003 +strand -187 : -180 ATGGTATT AC RSP01017 Mean Expected Number 0.002 +strand -78 : -71 AGAAACAA Totally 2 motifs of 2 different REs have been found Description of REs found 318. Group TF: S1F /AC: RSP00332//OS: Spinacia oleracea /GENE: RPL21/RE: S1 /TF: S1F 942. Group TF: AEF /AC: RSP01017//OS: Arabidopsis thaliana /GENE: GapA/RE: AE box 2 /TF: AEF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.25|82138..85646 |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +43 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.27 T - 0.20 C - 0.31 1 aacggaaagc caaatgtcat agctggtctg ggctggacta ggctttgtga 51 tggaacggcc catataaaag cctcagtcag ctcgtgggcg gcttttgggc 101 gcgacccttg cttgttttgg cgccaagcga accagatttg gcgccaaaat 151 ccccccgccc gcgccgcttc ttctccctcc ctcccgcccg cgaatccatt 201 CAGACTGCAA ACTCTGAGAG AGAGAGAGAG AGAGAGAGAG GCCATGCCCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.001 +strand +17 : +25 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +19 : +27 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +21 : +29 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +23 : +31 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +25 : +33 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +27 : +35 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +29 : +37 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand +31 : +39 AGAGAGAGA AC RSP01032 Mean Expected Number 0.002 -strand -81 : -90 CCAAAACAAG AC RSP01209 Mean Expected Number 0.002 +strand -90 : -81 CTTGTTTTGG AC RSP01283 Mean Expected Number 0.000 +strand +16 : +32 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +18 : +34 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +20 : +36 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +22 : +38 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +24 : +40 GAGAGAGAGAGAGAGAg Totally 15 motifs of 4 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 957. Group TF: FLC /AC: RSP01032//OS: Arabidopsis thaliana /GENE: SOC1/RE: CArG box /TF: FLC 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.27|complement(86565..88268) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +55 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.25 T - 0.26 C - 0.25 1 aaatcgtgat tgttattaag cgagaaggta gaaacatcga cagtagcact 51 tggcagtggg tgacacgagc aggtggtgag tggcgccaaa tgaagccagc 101 gcatgcagct gtactagtga agtgatcgat ccaccgccat cttttatttt 151 ctttttctct agcttgttgt acttggtact ccacaccact agctagtaat 201 GTGGCCGCTC TCTCCTCACC GACGGCATCT CCAGCAGCAC GGGCATTCCG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.004 +strand -12 : -5 CTAGCTAG AC RSP00503 Mean Expected Number 0.004 -strand -5 : -12 CTAGCTAG AC RSP00654 Mean Expected Number 0.008 -strand -139 : -148 CACCCACTgC AC RSP01014 Mean Expected Number 0.003 +strand -114 : -105 CAAATGAAGc AC RSP01016 Mean Expected Number 0.003 +strand -171 : -164 AGAAACAT Totally 5 motifs of 4 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown 939. Group TF: GAPF /AC: RSP01014//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 2 /TF: GAPF 941. Group TF: AEF /AC: RSP01016//OS: Arabidopsis thaliana /GENE: GapA/RE: AE box 1 /TF: AEF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.41|131101..132244 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +12 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.34 G - 0.25 T - 0.27 C - 0.15 1 gtatatataa tggtcaaaga tatgtttaag ttatgataaa gctaaaacga 51 tagttaattt aaaatggaga aagtgcaagt acattctgga tgggtagata 101 agaagagcag atggagatgt gtggggtgta ggtgtgatcg atcgagggac 151 gacaaaccaa ttaattaacc acgctagccc agagtgatcg atagcagaat 201 CGTACGTTTG TAATGACGTC ATCATTATCA TCATCCACAG CCTCTGCTGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01071 Mean Expected Number 0.008 -strand +10 : +1 CAAACGTACg AC RSP01654 Mean Expected Number 0.009 +strand +12 : +21 AATGACGTCA AC RSP01654 Mean Expected Number 0.004 -strand +23 : +14 GATGACGTCA AC RSP01664 Mean Expected Number 0.000 +strand +12 : +23 aATGACGTCATC AC RSP01664 Mean Expected Number 0.000 -strand +23 : +12 GATGACGTCATt AC RSP01731 Mean Expected Number 0.000 -strand +23 : +12 GATGACGTCATT AC RSP01732 Mean Expected Number 0.000 -strand +23 : +12 GATGACGTCATT Totally 7 motifs of 5 different REs have been found Description of REs found 989. Group TF: PvAlf /AC: RSP01071//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1c /TF: PvAlf ||Identical REs AC: RSP01153 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 1482. Group TF: HY5 /AC: RSP01664//OS: Arabidopsis thaliana /GENE: ARR9 (At3g57040)/RE: C-box (2) /TF: HY5 1539. Group TF: STF1/HY5 /AC: RSP01731//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: CRE (A/T) /TF: STF1/HY5 1540. Group RE: C-box /Group TF: STF1/HY5 /AC: RSP01732//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: C-box /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.44|138760..141356 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +126 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.28 T - 0.25 C - 0.22 1 gtgagtcgtc tggatggatg ttaccaaaat aaccaagcaa gataggaagg 51 gaagaggaag tttccagaag aagggaaggg caagaaagga aatactacta 101 ctacacctgt agtgggtgtg ggtgggtggc aggcagagga ggagccaaga 151 agcaacggtc acatttcctt tgcttaccgt gttgtgttgg tctcatcgtc 201 TGTCTCGCTC GGCGCTCGTC TTTCTCCCCT CCATTCCATT TTTCCTTCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00447 Mean Expected Number 0.005 -strand -27 : -36 AGCAAAGgAA AC RSP00792 Mean Expected Number 0.004 +strand -168 : -159 CCAAGCAAgA AC RSP00862 Mean Expected Number 0.001 +strand -118 : -110 AGAAAGGAA Totally 3 motifs of 3 different REs have been found Description of REs found 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 798. Group TF: BPC1 /AC: RSP00862//OS: Arabidopsis thaliana /GENE: STK/RE: GA-3 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.45|142403..144649 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +56 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.33 T - 0.24 C - 0.19 1 ggagcaagga gggagggagt gagtgagttt tataagggga aggaagagga 51 gtctggcacg tggggcccgc atcccatcgc acaccgtcca tttacacagc 101 aggggcggag atattatttt aggtgggacc cACAATtatt ttatttttaa 151 attgattttt ttttgtgtgt gttggccttc gccctggcct ggcctggccg 201 GCAGCGGTGC GGTCGTGCGG ATAACGAACG AACGAAGAGA AAGCATGGCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00024 Mean Expected Number 0.003 +strand -89 : -82 TATTATTT AC RSP00735 Mean Expected Number 0.004 -strand -41 : -48 AAAAATCA AC RSP01152 Mean Expected Number 0.008 -strand -137 : -146 CcCACGTGCC AC RSP01250 Mean Expected Number 0.007 -strand -41 : -50 AAAAaTCAAT AC RSP01480 Mean Expected Number 0.003 +strand -64 : -57 TATTTTAT Totally 5 motifs of 5 different REs have been found Description of REs found 23. Group TF: PCF1 /AC: RSP00024//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX3 /TF: PCF1 698. Group TF: DET1; CCA1 /AC: RSP00735//OS: Arabidopsis thaliana /GENE: CAB2/RE: CCA1 BS /TF: DET1; CCA1 1067. Group TF: EmBP-1 (+VP1) /AC: RSP01152//OS: Zea mays /GENE: Em/RE: Em1b /TF: EmBP-1 (+VP1) 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C 1348. Group TF: AT-1SNBP /AC: RSP01480//OS: Glycine max /GENE: GS15/RE: AT-cm /TF: AT-1SNBP ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.46|144887..147370 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +47 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.30 T - 0.18 C - 0.20 1 tgagcaagtt tgtaactgtg gacaggatga caagtgggaa ctcgatggac 51 aatgcatttg ctttggtgcg gaggcccatc aaatgcagcc cagcccaggg 101 aggtccctat cgagtagtaa gtgagtagaa gaaaagtctg atctccaccc 151 acgggcggag ttgacatact agtagtagta gtactagtac acgaggagaa 201 GAAGCAAGAG GAAGGGCATC CAGAATCAGA TCCACAAGGC AGCAGCTGCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00447 Mean Expected Number 0.001 -strand -134 : -143 AcCAAAGCAA Totally 1 motifs of 1 different REs have been found Description of REs found 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.47|149655..153251 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +537 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.22 T - 0.23 C - 0.25 1 ggtttgttga caccattcca taagttgaag ggcttcgaga aacgtgtgga 51 actacccgaa ccttctcata gacaagatga ttctgcagga caaactgaag 101 aagccatgga agcttccagg ATTGCtagag ttgctcagtc gctaaagcag 151 attgcacaga accgcccagc aaccaaattg cttgattcag agtctttacc 201 TAAGCTAGAT GCACCTGCTG CCCCATTTCA GAGACTTGGA AAACCCCTAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00040 Mean Expected Number 0.008 -strand -193 : -199 AACAAAC AC RSP00057 Mean Expected Number 0.006 -strand +40 : +31 TCCAaGTCTC AC RSP01641 Mean Expected Number 0.008 -strand -124 : -133 TCTTGTCTaT Totally 3 motifs of 3 different REs have been found Description of REs found 39. Group RE: AACA box (D) /AC: RSP00040//OS: Oryza sativa /GENE: GluB-1/RE: AACA box (D) /TF: unknown 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.50|complement(165722..167121) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +56 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.39 G - 0.29 T - 0.17 C - 0.15 1 tagaaatatc tttacaagag tacaaagatg cggggcattg ggggtggggc 51 cctgtagcga gcaagccaaa tgggagaaca ccacatatca gctgaatctt 101 atccatagaa aagagggaAT TGAaggggca ggaaggatat cccggccttg 151 tggcacactt gactggagat gtataaagag aggaggatgt gaagaaagaa 201 GATATCTACC ACCAAGCTAA TTAAGCAAAA GAAGAAGAAG AAGAAAGAAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00282 Mean Expected Number 0.004 +strand -101 : -95 TATCCAT AC RSP00394 Mean Expected Number 0.004 -strand -185 : -191 TGTAAAG AC RSP00471 Mean Expected Number 0.000 +strand -159 : -149 GgGTGGGGCCC AC RSP00593 Mean Expected Number 0.001 +strand -107 : -99 GAATCTTAT AC RSP00595 Mean Expected Number 0.001 -strand +26 : +18 GCTTAATTA AC RSP00713 Mean Expected Number 0.005 -strand -107 : -113 CAGCTGA AC RSP00722 Mean Expected Number 0.002 -strand -98 : -104 GATAAGA AC RSP01000 Mean Expected Number 0.005 -strand -163 : -172 ATGCCCCgCA Totally 8 motifs of 8 different REs have been found Description of REs found 273. Group RE: Amylase-element /AC: RSP00282//OS: Oryza sativa /GENE: Amy3D/RE: Amylase-element /TF: unknown ||Identical REs AC: RSP00675 377. Group TF: PBF-1 /AC: RSP00394//OS: Zea mays /GENE: gamma-27kDa zein/RE: P-box (s) /TF: PBF-1 ||Identical REs AC: RSP00396 RSP00429 RSP01402 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 569. Group RE: GATA/2 B /AC: RSP00593//OS: Lycopersicon esculentum /GENE: rbcS1/RE: GATA/2 B /TF: unknown 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 687. Group RE: I-box /AC: RSP00722//OS: Nicotiana plumbaginifolia /GENE: rbcS 8B/RE: I-box /TF: unknown 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0672D08.51|complement(167600..169946) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +72 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.20 T - 0.20 C - 0.31 1 aatttgatca agctaaaaaa ttaactaaga aaaaataagt caaatatgga 51 agggagggag tatgactaag gaggagaaag ggaatgaaat caaatccgat 101 taatggtatg ccggataggg ccttccctgg cCCAATccac agcagaattc 151 agcatggagc ccaacctccc gtcccccatt ccccttctcc atctcatctc 201 ACTCCCAACA CTCTCTCTCC TCGCTGCCGC TGCCGCCGCC GCCGCCGCCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00379 Mean Expected Number 0.003 +strand -89 : -80 CGGATAGGGC AC RSP00653 Mean Expected Number 0.001 +strand +11 : +21 cTCTCTCTCCT AC RSP00865 Mean Expected Number 0.001 -strand +20 : +12 GGAGAGAGA AC RSP00913 Mean Expected Number 0.005 -strand -3 : -12 GATGAGATGG AC RSP00914 Mean Expected Number 0.007 -strand -3 : -12 GATGAGATGG AC RSP01499 Mean Expected Number 0.007 +strand -22 : -13 TTCCCCtTCT AC RSP01772 Mean Expected Number 0.007 +strand -101 : -95 TTAATGG Totally 7 motifs of 7 different REs have been found Description of REs found 364. Group RE: LS7 /AC: RSP00379//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS7 /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 844. Group TF: Opaque-2 /AC: RSP00913//OS: Zea mays /GENE: b-32/RE: B1 /TF: Opaque-2 845. Group RE: B2 /Group TF: Opaque-2 /AC: RSP00914//OS: Zea mays /GENE: b-32/RE: B2 /TF: Opaque-2 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 1572. Group TF: WOX11 /AC: RSP01772//OS: Oryza sativa /GENE: PR2/RE: WOX11 BS /TF: WOX11 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.6|175408..177350 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +36 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.19 T - 0.28 C - 0.17 1 aaaacgaaaa gttgtgctta aagtacgtag atgacaaatt aagtcacaaa 51 taaaataaat aataatttta aaattttttg aataagacga gtggtcaaat 101 gttataagca aaaactcaaa atctcttata ttatggaacg gagggagtag 151 tattcaattc agatcagttg atttgagccg ccgtcgacga tccggccggc 201 CGCTTGCTTC TTCCATATTG ATCGAGGAGA CATCACATGG ATCATCATCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00030 Mean Expected Number 0.003 +strand -25 : -19 AGCCGCC AC RSP00438 Mean Expected Number 0.007 -strand -19 : -24 GGCGGC AC RSP00807 Mean Expected Number 0.007 +strand -24 : -19 GCCGCC AC RSP00933 Mean Expected Number 0.001 +strand -134 : -122 TTTAaAATTTTTT AC RSP00996 Mean Expected Number 0.004 +strand -34 : -25 GTTGATTTGA Totally 5 motifs of 5 different REs have been found Description of REs found 29. Group TF: EREBP /AC: RSP00030//OS: Nicotiana sylvestris /GENE: OLP/RE: ERRE /TF: EREBP ||Identical REs AC: RSP00082 RSP01344 RSP01523 RSP01764 RSP01775 418. Group RE: PR-box /AC: RSP00438//OS: Arabidopsis thaliana /GENE: PR-1/RE: PR-box /TF: unknown 760. Group RE: GCC box /Group TF: Pti4 /AC: RSP00807//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: GCC box /TF: Pti4 ||Identical REs AC: RSP00809 RSP00811 RSP00814 RSP00921 RSP01328 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.8-1|complement(183052..187064) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +31 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.25 T - 0.22 C - 0.30 1 caaaggaata ctagtcttcg cttttttggg ttgaggctga atgccacgtc 51 ggcccattgt gaatgccctt taacaaaaca agggtttatg gctatgggat 101 ctggctgagg cATTGAccta ccttggtcct tggcagagag agagagagac 151 tccccctcac tccttccccg acgacctgct cgatccgatc caatccgctc 201 CTCTCCAGTC CAGATCGGAA GGAAGCCAGG AATGGGGCAC CCCCACCCCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00092 Mean Expected Number 0.010 +strand -130 : -124 TAACAAA AC RSP00445 Mean Expected Number 0.003 -strand -174 : -183 AAAAAAGcGA AC RSP00755 Mean Expected Number 0.009 +strand -197 : -191 AGGAATA AC RSP00864 Mean Expected Number 0.001 +strand -66 : -58 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -64 : -56 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -62 : -54 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -60 : -52 AGAGAGAGA AC RSP00986 Mean Expected Number 0.006 +strand -157 : -150 CCACGTCG AC RSP01174 Mean Expected Number 0.005 +strand -1 : +10 CCTCTCCaGTC AC RSP01209 Mean Expected Number 0.003 +strand -180 : -171 CTTTTTTGGG Totally 10 motifs of 7 different REs have been found Description of REs found 90. Group TF: GAmyb /AC: RSP00092//OS: Hordeum vulgare /GENE: Amy pHV19/RE: TAACAAA box /TF: GAmyb ||Identical REs AC: RSP00393 RSP01051 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.9|187837..193089 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +2829 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.30 T - 0.22 C - 0.19 1 agtgaaagag aagtgaaaat gtggtagtcc accataccta cttgtatcgt 51 ggtcttgtag attttgcact gtggaacata tggcttaaca tagttgttgg 101 tctaggtgac ataccaggaa caccaaagtg tggagagtgg cttgtggggg 151 tgggggccca ccaccttcat tccattacac ggtcgaatcg aggccccact 201 GTAAGTAGAA AGAAACACAA GAAGAAGAAG AAGGGTTACC GGCGGGCGGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00441 Mean Expected Number 0.008 +strand -79 : -70 AcCAAAGTGT AC RSP00860 Mean Expected Number 0.003 +strand +7 : +15 AGAAAGAAA AC RSP01601 Mean Expected Number 0.009 -strand -183 : -190 TTTCACTT Totally 3 motifs of 3 different REs have been found Description of REs found 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.10|194448..197605 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +484 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.34 G - 0.24 T - 0.26 C - 0.16 1 cattgacatg tgggtcatag taaagtggaa tccacgtatc actgactcaa 51 ctgtaagaga atctgttttc tatcaagagg caatgaagta cagtaagttg 101 ACAATagcat gaatctaaca tatagtagta ggctataatt gctttgtttg 151 tgtgcccatg aaaaagaaaa gaagaggtaa tctcttgtgc gtgcgtcccc 201 TGTGCTGTCG CTGTGCCTGT GCGTCGGAAA GAAAAGAAAA GAAAAGAAAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00057 Mean Expected Number 0.001 +strand -170 : -161 TCCACGTaTC AC RSP00189 Mean Expected Number 0.002 +strand -170 : -161 TCCACGTAtC AC RSP00340 Mean Expected Number 0.002 +strand -170 : -161 TCCACGTaTC AC RSP00447 Mean Expected Number 0.002 -strand -53 : -62 AaCAAAGCAA AC RSP01000 Mean Expected Number 0.006 -strand -183 : -192 ATGaCCCACA AC RSP01274 Mean Expected Number 0.002 +strand -170 : -161 TCCACGTATC AC RSP01734 Mean Expected Number 0.006 +strand -170 : -164 TCCACGT Totally 7 motifs of 7 different REs have been found Description of REs found 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 1173. Group RE: ACE 1 /AC: RSP01274//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 1 /TF: unknown 1542. Group TF: CAMTA3 /AC: RSP01734//OS: Arabidopsis thaliana /GENE: CBF2/RE: CM4 /TF: CAMTA3 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.11|198745..203004 |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +99 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.22 T - 0.31 C - 0.18 1 acatatccaa ttgctaccat tattggtaat atggccttac gcatgtgtat 51 attagcatta tgatttatgt ccttatactc ctcctccctc ctgtcctgta 101 ttcaaaaaaa aaaagaaaag aaaaagaaag gataggtcag tgaggttgag 151 tcggtcgcat attgaaaaag aaagagtggc ttggcttggc ttggctcgcg 201 CGGCGTCTCC GAAATTCAAA CGGATCGATT TGGTTTTGTT GATTTGATCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00080 Mean Expected Number 0.003 +strand -187 : -172 cTACCATTATTGGTAA AC RSP00080 Mean Expected Number 0.003 -strand -172 : -187 TTACCAATAATGGTAg AC RSP00085 Mean Expected Number 0.002 +strand -187 : -172 cTACCATTATTGGTAA AC RSP00085 Mean Expected Number 0.002 -strand -172 : -187 TTACCAATAATGGTAg AC RSP00142 Mean Expected Number 0.003 -strand +5 : -2 CGCCGCG AC RSP00445 Mean Expected Number 0.009 +strand -92 : -83 AAAAAAGAaA AC RSP00716 Mean Expected Number 0.002 -strand +38 : +30 CAAAACCAA AC RSP00996 Mean Expected Number 0.006 +strand +38 : +47 GTTGATTTGA Totally 8 motifs of 6 different REs have been found Description of REs found 79. Group TF: MADS-domain AGAMOUS BF /AC: RSP00080//OS: Arabidopsis thaliana /GENE: STE2; other genes/RE: AGAMOUS MADS BS /TF: MADS-domain AGAMOUS BF 83. Group TF: AGL3 /AC: RSP00085//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AGL3-BE /TF: AGL3 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 917. Group TF: Opaque-2 (O2) /AC: RSP00996//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.12-1|complement(202936..206409) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +82 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.25 T - 0.19 C - 0.28 1 gatgagaggg gatcgattcg attgatttgc caaccacaag ctactacaac 51 gaagacggga ggaggaggaa gacgcgacgc accgcaacgc aaacgaatcg 101 aggagtaggc ccacagaagc ccataatgga gtatgttggg ccgatagccc 151 atttgcatta atggtggtag tccccacccc accacaccac cgcttcctcc 201 CACCTCTACT CCATTCCTCT TTCTTTGTTC ATCATCAAGG AAGGAAGGGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01185 Mean Expected Number 0.001 -strand -62 : -73 CCAACAtACTCC AC RSP01772 Mean Expected Number 0.008 +strand -43 : -37 TTAATGG Totally 2 motifs of 2 different REs have been found Description of REs found 1097. Group RE: box 2 /AC: RSP01185//OS: Petunia hybrida /GENE: chsA/RE: box 2 /TF: unknown 1572. Group TF: WOX11 /AC: RSP01772//OS: Oryza sativa /GENE: PR2/RE: WOX11 BS /TF: WOX11 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.13|206572..210975 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +489 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.29 T - 0.26 C - 0.24 1 ttgatgatga acaaagaaag aggaatggag tagaggtggg aggaagcggt 51 ggtgtggtgg ggtggggact accaccatta atgcaaatgg gctatcggcc 101 caacatactc cattatgggc ttctgtgggc ctactcctcg attcgtttgc 151 gttgcggtgc gtcgcgtctt cctcctcctc ccgtcttcgt tgtagtagct 201 TGTGGTTGGC AAATCAATCG AATCGATCCC CTCTCATCCG CTCGCGGACA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01185 Mean Expected Number 0.001 +strand -101 : -90 CCAACAtACTCC AC RSP01772 Mean Expected Number 0.008 -strand -120 : -126 TTAATGG Totally 2 motifs of 2 different REs have been found Description of REs found 1097. Group RE: box 2 /AC: RSP01185//OS: Petunia hybrida /GENE: chsA/RE: box 2 /TF: unknown 1572. Group TF: WOX11 /AC: RSP01772//OS: Oryza sativa /GENE: PR2/RE: WOX11 BS /TF: WOX11 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.19|223698..226103 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +3 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.22 T - 0.30 C - 0.25 1 aataatcccc atggggatgt taacgggcga aattcatacc catcgggtga 51 gcggggatgg ggacccggta actgcctgcc tgtcatgtgg gtcctatctt 101 tctcacacac atatagcctg tgtgtacgtc tatttcttca agcaaggaga 151 ctagctagct agttactcca catctgtatc tgtacgcatg caaagtaaac 201 TAGTCCTATT TATTTGTAAA TCGTGTGTCT CGTTCTCGTC GATCTCCATC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00442 Mean Expected Number 0.004 -strand -3 : -12 TtACTTTGCA AC RSP00503 Mean Expected Number 0.004 +strand -50 : -43 CTAGCTAG AC RSP00503 Mean Expected Number 0.004 +strand -46 : -39 CTAGCTAG AC RSP00503 Mean Expected Number 0.004 -strand -39 : -46 CTAGCTAG AC RSP00503 Mean Expected Number 0.004 -strand -43 : -50 CTAGCTAG AC RSP00837 Mean Expected Number 0.008 -strand +45 : +36 AGATCGACGa Totally 6 motifs of 3 different REs have been found Description of REs found 422. Group TF: Dof1 /AC: RSP00442//OS: Zea mays /GENE: cyPPDK1/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.25|complement(245630..253678) |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +130 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.25 T - 0.13 C - 0.30 1 gttgagaaaa gctaacgagc tgagccaagg gtttagctcg agctggctcg 51 caagctgctc acgaggccaa cgagccagag aaacaccagg accaggagtc 101 cactccgagc cgggctacct aaccagaaaa gcccattagt ggcCCAATag 151 cctatttcct tgagtaaaca aaccctagaa tccctaattc acagagaaga 201 GGCACGCAGA CAGTAAGGAA CACAGGCGCC GCGGCCACAA CCCACACGCG 251 A Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.27|258331..264947 |SUPPORT|16 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +33 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.25 T - 0.18 C - 0.29 1 acaagttgag ggaccttggg tgcacttttt ccataaaaaa atggaaagag 51 agagaaataa tcacgtactg ggccaggcca gtggtctcct gtgaagccca 101 ataggaggag gcagaaaagc ccatgtgggt gttgccccgc ctcctctcct 151 gcaccgccgc aacatctcca aaaccctaaa accccacaaa tcaacaacaa 201 CGCCGCCGCC TCATCCGCTC TGCTTCTGCT CGCATGGGGA AGGAGAAGGG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00279 Mean Expected Number 0.002 -strand -22 : -30 TTAGGGTTT AC RSP00369 Mean Expected Number 0.002 +strand -30 : -22 AAACCCTAA AC RSP00653 Mean Expected Number 0.004 -strand -145 : -155 TTCTCTCTCtT AC RSP00864 Mean Expected Number 0.002 +strand -154 : -146 AGAGAGAGA AC RSP01168 Mean Expected Number 0.001 -strand -184 : -192 AAGGTCCCT AC RSP01303 Mean Expected Number 0.004 +strand -31 : -22 aAAACCCTAA Totally 6 motifs of 6 different REs have been found Description of REs found 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1080. Group RE: GC element /AC: RSP01168//OS: Vicia faba /GENE: LeB4/RE: GC element /TF: Uunknown TF 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0436E04.28-2|complement(267052..268322) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +3437 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.22 T - 0.29 C - 0.23 1 atttattttt tatgagacga agggagtata cggtaggaga tgcggaacat 51 gttaacattc aaatttgagt cggtcgatcg cttactaccc tccactgcca 101 ataatcttga ttatcactag taggagtaca ctcagtcgtc agtcagtgtc 151 ctgcgagctc tgcttttaac tcatcctgtc cagcactcga gtaggaagga 201 GTACACTACA GTCTACAGTG CAGTGCAGTA CTCCCTCAGA TTGATCGATC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00255 Mean Expected Number 0.001 +strand -32 : -24 ACTCATCCT Totally 1 motifs of 1 different REs have been found Description of REs found 248. Group RE: ACTCAT motif /AC: RSP00255//OS: Arabidopsis thaliana /GENE: ProDH/RE: ACTCAT motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.10|<300064..303538 |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +70 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.19 T - 0.31 C - 0.20 1 aaagagagaa agcggcgagg aagccttagc ttatgggcac ctggatccat 51 tatttcccaa tctcaatagt caatagtata cttcttctct ccttttacac 101 acatgcatgt tgttgagaga ttctaaaagc tcattcagta gctagtagta 151 gtacgtgcat cgatcatgtg tcaatgtgtg cgtgtgtggc ctatcttttc 201 TTACTCTCTT GGAAGGAACA TCAAATAAAA AGATCATCAT CATTATAAAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00029 Mean Expected Number 0.008 -strand -102 : -109 TGTAAAAG AC RSP00072 Mean Expected Number 0.010 +strand -50 : -44 GTACGTG AC RSP00108 Mean Expected Number 0.003 +strand -99 : -92 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -92 : -99 CATGCATG AC RSP00534 Mean Expected Number 0.001 -strand +46 : +34 ATAATGATGATgA AC RSP01470 Mean Expected Number 0.009 +strand -100 : -91 aCATGCATGT AC RSP01470 Mean Expected Number 0.008 -strand -91 : -100 aCATGCATGT Totally 7 motifs of 5 different REs have been found Description of REs found 28. Group RE: P-box 1 /AC: RSP00029//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 1 /TF: unknown 71. Group RE: ACGT box /AC: RSP00072//OS: Oryza sativa /GENE: GluB-1/RE: ACGT box /TF: unknown 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 510. Group RE: LRE-TATA O2 /AC: RSP00534//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: LRE-TATA O2 /TF: unknown 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.11|complement(303673..305645) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +242 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.19 G - 0.25 T - 0.27 C - 0.29 1 atcagccaag tcagcacccg cgcgtgcgac tccgtccagg ccttattggg 51 ctggattttg tgctatgatg ggatttgagg cggcttgggc ccagtacagt 101 tgataggccg gaagtaatag gcttgtgggc ctcggcccat acatacatcg 151 agaatcttct tcctttttgt gccgttctcc acgagtcctc ctcttcttct 201 TCTTCTTCCT TCCTCCTCCT TCCCAAGGCC AAGGCCAAGA AGAAGAAGAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00229 Mean Expected Number 0.001 -strand -151 : -160 CCCAATAAGG AC RSP00248 Mean Expected Number 0.008 +strand -196 : -187 GCCAaGTCAG AC RSP00550 Mean Expected Number 0.002 +strand -149 : -139 TGGATTtTGTG AC RSP01025 Mean Expected Number 0.009 +strand -50 : -44 AGAATCT AC RSP01031 Mean Expected Number 0.003 +strand -50 : -43 AGAATCTT AC RSP01214 Mean Expected Number 0.008 +strand -160 : -151 CCTTATTGGG Totally 6 motifs of 6 different REs have been found Description of REs found 222. Group RE: CArG Box 1 /AC: RSP00229//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CArG Box 1 /TF: unknown 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 526. Group RE: CAAT/13 M /AC: RSP00550//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: CAAT/13 M /TF: unknown 950. Group RE: R2 /AC: RSP01025//OS: Arabidopsis thaliana /GENE: GapB/RE: R2 /TF: unknown 956. Group TF: AEF /AC: RSP01031//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 2 /TF: AEF 1122. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01214//OS: Brassica oleracea /GENE: BoCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.12|complement(306322..309973) |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +107 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.33 T - 0.25 C - 0.19 1 ctgtttgagg gtggcatttt aacgaaacca cttttgggag tggcattcca 51 gcgaaacccc gttttgacaa tggttaaatg tcaattttct cgttgggagt 101 tgggagggat gggtggtgca tcaagATTGA tgcaaggaag gaaggagcag 151 tggtgaggaa ggaagatgct ataaaatggg ggcattggtt ccttgagagc 201 TGGAGCCTGG ACCTGGAGGA GCGGTGCGTT CTCCTTCTCC CTCCCCGGCC 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.16|316556..319007 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +121 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.25 T - 0.19 C - 0.24 1 atatgtgtaa ctgcaacggc ccatgcatga taaatatgag gcagcccaaa 51 ccaacctctc tctctataat gtatagaagc ccaaaagaag agcgaggccc 101 aataataagt ccagcagtag taggcttcgc tagtagtgtt gtccaaagac 151 acaagtagta ggaggagatt agagagagag ggaagggaac accgacccgc 201 ATCGCATCTG ATCGGCATCG GCATCGTCCT CGTCCTCGGC ATCAGCAGCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -179 : -172 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -172 : -179 CATGCATG AC RSP00864 Mean Expected Number 0.003 +strand -30 : -22 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand -136 : -144 AGAGAGAGA AC RSP01470 Mean Expected Number 0.010 -strand -171 : -180 TCATGCATGg Totally 5 motifs of 3 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.17|complement(319370..320727) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.24 T - 0.25 C - 0.19 1 atcccgtaca aagttacagc aattaatgat ttattgtacg tgaaagagaa 51 tcaccaagag tagctaggaa gcactgaaac agtagtgtgc atgatactat 101 atagctagct agtgacgtgc gaactgaaac gagggaggcg aggcttaatt 151 ggtggtgata gcgttacgtt actaaccaaa ttaaaaggcc atcaacgcgc 201 GCAATGGTCT CTCACACACG CTCGATTGCA TATTTGCATT AGCTCTAGTT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00399 Mean Expected Number 0.002 -strand -81 : -88 GCACGTCA AC RSP00442 Mean Expected Number 0.008 -strand -185 : -194 TAACTTTGtA AC RSP00503 Mean Expected Number 0.003 +strand -96 : -89 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -89 : -96 CTAGCTAG AC RSP01654 Mean Expected Number 0.009 +strand -90 : -81 AGTGACGTGC Totally 5 motifs of 4 different REs have been found Description of REs found 381. Group TF: AP1-like leucine zipper TF /AC: RSP00399//OS: Nicotiana tabacum /GENE: RNP2/RE: ATF /TF: AP1-like leucine zipper TF ||Identical REs AC: RSP00884 422. Group TF: Dof1 /AC: RSP00442//OS: Zea mays /GENE: cyPPDK1/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.19|complement(323930..325253) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +53 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.24 T - 0.24 C - 0.16 1 tcaagatcat gattgggagg acgtcgatta ataaataaat taacggtacg 51 aattactagt acacgggcgt ggtggttggc ccagacgttc tagaaacaac 101 attctgATTG Ggacaaaaat gaagagaaat ttgaataaga aatacttaat 151 ttccccgtct tggaaaaaag tataaaaggg gccggaatcg atgaaggcga 201 TGCAAGCTGT GACACACTAA CACTCTACTT GTACTAGGTA GATCGCTAGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00021 Mean Expected Number 0.009 +strand -36 : -25 AAAAAGTAtAAA AC RSP00710 Mean Expected Number 0.002 -strand -53 : -65 TAAgTATTTCTTA AC RSP00933 Mean Expected Number 0.003 -strand -25 : -37 TTTATAcTTTTTT AC RSP01499 Mean Expected Number 0.001 +strand -50 : -41 TTCCCCGTCT AC RSP01755 Mean Expected Number 0.003 -strand -123 : -130 CAACCACC Totally 5 motifs of 5 different REs have been found Description of REs found 20. Group TF: GT-1 /AC: RSP00021//OS: Catharantus roseus /GENE: TDC/RE: GT-1#Box7 /TF: GT-1 676. Group RE: AT1-box /AC: RSP00710//OS: Pisum sativum /GENE: TOP2/RE: AT1-box /TF: unknown 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 1560. Group TF: C1 /AC: RSP01755//OS: Glycine max /GENE: a2/RE: C1BS1 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.21|complement(329469..330491) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +53 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.31 C - 0.26 1 gaagaatcag atgcctaaac aacccaccca ttttcctgct cctgctcctg 51 cactgtactt ggattgcaaa tgcggcagag aatcgtttcg tttcgcttca 101 ttttccgcaa gctgaaaGCA ATcgaaagat acgaatagga tcctcctctc 151 ttctttccgt cttgtatata tagatttctg tgggttattc ccgccatttc 201 AAGCAATCCA TATTCCGTCC GTCAGCTACT GCTAGTGGTA GGCTAGATCA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00299 Mean Expected Number 0.001 +strand -14 : -3 ATTCCCGCCAtT AC RSP01237 Mean Expected Number 0.003 -strand -26 : -35 aTCTATATAT Totally 2 motifs of 2 different REs have been found Description of REs found 288. Group TF: E2F /AC: RSP00299//OS: Nicotiana benthamiana /GENE: PCNA/RE: E2F-2 /TF: E2F 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.23|368633..371215 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.37 G - 0.24 T - 0.23 C - 0.16 1 acaatatgag caaccccaaa atacttcagg gcgtatttat atattactaa 51 tagataagaa gttattgttt ccgaaataaa gaactggaaa agaaaaggag 101 gaaagggtga aagagaaggc acggcccagt ggatgcatga tgatgggcca 151 tggcctgctt tgtggagtcc atatctgatc tgatctgagg gataaaaaga 201 AAAAAAGAAA AAAAATCTCA TCTTCCAATC CCAACCTGGT CTGGTGGAAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00683 Mean Expected Number 0.007 +strand -77 : -68 GCCcAGTGGA AC RSP01347 Mean Expected Number 0.000 +strand +27 : +37 AATCCCAACCT Totally 2 motifs of 2 different REs have been found Description of REs found 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 1230. Group RE: IMH2 /AC: RSP01347//OS: Cucumis sativus /GENE: ICL/RE: IMH2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.24|complement(371530..377517) |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.23 T - 0.30 C - 0.15 1 gagataagta tttaacccat aaggaaagcc agtaacatac gaatgtacga 51 agaatattat aaatttgacc gagtttgaat aaaatttatg caagtgatga 101 atatgaaata aataaagtac ggtacagtga tagagagggc atttcgtcct 151 cacgttttgt ttttgttttt tcttttcttt tctgttggga gtggcattcg 201 GAAGAAGAAG AGAGAAGTCC ATCTCCCTCA AGGAGCATCG GCTGCTGGCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00653 Mean Expected Number 0.005 -strand +16 : +6 TTCTCTCTtCT Totally 1 motifs of 1 different REs have been found Description of REs found 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.25-1|complement(380137..383424) |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.22 T - 0.25 C - 0.24 1 gaataaatgc cgaactgcaa gtgaccatca gtcctcacca cagttatcca 51 tggcaacaca gagagaagaa gagaagggga ttgctttgat gaaattgtgt 101 gtgagcgaag cgacacgttt cgtttcgttt tcttggagga aacaaaataa 151 acaccctccg cgtgcagata aagtacatgt gaatatcgca catgctcatc 201 GCTGCTTCTT TCCTCCGACG ACTCGCCGCC GCCTGAAATC TCTTTCTTGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.004 +strand -111 : -101 TGAAATTGTGt AC RSP00445 Mean Expected Number 0.004 -strand +48 : +39 AAgAAAGAGA AC RSP00447 Mean Expected Number 0.004 -strand -111 : -120 AtCAAAGCAA AC RSP00613 Mean Expected Number 0.004 -strand +51 : +44 ATCAAGAA AC RSP00861 Mean Expected Number 0.001 -strand +47 : +39 AGAAAGAGA Totally 5 motifs of 5 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 589. Group RE: UN Z1 /AC: RSP00613//OS: Lycopersicon esculentum /GENE: rbcS2/RE: UN Z1 /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.35|409426..412625 |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +51 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.25 T - 0.26 C - 0.25 1 agaattctat cctactaaaa tattgttagt gctaaacatg cctagatttt 51 gtcagtatac taccaatgtt tgatatgtac taaaccaaac gagccctcct 101 gtacttggaa aaaagtttga tgcaaatggg aaATTGGcgt gtggggccgg 151 agggcaaagg cgtaaattcg actccccacc gctgtgtcct cgatcttctc 201 TGTCTGTACT GGTCCGGGCT CCGGCGCGGC GGCCGGCCGT CGCCCTCCGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00471 Mean Expected Number 0.001 +strand -62 : -52 GTGTGGGGCCg Totally 1 motifs of 1 different REs have been found Description of REs found 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.36|complement(413066..417299) |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +95 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.25 T - 0.25 C - 0.20 1 tgatcaaagt caataacccg aaacggaggg tgtatgagat gatcaaatac 51 acattttgtt cttgaaaagg aaatagtagt gacagattct caaaaggtcc 101 aaacgtttgg acgtgaaatt cacttggacA TTGActtgca cggtttgtat 151 ttgtgatcca agtgaaaagg ctactaaagg agggggggta gcagcagcgg 201 GGGGCCCCAG TTGGCAGCCA CTTATCTCAT CGTAGCCCTT ATCTTCCTCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.007 +strand -55 : -45 TGtATTTGTGA AC RSP00056 Mean Expected Number 0.004 +strand +17 : +26 GCCACTTaTC AC RSP01205 Mean Expected Number 0.007 -strand -131 : -140 CCTTTTCAAG AC RSP01601 Mean Expected Number 0.009 -strand -34 : -41 TTTCACTT AC RSP01735 Mean Expected Number 0.001 +strand -117 : -109 AGATTCTCA Totally 5 motifs of 5 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 1115. Group RE: EM2 /Group TF: MADS box TFs /AC: RSP01205//OS: Arabidopsis thaliana /GENE: AtCRC/RE: EM2 /TF: MADS box TFs 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown 1543. Group TF: CAMTA3 /AC: RSP01735//OS: Arabidopsis thaliana /GENE: CBF2/RE: CM6 /TF: CAMTA3 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0005A05.37|419339..428019 |SUPPORT|21 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.16 T - 0.27 C - 0.30 1 cactatattt ttttaataat aaatttaatt ttaaaagcat tgatttagga 51 taaatctaaa atagaaaaat gatgaagaag tagttattcc gatccaaatg 101 gcaaaaaagg cgaggaggct gggtcatcgt cttcctcgtg agcgtccgcg 151 cccacccacc taacccaaag cccacctcgc ctccgcctcc cctccgcctt 201 CAATTTCCAC TCTCTCCTCT CCTCTCTTGG ACTCCACTCG CCCTCGCGAC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01019 Mean Expected Number 0.009 +strand -129 : -123 ATGAAGA AC RSP01250 Mean Expected Number 0.009 -strand -169 : -178 AAAATTaAAT Totally 2 motifs of 2 different REs have been found Description of REs found 944. Group TF: GAPF /AC: RSP01019//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 1 /TF: GAPF 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0482C06.18|<436799..446040 |SUPPORT|13 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +757 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.17 T - 0.38 C - 0.15 1 atataacctg ttctgatgct tcttgtgaga tttcatgttt gattgatttt 51 ttttgaacat attagcaaat atacgtgtgt cactgcgtgt tttgatattt 101 gatttagtaa atatctccta taatttttca ctgccatcac tccaggaata 151 ttcaacttat gcttgtcata ttaaaaaata tgaggaaaaa cagtatatta 201 GGATCTTGTA AAATAGCATG TTGGACCCTA GTAGAACCTG GGCCCTAGTA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01167 Mean Expected Number 0.006 +strand -93 : -85 TAAATATCT AC RSP01192 Mean Expected Number 0.001 -strand +48 : +39 CTAGGGcCCA AC RSP01192 Mean Expected Number 0.001 -strand +31 : +22 CTAGGGTCCA AC RSP01288 Mean Expected Number 0.005 +strand -130 : -123 ATACGTGT AC RSP01715 Mean Expected Number 0.002 -strand -121 : -132 AcACACGTATAT Totally 5 motifs of 4 different REs have been found Description of REs found 1079. Group RE: TATA box /Group TF: HMG proteins /AC: RSP01167//OS: Zea mays /GENE: pMS1/RE: TATA box /TF: HMG proteins 1103. Group RE: D-box /Group TF: D factor /AC: RSP01192//OS: Nicotiana tabacum /GENE: Adh2/RE: D-box /TF: D factor 1185. Group RE: Z-DNA-motif /AC: RSP01288//OS: Arabidopsis thaliana /GENE: cab1/RE: Z-DNA-motif /TF: unknown 1523. Group TF: STF1/HY5 /AC: RSP01715//OS: Arabidopsis thaliana /GENE: ARF6 (At1g30330)/RE: G/A-box /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0482C06.20|456978..458198 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +231 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.18 T - 0.30 C - 0.24 1 tgttttttgg atggagaaag tactccattc atcataaaat ataataaccg 51 agaatcaaat aaaaagtatc tatgtccact cgtagtattt tctaggttgc 101 tatattatgt aaacagaggg agagggagta agtgtgaatt actaccgtgt 151 actccgatct ctctctggat atacatacct ccccgggaga aggcgaccga 201 TACTTTCCCC TTCTCTCGTT CCCCTCCTCC CTCTACAGTA CTCTCCCCAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00356 Mean Expected Number 0.000 +strand +30 : +43 cCTCTACAGTACTC AC RSP00621 Mean Expected Number 0.001 +strand +21 : +29 CCCCTCCTC AC RSP00864 Mean Expected Number 0.002 -strand -35 : -43 AGAGAGAGA AC RSP00868 Mean Expected Number 0.003 -strand -155 : -166 TATTATATTtTA AC RSP01499 Mean Expected Number 0.009 +strand +5 : +14 TTCCCCtTCT Totally 5 motifs of 5 different REs have been found Description of REs found 341. Group TF: TacBBF /AC: RSP00356//OS: Nicotiana tabacum /GENE: EAS4/RE: TAC box /TF: TacBBF 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0482C06.23-1|475285..521238 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +70 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.14 T - 0.28 C - 0.31 1 gttgaccgca tttcatttcc ctcctccctc aattgtgttg ttgttacaca 51 cacttgccac ccgctataaa atgaaccaga gcagatcgac cacccaatcc 101 aacccaacca ctcatcatcc atctgctact gctactgcta gctccatcca 151 ttttattcta gctccatcca tcctttaaga gaagctgaga tcaagaaacg 201 TACTCACTCT TGCCTGCATC GATCCTTGAG TTTAATTAAC TCAAGGAAGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00613 Mean Expected Number 0.004 +strand -11 : -4 ATCAAGAA AC RSP01046 Mean Expected Number 0.004 +strand -106 : -98 CAATCCAAC AC RSP01065 Mean Expected Number 0.002 -strand +26 : +16 AGGATCGATGc Totally 3 motifs of 3 different REs have been found Description of REs found 589. Group RE: UN Z1 /AC: RSP00613//OS: Lycopersicon esculentum /GENE: rbcS2/RE: UN Z1 /TF: unknown 970. Group RE: NON /AC: RSP01046//OS: Nicotiana tabacum /GENE: histone genes (oligo)/RE: NON /TF: unknown 984. Group RE: Fungus RE /Group TF: homeodomain TF /AC: RSP01065//OS: Arabidopsis thaliana /GENE: At5g64250/RE: Fungus RE /TF: homeodomain TF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0482C06.24|479134..479757 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +79 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.28 T - 0.25 C - 0.11 1 cagtgttacc gtcggagaga tgaaatgaag gcagtacagt gaagtgagtg 51 gctggtgtga gtgcttggcc cgcgaaatgt accattagga tgacataaaa 101 ccatactagt agtaacatga ttcaaacctg cttgagagag tgatgtttgg 151 aagaaaaaat aaaataaaat aaaatgtaga aaaaactagt cgaggatgaa 201 ATAATTGATG ATGCATGTGG GTGAATGCGA TTTGTGGATT GAAGGATGGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00455 Mean Expected Number 0.010 +strand -100 : -95 CCATAC AC RSP00838 Mean Expected Number 0.006 +strand -192 : -187 CCGTCG AC RSP01470 Mean Expected Number 0.004 +strand +9 : +18 TgATGCATGT Totally 3 motifs of 3 different REs have been found Description of REs found 433. Group RE: Motif I /AC: RSP00455//OS: Pisum sativum /GENE: PSPAL2/RE: Motif I /TF: unknown 783. Group RE: CCGTCG motif /AC: RSP00838//OS: Arabidopsis thaliana /GENE: H4A748/RE: CCGTCG motif /TF: unknown 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0482C06.31|507554..508944 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +94 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.14 G - 0.16 T - 0.41 C - 0.30 1 cttttcttct ttccttctcc ccacggaggt gtacgtactg agtgactggt 51 tggtgggccc cacccagcgt ctcttctctt ctcttctttt ttattgctgc 101 caggctggcc tggcacttgc tgtaattact tttctgtaat ttggattaat 151 ccttcgcgtc acattttcta catctcatcc ttccattcca ctcccttcat 201 CTTCTTCCTC TGATAGATAG ATCTTCTTCT TCTTCTTCGC GTCACATTTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00079 Mean Expected Number 0.001 -strand -144 : -153 CCCACCaACC AC RSP00471 Mean Expected Number 0.000 -strand -136 : -146 GgGTGGGGCCC Totally 2 motifs of 2 different REs have been found Description of REs found 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0482C06.33|complement(510692..519250) |SUPPORT|22 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +464 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.19 G - 0.29 T - 0.16 C - 0.36 1 cgcagccgca gcacatgcct ctggggcctg cctccgctgc agcgccgccg 51 cctcaggccg ccgctgctcc gcctgctcag ccgcccgccg gcggcgcaac 101 ggccggccag aagctcacca cgaacgatgc gctcgtctac ctcaaggccg 151 tcaaggataa gttccaggac aagagggaga aatacgagga gttcctcgag 201 GTCATGCGCG ATTTCAAGAG TGAGAGGTCT CTCTACTCTC TCCCTATCGG 251 A Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.5|complement(<540381..541312) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.31 T - 0.19 C - 0.23 1 gaatggcaat gtggtgcggt agaaaaggca gtggatcgtc ttctcttgga 51 ggagatggat caaacgggtt ggttgtcgtg tcacctccat tctcacccaa 101 cttccttacc tagcaagctt ccATTGCcat ggcgatggcg gcaccagcat 151 acgcagagag cgagctctat atactagcaa ctcgtgtggg agagcagagc 201 AGAAGCAGAA GCAGAGCCGA ACCGAGCTAG ACGACGAAAG AGGAGAGGGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00489 Mean Expected Number 0.004 +strand -94 : -85 TACCTAgCAA Totally 1 motifs of 1 different REs have been found Description of REs found 465. Group RE: UVLRE2 /AC: RSP00489//OS: Glycine max /GENE: chs1/RE: UVLRE2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.9|545958..549396 |SUPPORT|13 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +99 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.19 T - 0.26 C - 0.25 1 atagccctcc cagagagcgg cgggcgacta cttttgtcaa tttttgaaat 51 agaaaattat ttttgtaaaa cttttaataa aaaaattaaa aaaaaaattc 101 taataggaga atagaaggcc ccacatatgg tagtagaatc gaagcCCAAT 151 acggcatctt gtttgttgct ttaactaaga aggctgacac gccgcttcac 201 CTCTCCACGT CTCCACGCCG TCGTCGTCGA CCTCACCGGC GGCTGCCTCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00030 Mean Expected Number 0.005 -strand +44 : +38 AGCCGCC AC RSP00057 Mean Expected Number 0.007 +strand +4 : +13 TCCACGTCTC AC RSP00340 Mean Expected Number 0.006 +strand +4 : +13 TCCACGTcTC AC RSP00385 Mean Expected Number 0.006 -strand -151 : -158 ATTTCAAA AC RSP00933 Mean Expected Number 0.001 -strand -109 : -121 TTTtTAATTTTTT AC RSP01000 Mean Expected Number 0.009 +strand -85 : -76 AgGCCCCACA AC RSP01274 Mean Expected Number 0.005 +strand +4 : +13 TCCACGTcTC Totally 7 motifs of 7 different REs have been found Description of REs found 29. Group TF: EREBP /AC: RSP00030//OS: Nicotiana sylvestris /GENE: OLP/RE: ERRE /TF: EREBP ||Identical REs AC: RSP00082 RSP01344 RSP01523 RSP01764 RSP01775 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 370. Group RE: ERE-core /AC: RSP00385//OS: Dianthus caryophillus /GENE: GST1/RE: ERE-core /TF: unknown ||Identical REs AC: RSP00893 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 1173. Group RE: ACE 1 /AC: RSP01274//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.10|complement(550827..554819) |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +712 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.24 C - 0.23 1 gaatgaaggt actgatacag aaagtttatt agatatggta tggaggtgct 51 actcctaata aaacacaaat acgaaggggt ggaactggaa aagtagagaa 101 tttcacacgt caagcattct acacaacgct agtgtactga ctttttcaaa 151 cccccccagc atggcactgg cagaccagac actgcgcaat agtagtagca 201 CACTAGCATG TACTACTACA CTCCTAATCT CTCTCTCTTT CTCGAGTGGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00110 Mean Expected Number 0.003 +strand -97 : -90 CACACGTC AC RSP00861 Mean Expected Number 0.001 -strand +42 : +34 AGAAAGAGA AC RSP00864 Mean Expected Number 0.001 -strand +38 : +30 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand +36 : +28 AGAGAGAGA AC RSP01258 Mean Expected Number 0.005 -strand -89 : -96 TGACGTGT AC RSP01663 Mean Expected Number 0.000 -strand -87 : -98 cTTGACGTGTGA Totally 6 motifs of 5 different REs have been found Description of REs found 108. Group RE: ACGT motif /AC: RSP00110//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: ACGT motif /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 1481. Group TF: HY5 /AC: RSP01663//OS: Arabidopsis thaliana /GENE: ARR9 (At3g57040)/RE: C-box (1) /TF: HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.13|complement(558890..568895) |SUPPORT|20 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +91 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.18 T - 0.30 C - 0.29 1 attttatccg caaattactt acggctccgg gagaaaacat tgtgagagat 51 gaaaataaaa caaaaatgca gggggttgtt tgtaatttgg tattgtaact 101 cctcgcgtgg cgtgcttgag gctgtccgcg ctctccgcct tggtctcctc 151 tcctctcctc gctttccatt ccattcaacc atctcaatca atctcaatcc 201 CAATCCCAAT CAATCCCTCT CTCCATCTGG TGCTCTCTAT CTGAGGAATC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00155 Mean Expected Number 0.000 -strand -6 : -18 gAGATTGATTGAG AC RSP01020 Mean Expected Number 0.009 +strand -152 : -146 ATGAAAA AC RSP01075 Mean Expected Number 0.005 +strand -99 : -90 CtCGCGTGGC AC RSP01602 Mean Expected Number 0.009 +strand -19 : -12 TCTCAATC AC RSP01602 Mean Expected Number 0.009 +strand -9 : -2 TCTCAATC Totally 5 motifs of 4 different REs have been found Description of REs found 150. Group RE: 13 bp CytRE /AC: RSP00155//OS: Cucumis sativus /GENE: hpr-A/RE: 13 bp CytRE /TF: unknown 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 993. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01075//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE II /TF: CpbZIP1; CpbZIP2 (short) 1423. Group RE: Inr /AC: RSP01602//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.16|complement(573295..576372) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +292 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.20 T - 0.25 C - 0.28 1 gctgctgata agccgaagac caaacaatga gaacgtcgat gtattataca 51 aaaatgcccc atacatttct gattgctccc atacgatttg ggcgggggcc 101 aatctagttg tcaacttcta ctactgctag gaggagtagt cacatgatcc 151 aatctctcct ctcctcgcct acaaaaccaa agccacactc cttccttcct 201 TGGGATCCCC AGACCCAGTG CAGGGTTGCA GCGCTTTGCA TAGGAATGTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00333 Mean Expected Number 0.002 +strand -142 : -134 CCATACATT AC RSP00550 Mean Expected Number 0.004 -strand -50 : -60 TGGATcATGTG AC RSP00716 Mean Expected Number 0.002 +strand -29 : -21 CAAAACCAA AC RSP01501 Mean Expected Number 0.005 +strand -111 : -105 GGGCGGG Totally 4 motifs of 4 different REs have been found Description of REs found 319. Group TF: S2F /AC: RSP00333//OS: Spinacia oleracea /GENE: RPL21/RE: S2 /TF: S2F 526. Group RE: CAAT/13 M /AC: RSP00550//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: CAAT/13 M /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 1361. Group RE: GC-box /AC: RSP01501//OS: Triticum aestivum /GENE: H1 (TH315)/RE: GC-box /TF: unknown ||Identical REs AC: RSP01502 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.20|complement(583247..584499) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +10 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.24 C - 0.33 1 ttatgtttag cagtagattg attatcttgt caagttgcag aaaatcccag 51 gtacgtcgtc ctacgtagca agcagatgga ttatcttatc caatccagcc 101 acgcctcgtc actcgccacc cacactgcgc aagcgcaacg catatgccaa 151 atcgccatcc ttgcgatgtg atgcgatgcg atgcagctct cacctctcgt 201 CTCGCCAGCA ATGTCGCACC AGATTCTCCA CACCTCCAAC CCCACGCTGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01053 Mean Expected Number 0.001 -strand -111 : -119 GATAAGATA Totally 1 motifs of 1 different REs have been found Description of REs found 973. Group TF: HvMCB1 /AC: RSP01053//OS: Hordeum vulgare /GENE: ITR1/RE: GATA-core /TF: HvMCB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.21|585718..590518 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +59 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.18 T - 0.21 C - 0.35 1 tagaggtaaa tttgatcagg catcttcttg cattggtagc aagaaaacgg 51 caacatatgg gcctccgatg gaagccacgt cctgtccaat tcccaaacta 101 acccaaacga cccgtttaat aggctaaaac accatccaaa ccaaagcgca 151 catcccaaac ggatcagccg cttagggttt cgtttctccc tctttcgcat 201 CGCATCGCAT CCCTAACCCT AGCTCCCGGC CCTCGCCCAC ACCCGCGCCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00279 Mean Expected Number 0.000 +strand -29 : -21 TTAGGGTTT AC RSP00369 Mean Expected Number 0.000 -strand -21 : -29 AAACCCTAA AC RSP00819 Mean Expected Number 0.005 +strand -127 : -118 GCCACGTCcT AC RSP00821 Mean Expected Number 0.008 +strand -127 : -118 GCCACGTCCT AC RSP00948 Mean Expected Number 0.006 +strand -196 : -190 GGTAAAT AC RSP01303 Mean Expected Number 0.000 -strand -20 : -29 gAAACCCTAA Totally 6 motifs of 6 different REs have been found Description of REs found 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 765. Group TF: ACE-binding TF /AC: RSP00819//OS: Arabidopsis thaliana /GENE: F3H/RE: ACE-core (AtF3H) /TF: ACE-binding TF 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.24|complement(600445..602445) |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +214 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.13 T - 0.30 C - 0.26 1 tgatctctag ttaattacct cctcccatat atgatcctag ctagctaaca 51 agtgtttatc tcaccatgca taattgcaag tatattccgt tcattgccag 101 ctcaaaacct ctctaaaata ccacaccgtc ttaacaagaa tcctcttctc 151 aactctctct atataagtag ctagaagcta ggtataccta catatgtttc 201 ATGCATACTG AGATCGATCG ATCCATCAGG TTGCTACTAC CAAGAACAGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.002 +strand -164 : -157 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand -157 : -164 CTAGCTAG Totally 2 motifs of 1 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.26|609366..612433 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +153 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.24 T - 0.22 C - 0.27 1 cagatcatat catgcatgag gatacacaca gggcacagac gccgcttgta 51 gacagcccca tcctgtcgcc acgtgtcgcg tctcccaacg catggtgcca 101 acgatccaag tcccatgcat gacgaggcta agctaaagaa acccatagcc 151 gcataccgta tttgtagcta tatactccta gtcctagata gagcttagct 201 ATAGCATGAT CGAGTGAGTG GGCGCGTGCG TGCTGCCGCT AGAATTAAGT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00002 Mean Expected Number 0.001 -strand -125 : -133 ACACGTGGC AC RSP00056 Mean Expected Number 0.007 +strand -133 : -124 GCCACgTGTC AC RSP00073 Mean Expected Number 0.008 +strand -133 : -124 GCCACGTGtC AC RSP00073 Mean Expected Number 0.008 -strand -124 : -133 GaCACGTGGC AC RSP00108 Mean Expected Number 0.004 +strand -190 : -183 CATGCATG AC RSP00108 Mean Expected Number 0.004 +strand -87 : -80 CATGCATG AC RSP00108 Mean Expected Number 0.004 -strand -80 : -87 CATGCATG AC RSP00108 Mean Expected Number 0.004 -strand -183 : -190 CATGCATG AC RSP00175 Mean Expected Number 0.004 -strand -126 : -133 CACGTGGC AC RSP00204 Mean Expected Number 0.005 -strand -124 : -133 GACACGTGGC AC RSP00340 Mean Expected Number 0.007 +strand -133 : -124 gCCACGTGTC AC RSP01255 Mean Expected Number 0.004 -strand -125 : -132 ACACGTGG AC RSP01301 Mean Expected Number 0.004 -strand -34 : -43 CTAcAAATAC AC RSP01470 Mean Expected Number 0.005 +strand -191 : -182 TCATGCATGa AC RSP01470 Mean Expected Number 0.008 -strand -79 : -88 TCATGCATGg AC RSP01470 Mean Expected Number 0.008 -strand -182 : -191 TCATGCATGa Totally 16 motifs of 10 different REs have been found Description of REs found 2. Group RE: ABRE-3 /AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /TF: unknown 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 72. Group TF: TAF-1 /AC: RSP00073//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: PA /TF: TAF-1 ||Identical REs AC: RSP00274 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.27|complement(617374..618318) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +54 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.28 T - 0.20 C - 0.31 1 agaacagagt atatagccat ccatccggtc aaagcagccg gccacgtggc 51 gtgtccccgt tggctgtact ggacgcgcgc gtgcagcctg cagcggagac 101 cgacttgacc gctggtctcc ggcgacgact tgtcagccgg tcaacatgaa 151 gtgtgtagca cggcgacgat ttccggtgca cacatgctca ctactgtcgc 201 AATGGCAAGC TCATATACTG TCTGACCAGC ATTAATTCCG GCCAGCCGCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00073 Mean Expected Number 0.001 +strand -160 : -151 GCCACGTGGC AC RSP00073 Mean Expected Number 0.001 -strand -151 : -160 GCCACGTGGC AC RSP00153 Mean Expected Number 0.001 -strand -152 : -161 CCACGTGGCC AC RSP00175 Mean Expected Number 0.007 +strand -158 : -151 CACGTGGC AC RSP00175 Mean Expected Number 0.007 -strand -153 : -160 CACGTGGC AC RSP00204 Mean Expected Number 0.007 +strand -160 : -151 GcCACGTGGC AC RSP00204 Mean Expected Number 0.007 -strand -151 : -160 GcCACGTGGC AC RSP00682 Mean Expected Number 0.007 +strand -160 : -151 GCCACGTGGc AC RSP00682 Mean Expected Number 0.007 -strand -151 : -160 GCCACGTGGc AC RSP00718 Mean Expected Number 0.007 +strand -159 : -152 CCACGTGG AC RSP00718 Mean Expected Number 0.007 -strand -152 : -159 CCACGTGG Totally 11 motifs of 6 different REs have been found Description of REs found 72. Group TF: TAF-1 /AC: RSP00073//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: PA /TF: TAF-1 ||Identical REs AC: RSP00274 149. Group RE: Box II /AC: RSP00153//OS: Petroselinum crispum /GENE: CHS/RE: Box II /TF: CPRF-1; CPRF-2; CPRF-3; ||Identical REs AC: RSP00154 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 683. Group TF: GBF /AC: RSP00718//OS: Arabidopsis thaliana /GENE: Adh/RE: G-box-1 /TF: GBF ||Identical REs AC: RSP01254 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.28|620889..621561 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +48 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.24 T - 0.24 C - 0.24 1 aataagattg caataagaac atagtggatc atgttcagaa gagaaggaag 51 aagacgaaat gaagcctatc attctgccgc cgctcaactg caagaacggg 101 cagccgtccg atcggcatcg gacggtcacc gacgtctctc aaggcggcga 151 acatctccat ctttcttact acttttagcc attagcttgg tggattagtg 201 AGCTCGCTCC TCCTTTTGGC ACAAATTCTC TCGAGAAGGA GAGCGAATAT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00653 Mean Expected Number 0.003 -strand +47 : +37 TTCgCTCTCCT AC RSP01058 Mean Expected Number 0.004 +strand -179 : -172 TAGTGGAT AC RSP01497 Mean Expected Number 0.006 +strand -98 : -89 GCCGTCcGAT AC RSP01505 Mean Expected Number 0.001 -strand -88 : -96 GATCGGACG AC RSP01703 Mean Expected Number 0.002 +strand -72 : -63 CCGACGTCTC Totally 5 motifs of 5 different REs have been found Description of REs found 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 978. Group TF: GT-3a /AC: RSP01058//OS: Brassica napus /GENE: extA/RE: GT-3a Box III /TF: GT-3a 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 1512. Group RE: ACGT2/DRE2 /AC: RSP01703//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT2/DRE2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.29|622787..623811 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +213 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.39 G - 0.20 T - 0.24 C - 0.17 1 ataaaattaa aagtgaggtt ttaaatctcg gttatagcta tttgaaaaag 51 ggtctagcta tttgctctta tatagtacaa tttagccgat acagctgttt 101 gagaagacca accattaaat gtttatctga ttagtaggca ctaccaaaaa 151 agagagacat aaacggagag ataaaaagga gcagagaaga agacctccac 201 TGGCATTGGC CAATTCCAAA AGCGAAAGCA GAAGCCAACC ATTATAACCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00421 Mean Expected Number 0.004 -strand -169 : -175 ACCGAGA AC RSP00445 Mean Expected Number 0.005 +strand -55 : -46 AAAAAAGAGA AC RSP01103 Mean Expected Number 0.002 -strand -180 : -187 AAACCTCA Totally 3 motifs of 3 different REs have been found Description of REs found 402. Group RE: DRE1 /AC: RSP00421//OS: Zea mays /GENE: rab17/RE: DRE1 /TF: unknown 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 1021. Group RE: AC1 /AC: RSP01103//OS: Spinacia oleracea /GENE: rps22/RE: AC1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.31|628940..629592 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.16 T - 0.31 C - 0.27 1 tataattctc ttttgtttag taagatttgc ataagattta tgatattcga 51 ataaaccttg gtcaaatgat cgatgataaa cttgtttatt cagtaaagta 101 aaaaaagtgt agttaacgag acgctcccgg ccatgtcgac agctgagctg 151 acaaaaggcg cgccagctat aaccccttcg tcccctctcc tcttcttcta 201 CCTCGCGACC ACTTCACTGG ACTACACTAC CACCTCTCTC TCGCTCTCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00035 Mean Expected Number 0.008 +strand -49 : -43 CAAAAGG AC RSP00320 Mean Expected Number 0.001 -strand -123 : -133 tATCATCGATC AC RSP00383 Mean Expected Number 0.010 +strand -141 : -135 GGTCAAA AC RSP00441 Mean Expected Number 0.004 +strand -100 : -91 AAaAAAGTGT AC RSP00713 Mean Expected Number 0.010 +strand -61 : -55 CAGCTGA AC RSP01065 Mean Expected Number 0.000 +strand -135 : -125 AtGATCGATGA AC RSP01621 Mean Expected Number 0.004 -strand -90 : -99 TACACTTTTt Totally 7 motifs of 7 different REs have been found Description of REs found 34. Group RE: D1 /Group TF: Dof family /AC: RSP00035//OS: Hordeum vulgare /GENE: Al21/RE: D1 /TF: Dof family 306. Group RE: Box I /Group TF: RNFG1 /AC: RSP00320//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: Box I /TF: RNFG1 368. Group TF: WRKY1 /AC: RSP00383//OS: Petroselinum crispum /GENE: WRKY1/RE: WA /TF: WRKY1 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 984. Group RE: Fungus RE /Group TF: homeodomain TF /AC: RSP01065//OS: Arabidopsis thaliana /GENE: At5g64250/RE: Fungus RE /TF: homeodomain TF 1441. Group TF: GmDof4; GmDof22 /AC: RSP01621//OS: Glycine max /GENE: Synthetic OLIGO/RE: E4 /TF: GmDof4; GmDof22 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.35|complement(642400..643524) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +25 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.34 G - 0.24 T - 0.22 C - 0.20 1 gaatgatcaa ccgcttatgg tttgatgaaa caagaagtgg gggagcacac 51 aaagcgagtc aactcgaata gttcagttga ttcagtaaca agagcagttt 101 cccattcagt tttgacacgc caagagtgtg caggtgATTG Cagttaacac 151 aaccagtcga gcgcattaca tatggtccaa gaagattaac cgcccggtca 201 GAATGAGATA CTAATTAATA CTGAAATGAC AACGGATCAT GCCGGGAAGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00559 Mean Expected Number 0.004 -strand +31 : +21 TGTcATTTCAG AC RSP00654 Mean Expected Number 0.009 -strand -158 : -167 CcCCCACTTC Totally 2 motifs of 2 different REs have been found Description of REs found 535. Group RE: 2'/Box II J1 /AC: RSP00559//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: 2'/Box II J1 /TF: unknown 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0439B06.36|complement(645090..648672) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +125 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.24 T - 0.21 C - 0.25 1 aagaaagtga aaagaattga caataattcg atactgcaaa aaagataatg 51 ttcatcaaaa gaagaaaata aatgcgaaga aaataacgga acggaagggg 101 ggtgaccccg ccgtcgccgt cgccgttaac catggtgtgg tggtcgtctt 151 cttcctcaat aagaaggcga tggattgagc ccccaccctc tcctctcctc 201 CCTGCTTCTC TCTCTCTCTC TCTACCCAGC GAGCAAGAGA GAGAGACAGG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.002 +strand +36 : +44 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +38 : +46 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand +23 : +15 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand +21 : +13 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand +19 : +11 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand +17 : +9 AGAGAGAGA AC RSP00864 Mean Expected Number 0.000 -strand +15 : +7 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 -strand +22 : +6 GAGAGAGAGAGAGAGAA AC RSP01601 Mean Expected Number 0.008 -strand -189 : -196 TTTCACTT Totally 9 motifs of 3 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBb0032H19.28|720493..722901 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +53 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.14 T - 0.33 C - 0.30 1 aagcctgtgt gcacccatgt gcttcattct atctggtcaa caatgtatta 51 cacactgctt tgactacttc ccccaaaaaa gtacacactg ctttgactca 101 ggtcaaactt ggactttatc catcattcca tcctctctcc cagtcccatc 151 ctcaacctca taacactttc ctaattgcct catatgcggc cttcccatcc 201 GTATTGTTTT CAGTTTATCA CACTTGTTGG GTCATGAATT TCTGAAGCTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.002 +strand +35 : +45 TGAATTTcTGA AC RSP00314 Mean Expected Number 0.002 +strand -98 : -88 TCaAACTTGGA AC RSP00383 Mean Expected Number 0.006 +strand -100 : -94 GGTCAAA AC RSP01209 Mean Expected Number 0.002 -strand -120 : -129 CTTTTTTGGG Totally 4 motifs of 4 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 300. Group TF: RSG /AC: RSP00314//OS: Arabidopsis thaliana /GENE: GA3/RE: rbe /TF: RSG 368. Group TF: WRKY1 /AC: RSP00383//OS: Petroselinum crispum /GENE: WRKY1/RE: WA /TF: WRKY1 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBb0032H19.31|complement(728099..734824) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +4805 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.24 T - 0.26 C - 0.29 1 aaacaggaac tcagcgcgcc catttgcgta atgccttgag ttcatctcac 51 tttcgatctt tgtatgcatt ttatctactg ctcatctgcg tcaacttaag 101 cccggcctac gtctagctgt gggccggatt cagcaaggtt gcctctgtga 151 tgggccagga cggaataaca ttgaatgagc ttgggcccga acgggatagt 201 GTGTTGGGCT TGAACCCAGT CCCCACAGTT CCCCCCTCCC CATCGACCTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC SP017556 Mean Expected Number 0.005 +strand +40 : +47 CCATCGAC Totally 1 motifs of 1 different REs have been found Description of REs found 1561. Group TF: C1 /AC: SP017556//OS: Glycine max /GENE: a2/RE: C1BS2 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1212_B09.8|742253..745747 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +131 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.30 C - 0.23 1 cgtgctccct gattttgttg actaatccag acatattgca atcagtcaat 51 attatccata gtctctgata gagatggggc agggatggac caaccgaagt 101 atctgataga gtaaagccaa attagtacca aactttgacc aactttcgct 151 aggaaatagg agtatatgat tgattgtccc ctattatagc aagcagtgat 201 CATACAGCCT TCCTGCTCTC TCTATTCTGT TTGCAATCCT CTTCACCCTA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00949 Mean Expected Number 0.004 -strand -177 : -184 TAGTCAAC AC RSP01305 Mean Expected Number 0.003 +strand +42 : +51 TtCACCCTAA AC RSP01527 Mean Expected Number 0.001 -strand -180 : -191 TCAACAAAaTCA Totally 3 motifs of 3 different REs have been found Description of REs found 878. Group RE: TAGTCAAC motif /AC: RSP00949//OS: Petroselinum crispum /GENE: 4CL-1/RE: TAGTCAAC motif /TF: unknown 1198. Group RE: Telo box /AC: RSP01305//OS: Nicotiana tabacum /GENE: Thio h2/RE: Telo box /TF: unknown 1375. Group RE: Box II /AC: RSP01527//OS: Pisum sativum /GENE: PsCHS2/RE: Box II /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1212_B09.10|complement(748882..751795) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +48 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.17 T - 0.33 C - 0.18 1 gattcgccac cctgcaaaga tcctaaagtt aaaatatctc tcaaagtgaa 51 cagtgttttt tgatcagtaa tttaaacagt aaactgaata gtgtttttga 101 atagtattca gccgaataaa cagtaaactg aatagtattc agccgaataa 151 atattgtaca tatatgtata tgtatgtata tatatgtata tatgcgtacg 201 TCTGATTCAT CGTTCATCTC CGGCTCTGGC CCTGCAAACT AAGCTGCCAT 251 G Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1212_B09.13|complement(763983..766477) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +60 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.20 T - 0.33 C - 0.24 1 tgttaagcta tcctaaacga acgaatctgt ctcagactct cagtcaacag 51 catcacagtc aagggcaggc agccctgatt agctaaacac gtcattgctc 101 aggtattcgg atattatttt tttttctttt tgcttattca actggaacac 151 ggaagcgctt gcaatatcaa ccatgtcgtt cgtccatctt gttctgacct 201 GTGCGCTTTT CTTTGAACCT GGCAATTGCG ATTCATGGTG CTCTGCATTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00195 Mean Expected Number 0.001 -strand -48 : -58 TCCGTGTtCCA AC RSP01072 Mean Expected Number 0.006 -strand -106 : -115 ATgACGTGTT AC RSP01258 Mean Expected Number 0.003 -strand -107 : -114 TGACGTGT AC RSP01654 Mean Expected Number 0.008 -strand -105 : -114 AATGACGTGT Totally 4 motifs of 4 different REs have been found Description of REs found 188. Group RE: Box II /AC: RSP00195//OS: Oryza sativa /GENE: Gt2/RE: Box II /TF: unknown 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1212_B09.20|complement(789257..793223) |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +2944 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.19 G - 0.28 T - 0.25 C - 0.28 1 aggagagggt gatgacgtgg cccgctgaca tgtggggccc acgtgggtcc 51 cacgctgact cagccgtcac gtcggacaaa accgggatga aaaccaccga 101 gggacctcgg gtgaccggtt ttgtatagtt gagagatccc gcatatctgg 151 ttttgcggtt tgaggatgtt ttcgtatccc gatgacaagt tgaggaacct 201 TCGGTGTACT TTTTCCATCC CCTTTCCTCC CCCTCTTGCC ACGAACCCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00113 Mean Expected Number 0.001 +strand -188 : -180 TGACGTGGC AC RSP00214 Mean Expected Number 0.005 +strand -188 : -181 TGACGTGG AC RSP00215 Mean Expected Number 0.005 -strand -181 : -188 CCACGTCA AC RSP00471 Mean Expected Number 0.003 +strand -171 : -161 aTGTGGGGCCC AC RSP00718 Mean Expected Number 0.006 +strand -162 : -155 CCACGTGG AC RSP00718 Mean Expected Number 0.006 -strand -155 : -162 CCACGTGG AC RSP00819 Mean Expected Number 0.004 -strand -180 : -189 GCCACGTCaT AC RSP00821 Mean Expected Number 0.005 -strand -180 : -189 GCCACGTCaT AC RSP00847 Mean Expected Number 0.008 -strand -181 : -190 CCACgTCATC AC RSP00913 Mean Expected Number 0.003 +strand -190 : -181 GATGACGTGG AC RSP00915 Mean Expected Number 0.004 +strand -190 : -181 GATGACGTGG AC RSP00916 Mean Expected Number 0.003 +strand -190 : -181 GATGACGTGG AC RSP00997 Mean Expected Number 0.004 +strand -190 : -181 GATGACGTGG AC RSP01020 Mean Expected Number 0.004 +strand -114 : -108 ATGAAAA AC RSP01275 Mean Expected Number 0.004 -strand -180 : -189 gCCACGTCAT AC RSP01280 Mean Expected Number 0.002 +strand -190 : -180 GaTGACGTGGC Totally 16 motifs of 15 different REs have been found Description of REs found 111. Group RE: TGA2 /AC: RSP00113//OS: Glycine max /GENE: GH3/RE: TGA2 /TF: unknown 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 683. Group TF: GBF /AC: RSP00718//OS: Arabidopsis thaliana /GENE: Adh/RE: G-box-1 /TF: GBF ||Identical REs AC: RSP01254 765. Group TF: ACE-binding TF /AC: RSP00819//OS: Arabidopsis thaliana /GENE: F3H/RE: ACE-core (AtF3H) /TF: ACE-binding TF 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown 844. Group TF: Opaque-2 /AC: RSP00913//OS: Zea mays /GENE: b-32/RE: B1 /TF: Opaque-2 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 847. Group TF: Opaque-2 /AC: RSP00916//OS: Zea mays /GENE: b-32/RE: B4 /TF: Opaque-2 918. Group TF: Opaque-2 (O2) /AC: RSP00997//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-2 /TF: Opaque-2 (O2) 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1212_B09.41|840331..844201 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +14 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.17 T - 0.26 C - 0.29 1 gaatctacga acggtctccg aaggtcacat actcacatac ctttctaagc 51 aatacaacac ggcagaagtt tcagtggcag ttggaattcc tgctcacaga 101 cgcaGCAATc gtgacaaaca caggataaat cctcactgga gatcatagca 151 ataggtgatc ctttttctat agccacggcc ttctcttcat ctgccttcct 201 CGCCATTACA CTCCATGGAC TTGCCAAAAC TTCTCTTCAC AGTACTCATA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00431 Mean Expected Number 0.009 +strand -128 : -117 AGTGGCAGTTGG AC RSP00830 Mean Expected Number 0.001 +strand -16 : -5 CTTCATCTGCCt AC RSP01014 Mean Expected Number 0.006 -strand -8 : -17 CAgATGAAGA AC RSP01205 Mean Expected Number 0.006 +strand -161 : -152 CCTTTCTAAG Totally 4 motifs of 4 different REs have been found Description of REs found 411. Group TF: AtMYB77 /AC: RSP00431//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB77 BS /TF: AtMYB77 776. Group TF: BHLH factors R, C1, Sn /AC: RSP00830//OS: Arabidopsis thaliana /GENE: CHS/RE: RRE (AtCHS) /TF: BHLH factors R, C1, Sn 939. Group TF: GAPF /AC: RSP01014//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 2 /TF: GAPF 1115. Group RE: EM2 /Group TF: MADS box TFs /AC: RSP01205//OS: Arabidopsis thaliana /GENE: AtCRC/RE: EM2 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0463F06.47|complement(908537..911049) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +28 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.18 T - 0.35 C - 0.17 1 gttgtaattt ttttgaaaac aatatatata caatattgtt atttaaaagc 51 cacgttaatc tattttttta atttaaaata attaatatct aattaattat 101 gcgttaatgg ctaagacgta tacTCAATtt tctgttttcc ccttcttggt 151 agcgcgtacg tcgtactact tataagtagg agccggccga gcgagcaaca 201 AGTAGCTAGC TTGGTAGCCT ACACTAGAAT GGAAGCAGCT GCTTTGTCGA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00577 Mean Expected Number 0.000 -strand -104 : -123 AtTAATTAGATATTAATTAt AC RSP00709 Mean Expected Number 0.008 -strand -117 : -125 TAATTATTT AC RSP00892 Mean Expected Number 0.006 +strand -119 : -111 TTAATATCT AC RSP01034 Mean Expected Number 0.004 -strand -146 : -152 ACGTGGC AC RSP01499 Mean Expected Number 0.003 +strand -64 : -55 TTCCCCtTCT Totally 5 motifs of 5 different REs have been found Description of REs found 553. Group RE: AT-rich FF2 /AC: RSP00577//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: AT-rich FF2 /TF: unknown 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 824. Group TF: Dof family /AC: RSP00892//OS: Solanum melongena /GENE: SmCP/RE: EE 2 /TF: Dof family 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698G03.18|complement(917880..920433) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +49 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.20 T - 0.32 C - 0.27 1 tcttttgtca catccaggct cgattgtttc cttccccaag tcagtcaatg 51 ccatcactgt catctgctct cagccatgta attgttaccc acccgtgtcc 101 atttgcaatt gagatcctct gctgtattat ccctatATTG Aaagtcactg 151 acatgtgggc taagcatata gctagctagc ttggacagca ggcccctctc 201 TATTGTAATA GGCTTGTTTG CACTGCCTGT GAAGCTAGCT ACCGTAGCGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00503 Mean Expected Number 0.003 +strand -29 : -22 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -22 : -29 CTAGCTAG Totally 2 motifs of 1 different REs have been found Description of REs found 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698G03.21|complement(926686..931260) |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +54 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.18 T - 0.32 C - 0.28 1 aggcccccag gccctcgccg gagctcgccc gtcatcgtcg cccaccgagc 51 cacttcatac ttcaatcaag ctatttgttc aaagcctcct ttcttgattt 101 gatggtaggg ttagtgttat ttgtaaagag aaaaccagct tccagatctc 151 gaatttgcct caaacttatc ttctcttgta gatctggaag ctaggttttc 201 TCTTTACAAA TAACACTATT TTTTCCCCCA TTAGGTCTGC CCTGTGTCAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00394 Mean Expected Number 0.009 +strand -79 : -73 TGTAAAG AC RSP00613 Mean Expected Number 0.009 -strand -103 : -110 ATCAAGAA Totally 2 motifs of 2 different REs have been found Description of REs found 377. Group TF: PBF-1 /AC: RSP00394//OS: Zea mays /GENE: gamma-27kDa zein/RE: P-box (s) /TF: PBF-1 ||Identical REs AC: RSP00396 RSP00429 RSP01402 589. Group RE: UN Z1 /AC: RSP00613//OS: Lycopersicon esculentum /GENE: rbcS2/RE: UN Z1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698G03.30|complement(966142..970130) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +23 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.15 T - 0.33 C - 0.25 1 tagccctcaa cttctctttc gccgttaaat ggcacttctt ggctgccaac 51 aataataggg ctctccaatt gtaaatttat ttttttaatt attctatttg 101 cagTCAATgg caaagtcttc ctgttcagtc ttatctatac ttcattcccc 151 tagctccccc cacacaaata gtactagtaa tacggggaag caaatataat 201 CAGCTTGGCA GTTGCATGAA TGCATGGCCA ACTCCATTGC AATATTCCGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00055 Mean Expected Number 0.004 -strand -106 : -117 AGAATaATTAAA AC RSP00431 Mean Expected Number 0.009 +strand +4 : +15 cTTGGCAGTTGC AC RSP01150 Mean Expected Number 0.007 +strand -9 : +2 AAaTATAATCA AC RSP01499 Mean Expected Number 0.001 -strand -12 : -21 TTCCCCGTaT Totally 4 motifs of 4 different REs have been found Description of REs found 54. Group RE: Box 3 /AC: RSP00055//OS: horseradish (Armoracia lapathifolia) /GENE: prxC2/RE: Box 3 /TF: unknown ||Identical REs AC: RSP00645 411. Group TF: AtMYB77 /AC: RSP00431//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB77 BS /TF: AtMYB77 1066. Group RE: C-DP BS2 /AC: RSP01150//OS: Cucumis sativus/GENE: POR/RE: C-DP BS2 /TF: unknown 1360. Group RE: CS6 /AC: RSP01499//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS6 /TF: unknown ||Identical REs AC: RSP01500 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698G03.37|complement(991513..994065) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +40 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.35 G - 0.17 T - 0.24 C - 0.24 1 ctaaattcag cgccacacaa tttgacgctg aacaaaagag tcagttttga 51 aataagtttt gacgacggtt tatttataaa aatagtttta caaaggatca 101 aattatcaaa atttatgaca gtacggaGCA ATactgttcc tcttcagtct 151 tccggaaaaa atctccccag tgaaagcacc caccccaacc cccaccaaat 201 TATACTACTC GGCAAGGCAA ATCCTGCCAG ACTGGGAGCC ATGGCGAAAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00157 Mean Expected Number 0.003 +strand -129 : -118 ATTTATAaAAAT AC RSP00157 Mean Expected Number 0.003 -strand -118 : -129 ATTTtTATAAAT AC RSP00385 Mean Expected Number 0.006 -strand -148 : -155 ATTTCAAA AC RSP00601 Mean Expected Number 0.002 +strand -11 : -3 CCCCACCAA Totally 4 motifs of 3 different REs have been found Description of REs found 152. Group RE: D2 /AC: RSP00157//OS: Glycine max /GENE: GmAux28/RE: D2 /TF: unknown 370. Group RE: ERE-core /AC: RSP00385//OS: Dianthus caryophillus /GENE: GST1/RE: ERE-core /TF: unknown ||Identical REs AC: RSP00893 577. Group RE: C-rich R /AC: RSP00601//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich R /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698G03.41|1007063..1009205 |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +98 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.34 G - 0.16 T - 0.25 C - 0.25 1 atatggcaca aatatgatgt aataaagcac tacaccatgt gctgcaatta 51 ggcaattgta ctgaaactac tattagcgca ttgcattcat gcaattgaga 101 ggtctctata gtctatagtc tataggaacc atatcccttc atgaacttca 151 ggagtaacaa aaccctctat atatacgcac acgccctgca ctcctctcaa 201 AAACACAAGC AACAGCTTAG CTAGTAACAG TAGGCCACTA CTAGCATCAC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01237 Mean Expected Number 0.006 +strand -36 : -27 CTCTATATAT Totally 1 motifs of 1 different REs have been found Description of REs found 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0494A10.15|1012867..1016294 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +65 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.23 T - 0.23 C - 0.26 1 gaagcatatc cccagttatt aattccgcat tccagttgac cagttgtagt 51 gttttatggc tagaaaaagt tggtcaaaaa gggcttgaag taaataagag 101 gagaactggg ggggagtttt tattcataaa agcccctcca actttctcgt 151 ctgccaccaa cccacttcct atttgtcgcc gtcgcggcgc gtcccaaact 201 CCAAACACGC CGCAAAGCGA AGAAGCGATC GCACGTTCGC ACGCAGACGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00078 Mean Expected Number 0.001 +strand -47 : -36 CCACCAACCCaC AC RSP00405 Mean Expected Number 0.006 -strand +5 : -3 TTTGGAGT AC RSP00654 Mean Expected Number 0.010 +strand -42 : -33 aACCCACTTC AC RSP01711 Mean Expected Number 0.004 +strand -141 : -132 CTAGAAAAAG Totally 4 motifs of 4 different REs have been found Description of REs found 77. Group RE: AC-II /AC: RSP00078//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-II /TF: unknown 387. Group RE: adjb /AC: RSP00405//OS: Nicotiana tabacum /GENE: RNP2/RE: adjb /TF: unknown 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown 1519. Group TF: RIN /AC: RSP01711//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Others /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0494A10.26|complement(1068764..1071633) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +45 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.31 T - 0.20 C - 0.17 1 tggagtttgg ctaagtcctc ctgagagcag ccaggcataa aggacatcat 51 caagaactgg tctattgagg agaagagaag agaagagttc ttggaaggtt 101 ctccatctcc catgtcaggg agttggtgtc tctaggatac ctgcataggc 151 aggcaatcac acacacatat ttatcacgag aaagagtaga gctgcaaaga 201 GTAGGAAGGA TTCAGACATT CAGAGAGAGA GGAGAGGGAG GAGAGATGGG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00358 Mean Expected Number 0.009 -strand -76 : -83 CAACTCCC AC RSP00536 Mean Expected Number 0.006 -strand -24 : -30 GTGATAA AC RSP00613 Mean Expected Number 0.009 +strand -152 : -145 ATCAAGAA AC RSP00864 Mean Expected Number 0.008 +strand +22 : +30 AGAGAGAGA Totally 4 motifs of 4 different REs have been found Description of REs found 343. Group RE: CARE2 /AC: RSP00358//OS: Oryza sativa /GENE: Rep-1/RE: CARE2 /TF: unknown 512. Group RE: LRE-TATA AA2 /AC: RSP00536//OS: Lycopersicon esculentum /GENE: rbcS3C/RE: LRE-TATA AA2 /TF: unknown 589. Group RE: UN Z1 /AC: RSP00613//OS: Lycopersicon esculentum /GENE: rbcS2/RE: UN Z1 /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0494A10.28|complement(1075367..1078399) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +32 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.18 T - 0.27 C - 0.23 1 aatctgatgg atggattagt atgcttaaca aaacagcaag ttgatgctga 51 tatgcaaact ctacaaaagc gagctggcta agcttggaga aatccaagta 101 caccactcca tttctctctc tttctctcgc tttctttttg catagttttc 151 ttcatgctcc atgtaaacaa gcaagaaaag agaggaaaag gaggcagctc 201 GGTGCAATTC TCGAACGACC CAAAACCTTG AACAATTCAA TCCTTCTTCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00653 Mean Expected Number 0.002 +strand -89 : -79 TTCTCTCTCtT AC RSP00861 Mean Expected Number 0.001 -strand -76 : -84 AGAAAGAGA AC RSP00863 Mean Expected Number 0.001 +strand -22 : -14 AGAGAGGAA AC RSP00864 Mean Expected Number 0.001 -strand -80 : -88 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 -strand -73 : -89 GAGAGAaAGAGAGAGAA Totally 5 motifs of 5 different REs have been found Description of REs found 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 799. Group TF: BPC1 /AC: RSP00863//OS: Arabidopsis thaliana /GENE: STK/RE: GA-4 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0494A10.34|1100584..1103692 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +90 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.25 T - 0.27 C - 0.24 1 ctttatccaa actcagcctt agaacgctgg gttgtgtggc aatccatcga 51 tcaatctaaa aaaatatcct agctggagct ggagggggtt ggaaatagcc 101 aatgtgcacc tggtccagga agaccttgtg cacgggtgtg tgtgttgagg 151 gttggcgtcc gtgtccagat ctacagacgc caagaaggaa gtaattcccc 201 AAACCTTAGA TCGCCTCTTC TTCTTCTTCT AATCTTGCTG TTGGACCCGA 251 C Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698A04.34|complement(1157000..1161422) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +51 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.22 T - 0.28 C - 0.30 1 ctataaattc ctggtttttt tcccagtgcc gatcaagttg ctagaatgat 51 ttcatgaatt tgtttgcata actaaactga cttgtcttca acatgctaat 101 cctggtttca gaatgagagt gaccaagtgg caggtggtgg ccactgggcg 151 agctaaccct gtccacgtct gctcgtcgcc atggcctctc gttccttccc 201 CAGCACTGCA GCCACACACA CCTGCGACTG CGAGCTCCCC GTCTCTCGCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00522 Mean Expected Number 0.009 -strand -71 : -77 CCACTTG AC RSP00695 Mean Expected Number 0.010 +strand -199 : -193 TATAAAT AC RSP01175 Mean Expected Number 0.003 +strand +33 : +43 AGCTcCCCGTC AC RSP01301 Mean Expected Number 0.006 +strand -200 : -191 CTATAAATtC Totally 4 motifs of 4 different REs have been found Description of REs found 498. Group TF: DPBF-1; DPBF-2 /AC: RSP00522//OS: Daucus carota /GENE: Dc3/RE: E2-core /TF: DPBF-1; DPBF-2 661. Group RE: TATA box /AC: RSP00695//OS: Oryza sativa /GENE: Gt1/RE: TATA box /TF: unknown 1086. Group TF: Zmhox1a /AC: RSP01175//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 2 /TF: Zmhox1a 1195. Group RE: TATA box /Group TF: TBF /AC: RSP01301//OS: Triticum aestivum /GENE: Amy2/54/RE: TATA box /TF: TBF ||Identical REs AC: RSP01302 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698A04.35|1162537..1165198 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +136 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.15 T - 0.33 C - 0.16 1 tgatatgagc tgatattgtt attcatctca acttttcttt ttgaatgcgc 51 ttataatttc tttcctctag ttatttattt attatagcta gacaaaacaa 101 taaacACAAT cagattacag cttccctgct gtttcgtttt ctaattctgg 151 gatgcacctt cttttctttc tgaagaagaa gaaaaaaaaa gagaggagaa 201 AGAAAAGAAA AAAAAAATTT CTCCAAAGAA GAAGAGAGCG TGTACAATTC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.002 +strand -16 : -7 AAAAAAGAGA AC RSP00631 Mean Expected Number 0.000 -strand -93 : -105 TGTGtTTATTGTT AC RSP00653 Mean Expected Number 0.002 -strand +4 : -7 TTCTtTCTCCT AC RSP00860 Mean Expected Number 0.004 +strand -4 : +5 AGAAAGAAA AC RSP00860 Mean Expected Number 0.003 -strand -30 : -38 AGAAAGAAA Totally 5 motifs of 4 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 607. Group TF: S2F /AC: RSP00631//OS: Spinacia oleracea /GENE: RPL21/RE: CII /TF: S2F 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0698A04.36|complement(1165539..1167929) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1366 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.18 T - 0.26 C - 0.35 1 aacattctac caccccagtt tcaaattttt tttttcgaaa gaaaacgaaa 51 agtgaaaaaa aaaagaaagg cgtcggcaac ttgagttggg caaagagcaa 101 ggttccacac gctgtcactg ccgtgtgggc catccccccc cccacgccac 151 gcgctctgct ctttctttat ctagtcggta ggctcggtcc actccgcctc 201 TCTCTCTCTC TCTCTTCCTC CTCCGCGCGC CGCCTTACCC CTCTCCTCCT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00161 Mean Expected Number 0.005 +strand -156 : -146 ACGAAAAGTGA AC RSP00445 Mean Expected Number 0.001 +strand -142 : -133 AAAAAAGAaA AC RSP00864 Mean Expected Number 0.004 -strand +15 : +7 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 -strand +13 : +5 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 -strand +11 : +3 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 -strand +9 : +1 AGAGAGAGA AC RSP00864 Mean Expected Number 0.004 -strand +7 : -2 AGAGAGAGA AC RSP00873 Mean Expected Number 0.009 +strand -156 : -146 ACGAAAAGTGA AC RSP01000 Mean Expected Number 0.002 -strand -68 : -77 ATGgCCCACA AC RSP01283 Mean Expected Number 0.000 -strand +14 : -3 GAGAGAGAGAGAGAGAg AC RSP01599 Mean Expected Number 0.004 +strand -182 : -175 TTTCAAAT AC RSP01601 Mean Expected Number 0.001 -strand -144 : -151 TTTCACTT AC RSP01711 Mean Expected Number 0.004 -strand -27 : -36 CTAGATAAAG Totally 13 motifs of 9 different REs have been found Description of REs found 156. Group TF: Dof1 /AC: RSP00161//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof1 BSopt /TF: Dof1 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 809. Group TF: Dof2 /AC: RSP00873//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof2 BSopt /TF: Dof2 921. Group TF: CBF /AC: RSP01000//OS: Agrobacterium tumefaciens /GENE: T-cyt/RE: 3'-III element /TF: CBF 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown 1519. Group TF: RIN /AC: RSP01711//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Others /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.5-1|complement(1168704..1176174) |SUPPORT|14 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +397 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.22 T - 0.15 C - 0.39 1 acttgtcgaa ctgggccaag cttgtcctcg tgtgcaggcg aaaaaaataa 51 ggaaacccga aggactcctc ccacgagatc ggacggccag aagaggccca 101 accccacaaa ccgacggcta gagatcactc cacgtcgtca ggaataaccc 151 ccggaagcgg gccgcgtcgt atttcacttg gaccctcgca accctaataa 201 ACCCCTCACC CCCGCGCCGC CGCCGCCTCC ACTCTCCTAC GCTTCCACCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00755 Mean Expected Number 0.006 +strand -61 : -55 AGGAATA AC RSP00986 Mean Expected Number 0.010 +strand -71 : -64 CCACGTCG AC RSP00297 Mean Expected Number 0.001 +strand -106 : -4 GGCCCA-- ** bp --ACCCTAA AC RSP01192 Mean Expected Number 0.005 -strand -13 : -22 CGAGGGTCCA AC RSP01275 Mean Expected Number 0.005 +strand -72 : -63 TCCACGTCgT AC RSP01505 Mean Expected Number 0.001 +strand -124 : -116 GATCGGACG AC RSP01601 Mean Expected Number 0.001 +strand -29 : -22 TTTCACTT Totally 7 motifs of 7 different REs have been found Description of REs found 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 925. Group TF: At-TCP20 /AC: RSP00297//OS: Arabidopsis thaliana /GENE: PCNA/RE: Box II/telo-box (motifs 2 & 3) /TF: At-TCP20 1103. Group RE: D-box /Group TF: D factor /AC: RSP01192//OS: Nicotiana tabacum /GENE: Adh2/RE: D-box /TF: D factor 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.5-2|complement(1174882..1176150) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +373 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.14 C - 0.42 1 tcctcgtgtg caggcgaaaa aaataaggaa acccgaagga ctcctcccac 51 gagatcggac ggccagaaga ggcccaaccc cacaaaccga cggctagaga 101 tcactccacg tcgtcaggaa taacccccgg aagcgggccg cgtcgtattt 151 cacttggacc ctcgcaaccc taataaaccc ctcacccccg cgccgccgcc 201 GCCTCCACTC TCCTACGCTT CCACCCCCCA TTCCCATCCC CTCCACCCAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00755 Mean Expected Number 0.005 +strand -85 : -79 AGGAATA AC RSP00986 Mean Expected Number 0.010 +strand -95 : -88 CCACGTCG AC RSP00297 Mean Expected Number 0.001 +strand -130 : -28 GGCCCA-- ** bp --ACCCTAA AC RSP01192 Mean Expected Number 0.004 -strand -37 : -46 CgAGGGTCCA AC RSP01275 Mean Expected Number 0.005 +strand -96 : -87 TCCACGTCGT AC RSP01505 Mean Expected Number 0.001 +strand -148 : -140 GATCGGACG AC RSP01601 Mean Expected Number 0.001 +strand -53 : -46 TTTCACTT Totally 7 motifs of 7 different REs have been found Description of REs found 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 925. Group TF: At-TCP20 /AC: RSP00297//OS: Arabidopsis thaliana /GENE: PCNA/RE: Box II/telo-box (motifs 2 & 3) /TF: At-TCP20 1103. Group RE: D-box /Group TF: D factor /AC: RSP01192//OS: Nicotiana tabacum /GENE: Adh2/RE: D-box /TF: D factor 1174. Group RE: ACE 2 /AC: RSP01275//OS: Petroselinum crispum /GENE: PcACO-IV/RE: ACE 2 /TF: unknown 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.6|1178118..1178949 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +38 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.14 T - 0.33 C - 0.29 1 ggtcatatgg ccatttttga tcggttgatc ctagctaagt cgtagataat 51 taaatcggat tagcattaga taatcaagca agctgctcct aaccccttac 101 acagcacact aatcatttgc ttgtcttctt ccctgcacta ccaaCCAATa 151 tgcaacttgt gcctcctgca tatagaccat ctcctccatt gcttcttcat 201 CACCATCTCA TTCTCATTCT CTTCTCTCTC TAGTTCTCAT GGGGATCACG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.007 -strand +31 : +23 AGAGAGAGA AC RSP01176 Mean Expected Number 0.002 +strand -120 : -110 AGCTGCTCCTA Totally 2 motifs of 2 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1087. Group TF: Zmhox1a /AC: RSP01176//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 3 /TF: Zmhox1a ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.7-2|1180267..1183451 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +39 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.17 G - 0.27 T - 0.18 C - 0.37 1 ccacccgacg cttctcctcg gtccccgctg caaatcccaa tcggctctca 51 caccgacacg tgggccaatc gagccagggc cccacctgtc attgaccctt 101 cttccaagcc cccacccctc gcatcattca ttcactcgtc gacttttcgt 151 cgtcctccgc gacgacgcga acaaattgcg acgcgacgca gcggccgggc 201 TAGGGCTAGG GCTAGGGTTT GAGGTCGGGC GCGCGCGGCA TGGCGGGGAT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00204 Mean Expected Number 0.006 +strand -146 : -137 GACACGTGGg AC RSP00304 Mean Expected Number 0.006 -strand -110 : -117 TGACAGGT AC RSP00340 Mean Expected Number 0.006 -strand -137 : -146 cCCACGTGTC AC RSP00426 Mean Expected Number 0.002 +strand -149 : -139 ACCGAcACGTG AC RSP00778 Mean Expected Number 0.000 -strand -67 : -76 TGAATGAATG AC RSP01255 Mean Expected Number 0.004 +strand -145 : -138 ACACGTGG AC RSP01460 Mean Expected Number 0.000 -strand -132 : -142 ATTGGCCCACG Totally 7 motifs of 7 different REs have been found Description of REs found 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 407. Group RE: DRE1/ABRE1 /AC: RSP00426//OS: Zea mays /GENE: rab17/RE: DRE1/ABRE1 /TF: unknown 733. Group RE: Box III /AC: RSP00778//OS: Arabidopsis thaliana /GENE: AtS1/RE: Box III /TF: unknown 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1330. Group RE: ERSE-II /AC: RSP01460//OS: Glycine max /GENE: BiP9/RE: ERSE-II /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.8|complement(1183469..1187815) |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1825 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.21 T - 0.27 C - 0.23 1 ttgcttagta caacatccag tatctttttt ttaaaaaaat aagaaaataa 51 taagtgcaag agagaatttc gcgcctactt cttcctagtc ctaaggaaga 101 ggagctaata tacagcacag tggccatcag aggggtagcc acgtaatttt 151 gacaggctgc tcttgcagtt agtggtgggc cacccacctc acaaggaatc 201 CGTATTCCTC TCGAGCTTTG CGTTCTTGCA AGCAGGTACT CCGTATACAC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00043 Mean Expected Number 0.003 -strand -56 : -63 TACGTGGC AC RSP00064 Mean Expected Number 0.006 -strand -54 : -63 AtTACGTGGC AC RSP00247 Mean Expected Number 0.006 +strand -63 : -54 GCCACGTAAt AC RSP00445 Mean Expected Number 0.006 -strand -171 : -180 AAAAAAGAtA AC RSP00654 Mean Expected Number 0.007 +strand -20 : -11 CACCCACcTC AC RSP01297 Mean Expected Number 0.001 +strand -79 : -71 GGCCATCAG Totally 6 motifs of 6 different REs have been found Description of REs found 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 240. Group TF: REB /AC: RSP00247//OS: Oryza sativa /GENE: alpha-globulin/RE: REB1 /TF: REB ||Identical REs AC: RSP00738 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown 1193. Group RE: Inr element /AC: RSP01297//OS: Avena fatua /GENE: Amy2/D/RE: Inr element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0684C01.11|complement(1195489..1200310) |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +134 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.30 T - 0.14 C - 0.36 1 cgtgtccttt ttcacgacgc gcaccgaaac gacactcact ggagggtggg 51 gaccgccacc accacgtgtc gccgaccgcc tgccacgtgg gcagggcgtc 101 tcccccgcta cgcgcaccca ggcgaaacgc acacgccgtt tcgcccgcca 151 caccgtcgcg tcggggtcgg taataactaa cccgagacag ggagagagac 201 GAGACCGACC GACGCCGCGG GCTTAGTCCA GTGGAAGGTG TTCGTCCACT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00175 Mean Expected Number 0.009 -strand -112 : -119 CACGTGGC AC RSP00204 Mean Expected Number 0.008 -strand -131 : -140 GACACGTGGt AC RSP00340 Mean Expected Number 0.007 +strand -140 : -131 aCCACGTGTC AC RSP00682 Mean Expected Number 0.008 +strand -119 : -110 GCCACGTGGg AC RSP00718 Mean Expected Number 0.009 +strand -118 : -111 CCACGTGG AC RSP00718 Mean Expected Number 0.009 -strand -111 : -118 CCACGTGG AC RSP00808 Mean Expected Number 0.007 -strand -20 : -26 GTTAGTT AC RSP00865 Mean Expected Number 0.001 +strand -10 : -2 GGAGAGAGA AC RSP01255 Mean Expected Number 0.004 -strand -132 : -139 ACACGTGG AC RSP01726 Mean Expected Number 0.000 +strand -120 : -109 TGCCACGTGGGc Totally 10 motifs of 9 different REs have been found Description of REs found 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 683. Group TF: GBF /AC: RSP00718//OS: Arabidopsis thaliana /GENE: Adh/RE: G-box-1 /TF: GBF ||Identical REs AC: RSP01254 761. Group TF: Pti4 /AC: RSP00808//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: Myb1 /TF: Pti4 ||Identical REs AC: RSP00810 RSP00812 RSP00813 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 1534. Group TF: STF1/HY5 /AC: RSP01726//OS: Arabidopsis thaliana /GENE: SAUR-AC1-like (At3g60690)/RE: G-box (1) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.4|complement(<1221648..1227309) |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +125 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.22 T - 0.16 C - 0.36 1 tgcggagtaa ggtacgtaaa aggtgtagcc atgggcctgt aggctatagc 51 ccactgcaac agaaggccca gcacaattgg gtgttactta caggtgggcc 101 catcagccta ctacgcaaaa ggcccatgac gaagaaggcc caaggcccat 151 tcgcatcggt cgcgcaacaa acaaagcaac caccaccaca cgaactccac 201 GCTAAACCCC CCCCCCCCCC TCGTCTTCCT CCTCTTCACT CCTCGTCGCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00303 Mean Expected Number 0.000 +strand -109 : -98 AGGTGGGCCCaT AC RSP00447 Mean Expected Number 0.008 +strand -31 : -22 AaCAAAGCAA Totally 2 motifs of 2 different REs have been found Description of REs found 290. Group TF: PCF1; PCF2 /AC: RSP00303//OS: Oryza sativa /GENE: PCNA/RE: IIa /TF: PCF1; PCF2 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.5|1229295..1233550 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +179 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.30 T - 0.19 C - 0.31 1 taccccgtac acccagccag aaagagccca ctgaccggtg ggccaggagg 51 agagtgtgcc ccacatgtca gtgatggtag aacagaaggg tctaggcggg 101 cgcggggtac gacgtgttcc gggtgtagaa agcgacagcg cccctcacaa 151 cgctcgcctc cctcctcctc cgtctcctcc tttcatctct tcttctgtgt 201 GTGCGTGTCT GCGAAGCGTG AGAGAGAAAC GTACGCGACG CGACGAGCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00660 Mean Expected Number 0.006 +strand -77 : -71 TGTAGAA Totally 1 motifs of 1 different REs have been found Description of REs found 632. Group RE: -300 box /AC: RSP00660//OS: Oryza sativa /GENE: Gt3/RE: -300 box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.8|1246683..1248223 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +200 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.34 G - 0.18 T - 0.29 C - 0.19 1 gtagaaaaat tttgatgtga tgaaaaaatt gaaagtttga agaaaaaaaa 51 tttgtaacta aacactacct tactgaacta gtccgtagta actcaacagt 101 aatgcgtgat gaatcaactt gtgtcaTCAA Tcaagtaaaa acaacaaatc 151 ttgggtccag aggctagtta atccccatat ccgtttctgg gaaccgactg 201 ATCCTGTGAT GTTGCACACT GTCTCACTTC ATTTGGCTCA TGAGCTCATG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01014 Mean Expected Number 0.006 -strand +35 : +26 CAAATGAAGt AC RSP01192 Mean Expected Number 0.002 +strand -51 : -42 CTTGGGTCCA Totally 2 motifs of 2 different REs have been found Description of REs found 939. Group TF: GAPF /AC: RSP01014//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 2 /TF: GAPF 1103. Group RE: D-box /Group TF: D factor /AC: RSP01192//OS: Nicotiana tabacum /GENE: Adh2/RE: D-box /TF: D factor ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.10|1250830..1252437 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +228 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.41 G - 0.09 T - 0.32 C - 0.18 1 taatcgtccg tcttatttaa aaaaattaaa aatataaatc acgagtaaaa 51 tattatttat attttatcat ctcataacaa taaaaatact aattttaaaa 101 ttttttaaat aagatggacg attaaaatta aacgtaaaaa ctcatggtta 151 cattaaaata ggatggacaa atacagtttt actacctcac ctcccactct 201 ACTGCTACTC AACAATGCAC CAGCAACAAA GTTCATGCCT TTTCAAAGTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00122 Mean Expected Number 0.005 +strand -10 : -4 CTCCCAC AC RSP00331 Mean Expected Number 0.003 -strand -50 : -58 GTAACCATG AC RSP00933 Mean Expected Number 0.005 +strand -107 : -95 TTTAaAATTTTTT AC RSP01086 Mean Expected Number 0.010 -strand -63 : -72 TTTACGTTTa AC RSP01600 Mean Expected Number 0.009 +strand +41 : +48 TTTCAAAG Totally 5 motifs of 5 different REs have been found Description of REs found 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 1004. Group TF: bZIP TF /AC: RSP01086//OS: Helianthus annuus /GENE: sHSP/RE: bZIP BS /TF: bZIP TF 1421. Group RE: Inr /AC: RSP01600//OS: Spinacia oleracea /GENE: RPS22/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.14|complement(1257656..1260677) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1792 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.29 T - 0.18 C - 0.29 1 tctagaattg agttttcttt ttggacggag ggagtatgaa aaaaaaagaa 51 agaactgtta gatggatctc cctccccttg agcccaacgg ctcaaggggg 101 ccttgacccg cgccctgatc gggggcgccc agcCCAATgg ctggtgggcc 151 cccgtcacac tgtgccatat aaagaggggt ggaagacggg acggcataac 201 GACACAAGGA ACGAGGTTCG TCGCCGCCGC CGCCACTCCA CCCCATAAAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00042 Mean Expected Number 0.006 -strand -192 : -198 AATTCTA AC RSP00397 Mean Expected Number 0.006 -strand +37 : +30 AGTGGCGG AC RSP00445 Mean Expected Number 0.006 +strand -159 : -150 AAAAAAGAaA AC RSP01250 Mean Expected Number 0.001 -strand -185 : -194 AAAAcTCAAT AC RSP01710 Mean Expected Number 0.009 +strand -36 : -27 CCATATAAAG Totally 5 motifs of 5 different REs have been found Description of REs found 41. Group RE: Motif h /AC: RSP00042//OS: Pisum sativum /GENE: PSPAL2/RE: Motif h /TF: unknown 379. Group RE: CDE /AC: RSP00397//OS: Nicotiana tabacum /GENE: RNP2/RE: CDE /TF: unknown 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C 1518. Group TF: RIN /AC: RSP01710//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Intermediate /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.37|complement(1335041..1335901) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +24 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.23 T - 0.24 C - 0.21 1 tcacaaaaaa aattgaataa gacgaacggt taaacatgtg ctaaaatgtc 51 aacggtgtca aacattttga aattgagggg tacgatatat gcgtgtgtgt 101 ggcaacggaa ggcggtcatg tgttcttatc tatccacggt tcagctctgc 151 tattggtctc agtgtcccga taaataacac accacagctg caacacagtt 201 CATCTCAAAG CAAGCAAGAC GTCCATGAAG ATGAAGCGCA CCATGGCTGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00385 Mean Expected Number 0.006 -strand -128 : -135 ATTTCAAA AC RSP01190 Mean Expected Number 0.003 +strand -67 : -58 CCACGGTTCA Totally 2 motifs of 2 different REs have been found Description of REs found 370. Group RE: ERE-core /AC: RSP00385//OS: Dianthus caryophillus /GENE: GST1/RE: ERE-core /TF: unknown ||Identical REs AC: RSP00893 1101. Group RE: C-box /Group TF: C factor /AC: RSP01190//OS: Nicotiana tabacum /GENE: Adhl/RE: C-box /TF: C factor ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.38|complement(1338170..1339080) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +97 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.21 T - 0.29 C - 0.19 1 gcagcgggct acagatttgt agccagctat agtacggact ccaagacgcg 51 gtgtatatat gacaggtggg actagttatt gatagtgtag tatgtaacta 101 ttgtataaat gagctatcag attggctata gataaATTGG agctaatagt 151 tgactatact attaaacttg ctcttatagc tagctctcag tttagttgct 201 CGATAAATAA CACCCCATGC ATGCATTTCA CCATGACCAA ACCACGCCTA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand +16 : +23 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand +23 : +16 CATGCATG AC RSP00304 Mean Expected Number 0.007 +strand -141 : -134 TGACAGGT AC RSP00949 Mean Expected Number 0.005 -strand -45 : -52 TAGTCAAC AC RSP01074 Mean Expected Number 0.001 +strand +15 : +24 cCATGCATGC AC RSP01074 Mean Expected Number 0.001 -strand +24 : +15 GCATGCATGg Totally 6 motifs of 4 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 878. Group RE: TAGTCAAC motif /AC: RSP00949//OS: Petroselinum crispum /GENE: 4CL-1/RE: TAGTCAAC motif /TF: unknown 992. Group TF: PvAlf /AC: RSP01074//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Sph /TF: PvAlf ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0445D12.39|complement(1341920..1342849) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +36 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.11 T - 0.35 C - 0.18 1 ttttttaaca tataaaaatt agatttggtt ttgtatattt gtgaagtgat 51 atatcacata ttaatttatc ttgttaattt ttttaaaaaa aaattatgat 101 cacctaagtt acatacaaac aactggacat cgctatggag tttagaatat 151 ttttccttgg tctatctatc tataataact aaactactcg actcatcact 201 AGCACAACAC CACAAACCAA GATGAGTAAC AACAGCATGG CTACTTCCAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00716 Mean Expected Number 0.001 -strand -168 : -176 CAAAACCAA AC RSP00943 Mean Expected Number 0.003 -strand -152 : -162 TCAcTTCACAA AC RSP01596 Mean Expected Number 0.003 +strand -162 : -152 TTGTGAAgTGA Totally 3 motifs of 3 different REs have been found Description of REs found 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 872. Group TF: GBF /AC: RSP00943//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box III /TF: GBF 1417. Group RE: Box III /AC: RSP01596//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0037C04.32|1401616..1403691 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +147 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.37 G - 0.27 T - 0.18 C - 0.18 1 aaaaaaaaaa ttactacacc gatggaggtg gtggggtcag gaagagaaga 51 ccctcaccca tgtgggaggg tcagtgagat tatagaagag aggaggtaga 101 ATTGTagtag tagaaaagag gaggagctag tagtagtaga agaagaagag 151 agcagataga aagaaccctt tcttaaatgc agggaagtag tggcttcact 201 TGCAACGGTA CAAGAACCAC CATCACTTCC CTACCACTCC ACTACTAGCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00642 Mean Expected Number 0.007 +strand -27 : -20 TAAATGCA AC RSP01039 Mean Expected Number 0.008 -strand -29 : -34 GAAAGG Totally 2 motifs of 2 different REs have been found Description of REs found 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 963. Group RE: Dof BS1 /Group TF: Dof family /AC: RSP01039//OS: Petroselinum crispum /GENE: Icy/RE: Dof BS1 /TF: Dof family ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0037C04.34|complement(1407789..1409896) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +161 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.22 T - 0.26 C - 0.31 1 aggccttggt tggaagccca ttataaagcc caaaaccagt gtaaaaatac 51 tgggccatat tttcctgagt tataataacc ttgtaggctc taaaatttct 101 cttggatggg ccggctttcg gATTGAgccc attccactgg gaggaaaaat 151 atagtgtact actagtactc ttttctccgt cgtcacccct cccctccgca 201 CTCCGCCGCG GGCCGGCGCC GTCGACCGCG TCCTCCGCTC CGCTCCGCCG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00565 Mean Expected Number 0.008 -strand -151 : -157 GTATTTT AC RSP00963 Mean Expected Number 0.009 +strand -135 : -129 TGAGTTA Totally 2 motifs of 2 different REs have been found Description of REs found 541. Group RE: AT-rich G /AC: RSP00565//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich G /TF: unknown 888. Group RE: GLM2 /AC: RSP00963//OS: Hordeum vulgare /GENE: ITR1/RE: GLM2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0037C04.35|1410639..1415784 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +81 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.15 T - 0.20 C - 0.37 1 aaataaaact gccaacattc tccatctagc ttttgcaaaa ggtgtgacac 51 cacccacggt acagctgtca ttttaaacac ggccctgttt cctcggaggc 101 atcagactga cattaggccc cacatctcct ccggccccac acgtcagacg 151 cacccaccat ctgtacgcag aaaacactac cgtgccgtaa ccgtattaac 201 CAGTTATTAA CCACCACCTC CTCCACCACT CGCGACCCCA CCCCAGATCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.008 -strand -131 : -138 TGACAGCT AC RSP00471 Mean Expected Number 0.005 -strand -59 : -69 GTGTGGGGCCg AC RSP00961 Mean Expected Number 0.002 +strand -167 : -160 TGCAAAAG AC RSP00961 Mean Expected Number 0.002 -strand -164 : -171 TGCAAAAG AC RSP01136 Mean Expected Number 0.006 -strand -152 : -158 TGTCACA AC RSP01190 Mean Expected Number 0.009 +strand -147 : -138 CCACGGTaCA AC RSP01258 Mean Expected Number 0.008 -strand -55 : -62 TGACGTGT AC RSP01598 Mean Expected Number 0.001 +strand -135 : -128 TGTCATTT Totally 8 motifs of 7 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 886. Group TF: BPBF /AC: RSP00961//OS: Hordeum vulgare /GENE: ITR1/RE: PB1 /TF: BPBF 1054. Group RE: TGTCACA motif /AC: RSP01136//OS: Cucumis melo /GENE: Cucumisin/RE: TGTCACA motif /TF: unknown 1101. Group RE: C-box /Group TF: C factor /AC: RSP01190//OS: Nicotiana tabacum /GENE: Adhl/RE: C-box /TF: C factor 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 1419. Group RE: Inr /AC: RSP01598//OS: Spinacia oleracea /GENE: RPL21/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0037C04.36|1418494..1424452 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1652 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.18 T - 0.31 C - 0.31 1 aactcgacgt taaagttgag atagcttaag tgaacttgtt ccatataata 51 agatgacgaa tcagtttcgg aaggttgaaa agcccatgta gctccgaccg 101 accgagccca aattctaccg gaatccggcc tgccaccgtt tcgtgtactg 151 cgtaaccgtg ccttcttttg ctttctctct ctctctagtc cctcctcttt 201 TGGTGGTCTC TCTCTCTCTC TCTTCTCTCG CCTCACTTCG CATCGCCTCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.007 -strand +23 : +15 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand +21 : +13 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand +19 : +11 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand +17 : +9 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand +15 : +7 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand -15 : -23 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand -17 : -25 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand -19 : -27 AGAGAGAGA AC RSP00875 Mean Expected Number 0.005 +strand -192 : -183 GTTAAAGTTG AC RSP01283 Mean Expected Number 0.000 -strand +22 : +6 GAGAGAGAGAGAGAGAc Totally 10 motifs of 3 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 811. Group TF: PBF /AC: RSP00875//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: PBF BSopt /TF: PBF 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.2|1433964..1442401 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +184 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.35 G - 0.14 T - 0.26 C - 0.24 1 gaatgatggc cacagaaaaa aaagaggaat ccaatagaca caaaagaatc 51 caagcggcat aaatccaaac tagcatttcc atgcttcgga ataaccagac 101 aattaagagg atatcaacag gccacatctt tctcccagca aagttaaatt 151 cgatgcccac tatgccacta tatatgaaca aattcctggc catctctttc 201 CATTCTCTCC TCACATCATC TTGATAGATT TTTTTTTTCA CTCAATGGAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00442 Mean Expected Number 0.007 -strand -55 : -64 TAACTTTGCt AC RSP00629 Mean Expected Number 0.005 -strand +33 : +26 AAAAATCT AC RSP00888 Mean Expected Number 0.001 -strand +33 : +25 AAAAATCTA AC RSP00915 Mean Expected Number 0.008 -strand +20 : +11 GATGATGTGa AC RSP00916 Mean Expected Number 0.005 -strand +20 : +11 GATGAtGTGA AC RSP01237 Mean Expected Number 0.007 +strand -35 : -26 CaCTATATAT Totally 6 motifs of 6 different REs have been found Description of REs found 422. Group TF: Dof1 /AC: RSP00442//OS: Zea mays /GENE: cyPPDK1/RE: box b /TF: Dof1 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 820. Group TF: CCA1 /AC: RSP00888//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: CCA1 motif (2) /TF: CCA1 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 847. Group TF: Opaque-2 /AC: RSP00916//OS: Zea mays /GENE: b-32/RE: B4 /TF: Opaque-2 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.5|1444491..1447275 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +174 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.35 T - 0.20 C - 0.22 1 atcacagggg tcacacgggg aacgccattg tggagttcgc caaagactgg 51 accggtttcg agaacgcgct cgcgttcgag gtccacttcg agcaacaagg 101 gtatggcagg agggcatgga tggggaacaa gtacaggggg tcacagatgt 151 ttgggtgggt cgccagggcc gatgatcaca actctccggg gccgattggg 201 GTTTATCTGC GCAAGAACGG TGATCTCAAG ACTGTTGCTG ATCTTGAGAA 251 T Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.15|complement(1487296..1489136) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +240 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.16 G - 0.27 T - 0.13 C - 0.44 1 aattccaccg cgacatgccg ccgacgccgg tgttcgtgta cgggcagtcg 51 ctgcagacgg cgacgttccc ggggcccacc atcgtggcgc gctacaacgt 101 gccgctctac gtgacgtggg agaaccacct ccccgacgcc cacatcctcc 151 cgtgggaccc caccgtcccc accgccattc ccaagaacgg cggcgtcccc 201 ACCGTCGTCC ACCTCCACGG CGCCGCCCAG GCCCCCGATT CCGACGGCCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00066 Mean Expected Number 0.004 +strand -104 : -96 ACGTGCCGC AC RSP00068 Mean Expected Number 0.003 -strand -86 : -95 GtCACGTAGA AC RSP00122 Mean Expected Number 0.007 -strand -79 : -85 CTCCCAC AC RSP00202 Mean Expected Number 0.006 +strand -187 : -179 CATGCCGCC AC RSP00214 Mean Expected Number 0.002 +strand -89 : -82 TGACGTGG AC RSP00215 Mean Expected Number 0.002 -strand -82 : -89 CCACGTCA AC RSP00233 Mean Expected Number 0.006 +strand -95 : -86 TCTACGTgAC AC RSP00866 Mean Expected Number 0.005 -strand -99 : -106 GCACGTTG Totally 8 motifs of 8 different REs have been found Description of REs found 65. Group TF: EmBP-1 /AC: RSP00066//OS: Triticum aestivum /GENE: Em/RE: Em1b /TF: EmBP-1 67. Group RE: UV LRE /AC: RSP00068//OS: Arabidopsis thaliana /GENE: CHS/RE: UV LRE /TF: unknown 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 195. Group TF: ABF /AC: RSP00202//OS: Zea mays /GENE: rab28/RE: ABRE GRA /TF: ABF 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 226. Group RE: LS5 /Group TF: TGA2 & NPR1/NIM1 /AC: RSP00233//OS: Arabidopsis thaliana /GENE: PR-1/RE: LS5 /TF: TGA2 & NPR1/NIM1 802. Group RE: G-box /AC: RSP00866//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: G-box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.19|complement(1500839..1504860) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +30 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.31 T - 0.16 C - 0.33 1 aggaagggac gggtgaggtg gagcgccatt gccgcggcga agcgagggcg 51 gggacgcgaa cggataaggc tgtgactcac tgggccgcca aattgggccc 101 accactcggc CCAATtatgc actgaatcaa gggggcccac ctgtcattct 151 cacgtagaaa ccaccaaacc cttcttcttc ccccatctct ccgcagccac 201 CGGTGGAGAA GATTCGCGCG GCCGCTCGCC ATGTCGTCGC CGTCGCCGGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00190 Mean Expected Number 0.008 -strand -122 : -128 TGAGTCA AC RSP00304 Mean Expected Number 0.005 -strand -55 : -62 TGACAGGT AC RSP00379 Mean Expected Number 0.007 +strand -140 : -131 CGGATAaGGC AC RSP00847 Mean Expected Number 0.007 -strand -180 : -189 CCACCTCAcC AC RSP01061 Mean Expected Number 0.001 -strand -121 : -129 GTGAGTCAC AC RSP01174 Mean Expected Number 0.005 -strand -183 : -193 CCTCaCCCGTC Totally 6 motifs of 6 different REs have been found Description of REs found 184. Group RE: GCN4 box /AC: RSP00190//OS: Oryza sativa /GENE: GluB-1/RE: GCN4 box /TF: unknown ||Identical REs AC: RSP00666 RSP00959 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 364. Group RE: LS7 /AC: RSP00379//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS7 /TF: unknown 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown 981. Group TF: Hahb-4 /AC: RSP01061//OS: Oryza sativa /GENE: GluA-3/RE: GCN4 motif /TF: Hahb-4 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.20|1509940..1511234 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +43 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.18 T - 0.25 C - 0.21 1 ttcaagctca tcatgcacac taaccttctc tagaaaagag taatactata 51 cctcgatctt cccatgacca acctaattca aaccggccaa cggagtttct 101 ttcttctaaa atgataatca aaggaagaaa taattaacat ttcgATTGCt 151 gagctcccca agttcagaat aaattaacgt catttcgaca taaagagatc 201 GCTCTCGGTA GTAAGCTAGA GATAGAGAGA GAGAGAGAGA GAGATGCCGG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00421 Mean Expected Number 0.006 -strand +9 : +3 ACCGAGA AC RSP00709 Mean Expected Number 0.008 -strand -65 : -73 TAATTATTT AC RSP00710 Mean Expected Number 0.001 -strand -65 : -77 TAATTATTTCTTc AC RSP00860 Mean Expected Number 0.001 -strand -97 : -105 AGAAAGAAA AC RSP00864 Mean Expected Number 0.002 +strand +24 : +32 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +26 : +34 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +28 : +36 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +30 : +38 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +32 : +40 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +34 : +42 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +36 : +44 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 +strand +25 : +41 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +27 : +43 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +29 : +45 GAGAGAGAGAGAGAGAt AC RSP01654 Mean Expected Number 0.008 -strand -17 : -26 AATGACGTTA Totally 15 motifs of 7 different REs have been found Description of REs found 402. Group RE: DRE1 /AC: RSP00421//OS: Zea mays /GENE: rab17/RE: DRE1 /TF: unknown 675. Group RE: I-box /AC: RSP00709//OS: Pisum sativum /GENE: TOP2/RE: I-box /TF: unknown 676. Group RE: AT1-box /AC: RSP00710//OS: Pisum sativum /GENE: TOP2/RE: AT1-box /TF: unknown 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.25|1530936..1536403 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +85 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.19 G - 0.13 T - 0.22 C - 0.46 1 caccaagcta gcgtggccat caaccaaccc cttttccatt ccgatccgac 51 ccgacgcggt caattccttc ccacgccgcg catcgcattc gcaaactccg 101 accgagccga gcgagtcgtc ttcttcttct tctccatcgc gtcgtctccc 151 tccctccttc cccctcccct ttaaaaatcc aaacccctct cctccacctc 201 CATCTCCATT CCCAACCCAA ACCCCCGCAA CCGCAAATCC CGCGCTGCTA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00467 Mean Expected Number 0.001 +strand -144 : -135 cGGTCAATTC AC RSP00874 Mean Expected Number 0.002 -strand -25 : -35 TTTTAAAGGGG AC RSP00958 Mean Expected Number 0.008 -strand -26 : -32 TTTAAAG Totally 3 motifs of 3 different REs have been found Description of REs found 445. Group RE: ERE1 /AC: RSP00467//OS: Dianthus caryophyylus /GENE: hcbt2/RE: ERE1 /TF: unknown 810. Group TF: Dof3 /AC: RSP00874//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof3 BSopt /TF: Dof3 884. Group TF: BPBF /AC: RSP00958//OS: Hordeum vulgare /GENE: Hor2/RE: PB2 /TF: BPBF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.27|complement(1546043..1547813) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +154 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.20 T - 0.31 C - 0.25 1 ctctgcagct aggccatatg catctctcct ccctcttctc ttgtacttac 51 ttgtgcttgc tctcttccat tcttttcttc cctaattgat ctcctagaga 101 gttgagagtt gagagagtag ttaaggggca agctaattaa gctagtgaga 151 gctagtggag gtacatggct atatatatgg ttgtatgagt tgcaccctcc 201 AAGGGGATCA TACATCGACC TCATCATCCA ATCCACCAAC TGACCAACAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00595 Mean Expected Number 0.001 -strand -59 : -67 GCTTAATTA AC RSP00847 Mean Expected Number 0.010 +strand +16 : +25 CgACCTCATC AC RSP00915 Mean Expected Number 0.005 -strand +28 : +19 GATGATGAGG AC RSP01237 Mean Expected Number 0.005 +strand -32 : -23 CTaTATATAT Totally 4 motifs of 4 different REs have been found Description of REs found 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0409B08.31|1562949..1566269 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +19 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.20 T - 0.20 C - 0.37 1 acgccagaga ctgttgtcgg catgataaaa atctgtataa aatttatggg 51 ccgaaattgc cctcagcatc acaagcatcc ggcccatccg gataatcttg 101 gcccactagc ccagcccatg ccaccgctac gttaccttct cctctcgtgc 151 tctttctccg cccaataaat agcccacgac ccaaccactc cggcgaggct 201 GAGCTGACCA CCACCGGAGA TGGCACTCGC AGCGCCTCTG CTCCGCCTCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00354 Mean Expected Number 0.003 -strand -67 : -74 TAACGTAG AC RSP00629 Mean Expected Number 0.002 +strand -174 : -167 AAAAATCT Totally 2 motifs of 2 different REs have been found Description of REs found 339. Group RE: GARE1 /AC: RSP00354//OS: Oryza sativa /GENE: Rep-1/RE: GARE1 /TF: unknown 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0408F06.4|complement(1568326..1573399) |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +65 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.24 T - 0.15 C - 0.30 1 cggggaagaa gattacatta catcggaaaa ggagaaaaaa aagagagaga 51 gaagagcccg aaacaaacgt gacaccaaag tgggtagtag acacagaggt 101 ggcgcaggca gcacacagaa aaccagcgag attttacaca cgcctcgccc 151 tcgcgttcgc gtcgacggga ataaaatccc ccgcgtctcc tcttctcctc 201 GCGCAACTCG CTCATCTCAT CGCTCTCGCC TCGACTCGCC TCCACGAAGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00132 Mean Expected Number 0.003 -strand -98 : -105 GCCACCTC AC RSP00445 Mean Expected Number 0.001 +strand -164 : -155 AAAAAAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -159 : -151 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand -157 : -149 AGAGAGAGA Totally 4 motifs of 3 different REs have been found Description of REs found 130. Group TF: ROM1; ROM2 /AC: RSP00132//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: vicilin box /TF: ROM1; ROM2 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0408F06.22|complement(1638036..1640954) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.29 C - 0.24 1 catctgacca tctttatatc acgttgggcc ccatgcttct ctaatcactc 51 gatctctccc agatgcttta tgcaaagcct atataaactt tgtgttgtcc 101 caaaccattc gcccgatttg atccacatca ccactttggt tcctcccatt 151 tttcatttca aagtgatact aataagcaag tgcaaggata gctagcttga 201 CAGTGTGGAA GTAGTAGTAG GAGCAAGAGG CAAATTAAGG GGAAGCTGCA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00385 Mean Expected Number 0.008 +strand -46 : -39 ATTTCAAA AC RSP00646 Mean Expected Number 0.000 -strand -42 : -55 GAAATgAAAAATGG AC RSP00915 Mean Expected Number 0.005 -strand -69 : -78 GGTGATGTGG AC RSP01600 Mean Expected Number 0.006 +strand -45 : -38 TTTCAAAG Totally 4 motifs of 4 different REs have been found Description of REs found 370. Group RE: ERE-core /AC: RSP00385//OS: Dianthus caryophillus /GENE: GST1/RE: ERE-core /TF: unknown ||Identical REs AC: RSP00893 620. Group RE: C1-box /AC: RSP00646//OS: Daucus carota /GENE: DC 59/RE: C1-box /TF: unknown 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 1421. Group RE: Inr /AC: RSP01600//OS: Spinacia oleracea /GENE: RPS22/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0408F06.27|complement(1667277..1667799) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +73 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.15 T - 0.30 C - 0.24 1 taactaatgt aatttaccta ggattttcag gtggtcaacc aagtaaattg 51 ttaatgtgtt gcacctgtaa aatcttcttc ttccagtaga aaacgaagtg 101 tattatacta ctccaaactt atatacttgg ggcaactctc cttgattccc 151 gcttctcaca cgcattattt gtttcagagc ggaaacagcc aacgctaacc 201 TAACTAGTTA AACCAAAAGC CTAGCTTTCC AAGCACAAAC ACCGACCATT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00036 Mean Expected Number 0.008 +strand +36 : +43 CAAACACC AC RSP00405 Mean Expected Number 0.010 -strand -84 : -91 TTTGGAGT Totally 2 motifs of 2 different REs have been found Description of REs found 35. Group TF: ABI3 /AC: RSP00036//OS: Brassica napus /GENE: napA/RE: ABRE Bp /TF: ABI3 387. Group RE: adjb /AC: RSP00405//OS: Nicotiana tabacum /GENE: RNP2/RE: adjb /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0408F06.28|complement(1670409..1673868) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +175 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.30 T - 0.18 C - 0.32 1 taccccaagg ttccgtgacg gcacatacat gcaccggcgc gcgcacgtca 51 cgacaacgga cggcgacgtg atcgcgtgcg ggggcggagc gaaacccgtg 101 cagcctatag cctttggatt ctgctcgcgt cgcgactATT GAaaccgatc 151 aactttcggt gatcagtaga tagatgtgga gagatcgatc cttggcgatc 201 GCTACCACGC GTGCCCCCAG ACGTATCAGT CGGCCTCACG CCCGCGCGCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00103 Mean Expected Number 0.006 +strand -180 : -171 GCACATACaT AC RSP00399 Mean Expected Number 0.005 +strand -158 : -151 GCACGTCA AC RSP01524 Mean Expected Number 0.002 -strand +35 : +27 GGCCGACTG AC RSP01699 Mean Expected Number 0.009 +strand -135 : -129 ACGTGAT Totally 4 motifs of 4 different REs have been found Description of REs found 101. Group RE: Z element /AC: RSP00103//OS: Agrobacterium tumefaciens /GENE: nos/RE: Z element /TF: unknown 381. Group TF: AP1-like leucine zipper TF /AC: RSP00399//OS: Nicotiana tabacum /GENE: RNP2/RE: ATF /TF: AP1-like leucine zipper TF ||Identical REs AC: RSP00884 1372. Group TF: StEREBP1 /AC: RSP01524//OS: Solanum tuberosum /GENE: Synthetic OLIGO/RE: DRE/CRT /TF: StEREBP1 1510. Group RE: CARE B1 /AC: RSP01699//OS: Arabidopsis thaliana /GENE: At2g21640/UPOX/RE: CARE B1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.10|complement(1697325..1699314) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +647 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.25 T - 0.22 C - 0.30 1 gctgatctag aacctaaaat aatcagagag acagaatgga gaaatgcaga 51 tgaaagcata agaaagcttc gatctatgct tcgatctgca tgttccaagt 101 catggtgaag ctcttgccca gcgGCAATgc cagccctccc acctccacca 151 tcacgctctt cttgtgtccc tccacgtcgc ggtgcccgtg cagctccgcc 201 TCGGCACCTG CAAAGTACGG CCTCGACGTT GCAATGGCGG TGGCGTTCGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00189 Mean Expected Number 0.006 +strand -30 : -21 TCCACGTcGC AC RSP00426 Mean Expected Number 0.002 -strand -18 : -28 ACCGcGACGTG AC RSP00682 Mean Expected Number 0.006 -strand -21 : -30 GCgACGTGGA AC RSP00986 Mean Expected Number 0.006 +strand -29 : -22 CCACGTCG AC RSP01015 Mean Expected Number 0.003 +strand -154 : -145 CAgATGAAAG AC RSP01201 Mean Expected Number 0.003 +strand -95 : -88 TGAAGCTC Totally 6 motifs of 6 different REs have been found Description of REs found 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 407. Group RE: DRE1/ABRE1 /AC: RSP00426//OS: Zea mays /GENE: rab17/RE: DRE1/ABRE1 /TF: unknown 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 940. Group TF: GAPF /AC: RSP01015//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 3 /TF: GAPF 1112. Group TF: NIT2 /AC: RSP01201//OS: Chlorella vulgaris /GENE: NR/RE: NIT2 BS II /TF: NIT2 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.13|complement(1708939..1709750) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +97 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.27 T - 0.12 C - 0.40 1 gttgcaagtt gcctcgccgc acgggctccc gtcacgactc ggacctggcc 51 cgatacaccg cacgccagga cagaggaggc gacgcgacct ggtccgcaca 101 taccggctgc gcgcgcgcgc ggcgacggcg gcgcgccaaa ccagccgagc 151 cactcgatgc tggagtacac tacaaaagcg cgaagaggcg gccgcctcgc 201 TGCCAAAACA CTCCCACTCT CACTGACTCA CACCCCGTCA CTCCCCTCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00190 Mean Expected Number 0.007 -strand +30 : +24 TGAGTCA AC RSP00876 Mean Expected Number 0.004 +strand -69 : -61 CGCGCCAAA Totally 2 motifs of 2 different REs have been found Description of REs found 184. Group RE: GCN4 box /AC: RSP00190//OS: Oryza sativa /GENE: GluB-1/RE: GCN4 box /TF: unknown ||Identical REs AC: RSP00666 RSP00959 812. Group TF: AtE2F /AC: RSP00876//OS: Arabidopsis thaliana /GENE: MCM3/RE: Site 1 E2F (D1) /TF: AtE2F ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.20|1735668..1736622 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +99 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.18 T - 0.15 C - 0.44 1 ccctccccga ccaaaaccaa ataaagaaaa cgtctctccg ctcacgagag 51 ccagccgtgc caaccaagcc ctcaccgcac cgcgccgcgc cgctcccacg 101 cacgcacgcc acacatgttt ttgcgcaaaa acccccccgc gagtgcgcac 151 ccggcacccg cgtccaacgc tatatattac gcggccccca actcggcgtc 201 GCACCGCAAA GCAACCCCCC CTTGCTTTTT GTACTCTTCC ATCTCACAAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00339 Mean Expected Number 0.003 +strand -84 : -78 GTTTTTG AC RSP00447 Mean Expected Number 0.004 +strand +5 : +14 cGCAAAGCAA AC RSP00456 Mean Expected Number 0.003 +strand -85 : -80 TGTTTT AC RSP00716 Mean Expected Number 0.003 +strand -189 : -181 CAAAACCAA AC RSP01209 Mean Expected Number 0.006 -strand -175 : -184 CTTTATTTGG AC RSP01237 Mean Expected Number 0.000 +strand -33 : -24 CgCTATATAT AC RSP01710 Mean Expected Number 0.006 +strand -184 : -175 CCAAATAAAG Totally 7 motifs of 7 different REs have been found Description of REs found 324. Group TF: SEF4 /AC: RSP00339//OS: Glycine max /GENE: beta-conglicinin alfa'/RE: SEF4 BScons /TF: SEF4 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 434. Group RE: Motif II /AC: RSP00456//OS: Pisum sativum /GENE: PSPAL2/RE: Motif II /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1518. Group TF: RIN /AC: RSP01710//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Intermediate /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.32|complement(1757112..1757867) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +83 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.35 G - 0.20 T - 0.23 C - 0.23 1 gtgagtgtga catggaagaa tacaaaatgt gttcaacgcc tcacactcta 51 gcagccgcgt cagtcaaagg cacgcctaac atgcatcccc aaaaaatata 101 ttcgatatca agcatgaaag aatggcattt ggcaacatgc taatatgttg 151 ttcagatctg aacgcctata tatacagatg ctctcctggg ctttggccat 201 AACCACAAAC ACAAAGCGTA AAGCCATCTA CTAGTACCAA GTAGAGGAAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00131 Mean Expected Number 0.009 -strand -168 : -174 AACACAT AC RSP00248 Mean Expected Number 0.005 +strand -147 : -138 GCCgCGTCAG AC RSP00756 Mean Expected Number 0.004 +strand -161 : -154 CTCACACT AC RSP00872 Mean Expected Number 0.005 +strand -197 : -188 aGTGTGACAT AC RSP00891 Mean Expected Number 0.005 +strand -108 : -100 AAAATATAT AC RSP01237 Mean Expected Number 0.006 -strand -24 : -33 CTgTATATAT Totally 6 motifs of 6 different REs have been found Description of REs found 129. Group RE: CACA box /AC: RSP00131//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: CACA box /TF: unknown 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 718. Group RE: submotif B /AC: RSP00756//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif B /TF: unknown 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown 823. Group TF: Dof family /AC: RSP00891//OS: Solanum melongena /GENE: SmCP/RE: EE 1 /TF: Dof family 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.35|complement(1768299..1769212) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +63 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.15 T - 0.33 C - 0.30 1 tgtttatgga gtgttatatc atatactaat taatcttttt aaattttttc 51 ttaaccatct gactgacata gaggatcaaa acggtttccc gtccgcaccc 101 ACAATtccgc tgcgaaattt gcacacacac atgcatgggt cccctgccct 151 tccaggcctc cgctctattt atccatttct tctctccaaa cccgcttcgc 201 CTCGATCTCG ATCTCTCGCT CGCTTGTGGT CTCACACTAC TACTAGCTGT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00108 Mean Expected Number 0.003 +strand -71 : -64 CATGCATG AC RSP00108 Mean Expected Number 0.003 -strand -64 : -71 CATGCATG AC RSP00200 Mean Expected Number 0.009 -strand -166 : -175 gATTAATTAG AC RSP00473 Mean Expected Number 0.000 -strand -68 : -80 CATGTGTGTGTgC AC RSP00681 Mean Expected Number 0.002 +strand -174 : -166 TAATTAATC AC RSP01470 Mean Expected Number 0.004 -strand -63 : -72 cCATGCATGT Totally 6 motifs of 5 different REs have been found Description of REs found 106. Group RE: RY4 /AC: RSP00108//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: RY4 /TF: unknown ||Identical REs AC: RSP01169 RSP01452 193. Group TF: GmHdl56; GmHdl57 /AC: RSP00200//OS: Glycine max /GENE: vspB/RE: PRD motif 1 /TF: GmHdl56; GmHdl57 451. Group TF: Alfin1 /AC: RSP00473//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS3 /TF: Alfin1 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0504H10.38|complement(1772846..1774907) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +85 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.18 G - 0.17 T - 0.27 C - 0.38 1 aagattctcg aagcggtcga tcctgtggac tgggtctacg ctgaatctac 51 ggaaccaacc gactaacgag gtaaccaact gtttactggt ctccatcaag 101 tttataaccg ctcgcgtcgc gcccatctcc aCCAATccac caccgccacg 151 ccacttcacc cttgtttttt ttttcccctt ctcgcaaagt tcaaaccccc 201 TCTTCTTCCC TCCCTCCTCT CCTCTCCTCG CTTCCGGGTT CCGCCGCGGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00395 Mean Expected Number 0.004 -strand -147 : -156 TTcCGTAGAT AC RSP00935 Mean Expected Number 0.002 +strand -2 : +12 CCTCTtCTTCCCTC AC RSP01031 Mean Expected Number 0.002 -strand -193 : -200 AGAATCTT Totally 3 motifs of 3 different REs have been found Description of REs found 378. Group TF: Opaque-1 /AC: RSP00395//OS: Zea mays /GENE: gamma-27kDa zein/RE: O2-like-box /TF: Opaque-1 864. Group RE: CT element /AC: RSP00935//OS: Pinus sylvestris /GENE: GS1a/RE: CT element /TF: unknown 956. Group TF: AEF /AC: RSP01031//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 2 /TF: AEF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.12|complement(1809813..1814404) |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +48 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.18 T - 0.25 C - 0.35 1 cctagcgatg aaaccgccta gccccgttag gtttcagggt aaccacgtaa 51 tgggccgaaa actccagccc aacatagatc ccctcgtatc cggcctggcc 101 caaattttcc tgcggcccac gtactccatc cttcacctgg gattaagata 151 ttttcatttt tctccctcca aagcaacacg aagggcggct aatgctaatc 201 TGAAATCTCC TCTCGCCCTA TCGGTTCCGC TTCTCCTCTC CCCTCGCCAT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00030 Mean Expected Number 0.009 -strand -11 : -17 AGCCGCC AC RSP00792 Mean Expected Number 0.010 +strand -32 : -23 CaAAGCAACA AC RSP01008 Mean Expected Number 0.005 -strand -169 : -175 ACCTAAC AC RSP01072 Mean Expected Number 0.005 -strand -150 : -159 ATTACGTGgT AC RSP01276 Mean Expected Number 0.008 -strand -77 : -84 GTACGTGG AC RSP01636 Mean Expected Number 0.001 +strand -35 : -25 CTCCAAAGCAA AC RSP01638 Mean Expected Number 0.001 +strand -35 : -25 CTCCAAAGCAA Totally 7 motifs of 7 different REs have been found Description of REs found 29. Group TF: EREBP /AC: RSP00030//OS: Nicotiana sylvestris /GENE: OLP/RE: ERRE /TF: EREBP ||Identical REs AC: RSP00082 RSP01344 RSP01523 RSP01764 RSP01775 745. Group RE: DAE /AC: RSP00792//OS: Hordeum vulgare /GENE: Amy32b/RE: DAE /TF: unknown 933. Group TF: PtMYB1; PtMYB4 /AC: RSP01008//OS: Pinus sylvestris /GENE: PsGS1b/RE: GS1b AC box 3 (AC-III) /TF: PtMYB1; PtMYB4 ||Identical REs AC: RSP01455 990. Group TF: PvAlf /AC: RSP01072//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1d /TF: PvAlf ||Identical REs AC: RSP01154 1175. Group RE: Box III /AC: RSP01276//OS: Petroselinum crispum /GENE: CHS/RE: Box III /TF: unknown 1456. Group RE: TERE /AC: RSP01636//OS: Arabidopsis thaliana /GENE: XCP2/RE: TERE /TF: unknown 1458. Group RE: TERE /AC: RSP01638//OS: Arabidopsis thaliana /GENE: AGP/RE: TERE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.18|complement(1835084..1835996) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.21 T - 0.19 C - 0.37 1 caagcagcat ttacatgcga tttaacgtgt taataaatcg aaaaggtaca 51 cgcgcctttt tccatccatc tacggctact ttcctgcacg atccaagcgg 101 ccggtcaggc aggccaggca gcggctgcac cgaacccgtg ccgctgcgcc 151 ccaaacccca ctaccataaa accccatcgc ctccacaccc cagcacaaac 201 CGACTCGGCC GCTGGCCCGC TGCTGCTGCT GCTGCACACG CCATTTTTGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00018 Mean Expected Number 0.003 +strand +43 : +49 ATTTTTG AC RSP00254 Mean Expected Number 0.007 -strand -155 : -161 CCTTTTC AC RSP01115 Mean Expected Number 0.003 -strand +49 : +43 CAAAAAT Totally 3 motifs of 3 different REs have been found Description of REs found 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.20|1841065..1845904 |SUPPORT|13 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +87 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.29 T - 0.30 C - 0.21 1 ggtctcaggt ttattattaa actcgttttc ccaatctcca actgcgagtt 51 tatcagtcac atagtcaacg ccgaattatg acgacttttt tctctccggg 101 tttttttttt gggtctaaaa aagcaagtgg ttttgtgtgg tggagtgcga 151 tggcagggac gggagcctcc gttaagatga ttcgttgcgt tgtaaagtgc 201 GGCGGGCAGC AGCAGCACGT CGTCGTCGCT GCGCGCGGTG ATCGGAAGTC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00495 Mean Expected Number 0.005 +strand -10 : -3 TGTAAAGT AC RSP00869 Mean Expected Number 0.001 +strand -10 : -2 TGTAAAGTG AC RSP00949 Mean Expected Number 0.002 +strand -139 : -132 TAGTCAAC Totally 3 motifs of 3 different REs have been found Description of REs found 471. Group RE: P-box 2 /AC: RSP00495//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 2 /TF: unknown ||Identical REs AC: RSP00686 805. Group RE: EM1 /AC: RSP00869//OS: Triticum aestivum /GENE: LMWG-1D1/RE: EM1 /TF: unknown 878. Group RE: TAGTCAAC motif /AC: RSP00949//OS: Petroselinum crispum /GENE: 4CL-1/RE: TAGTCAAC motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.21-2|1846721..1852212 |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +51 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.24 T - 0.25 C - 0.31 1 tgaaatttac tctttttttc tctcttggtc cacgtgctga tgttttttct 51 ccataatcac tgcacgaatt gccggccgca caagtagaaa tccatcgccc 101 tcacagatgg cctgtttcgt actggaagct actagagcat aaataggctg 151 gcggctggcc ccttctgcag ctacccgcct ggcgcctagt gccctggcca 201 GTATACAGCG AGGACATCGT CACCTCGCAG CGCCACAACG CCGGGGCGGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.006 -strand -183 : -192 AAAAAAGAGt AC RSP00817 Mean Expected Number 0.005 +strand -172 : -163 TcCACGTGCT Totally 2 motifs of 2 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 763. Group TF: ACE-binding TF /AC: RSP00817//OS: Arabidopsis thaliana /GENE: CFI/RE: ACE-core (AtCFI) /TF: ACE-binding TF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.28|1873714..1876705 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +560 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.22 T - 0.23 C - 0.28 1 tacgacccaa cacagtgagt agcccaatcc ttggcccaag caagcccaac 51 aaagagctag aaaggaaggg atgctacact ctcaggaaaa ggaacagaac 101 agagatcaaa caggcatcgg cggcttcggc ggcggcggcg acttggttta 151 ggctgaacct tgtcgatctt catctcttcc tctactacct ctcttgctac 201 TATCTCTACT GCAGCTACTA GGGCAATCCA GTCTCTCTAT TAGCTTGTAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00862 Mean Expected Number 0.001 +strand -142 : -134 AGAAAGGAA AC RSP00962 Mean Expected Number 0.010 +strand -185 : -179 TGAGTAG Totally 2 motifs of 2 different REs have been found Description of REs found 798. Group TF: BPC1 /AC: RSP00862//OS: Arabidopsis thaliana /GENE: STK/RE: GA-3 /TF: BPC1 887. Group RE: GLM1 /AC: RSP00962//OS: Hordeum vulgare /GENE: ITR1/RE: GLM1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.29|1885326..1889064 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.17 T - 0.24 C - 0.36 1 tggtgtgaac taaccatgac cttgaatagg cccatagtaa ctacagccca 51 ctggcctcca cccaaaggct taaaccggcc cgtgaatcgg tgggttttag 101 ccctatatat ttccacctgg caggctggca ttacctgcaa ctccccacgc 151 actactgtct gtctctcctt taaaacccac aaacgaaggt tgggtctccc 201 TACTCTCTCT CTCCACGCTT TACAACTCAA CCCCCGCACC ACCACCAGTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.003 -strand +12 : +4 AGAGAGAGA AC RSP00865 Mean Expected Number 0.004 -strand +14 : +6 GGAGAGAGA AC RSP00878 Mean Expected Number 0.007 -strand -81 : -88 CCAGGTGG AC RSP00938 Mean Expected Number 0.001 -strand -79 : -90 TGCCAgGTGGAA AC RSP01237 Mean Expected Number 0.002 +strand -100 : -91 CcCTATATAT Totally 5 motifs of 5 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 814. Group TF: RPCF-1 /AC: RSP00878//OS: Arabidopsis thaliana /GENE: PCNA/RE: Site I /TF: RPCF-1 867. Group TF: GBF /AC: RSP00938//OS: Arabidopsis thaliana /GENE: RbcS-1A/RE: G box-2 /TF: GBF 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.32|complement(1903519..1904933) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +479 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.38 G - 0.11 T - 0.27 C - 0.24 1 aatggcccac atgacaattc acgtacatga tcattgcgtt gagcaaatga 51 ccataaaatt tgcataggaa cattgtaaaa tgaaaggaaa acattacact 101 ttgcttcatt tgcttcacac tcactcaagc acaaaaattt tcaccccatc 151 taatcaaaga tccacccaat catacacgaa tttctttctc ccaatatagt 201 AACAAAATAT CATAACACTC GAAATTTCTG CAAAAACTAC TACATAGGTG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00441 Mean Expected Number 0.006 -strand -96 : -105 AgCAAAGTGT AC RSP00746 Mean Expected Number 0.002 -strand -52 : -63 ATGGGGTgAAAA AC RSP00860 Mean Expected Number 0.001 -strand -12 : -20 AGAAAGAAA AC RSP00943 Mean Expected Number 0.002 -strand -118 : -128 TCATTTtACAA AC RSP01014 Mean Expected Number 0.005 -strand -89 : -98 CAAATGAAGc AC RSP01093 Mean Expected Number 0.004 +strand -52 : -42 TCTAAtCAAAG AC RSP01596 Mean Expected Number 0.002 +strand -128 : -118 TTGTaAAATGA Totally 7 motifs of 7 different REs have been found Description of REs found 421. Group TF: Dof1 /AC: RSP00441//OS: Zea mays /GENE: cyPPDK1/RE: box a /TF: Dof1 708. Group TF: GT-1 /AC: RSP00746//OS: Nicotiana plumbaginifolia /GENE: Cab-E/RE: box 6 /TF: GT-1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 872. Group TF: GBF /AC: RSP00943//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box III /TF: GBF 939. Group TF: GAPF /AC: RSP01014//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 2 /TF: GAPF 1011. Group RE: box 2 /AC: RSP01093//OS: Pisum sativum /GENE: GS2/RE: box 2 /TF: unknown 1417. Group RE: Box III /AC: RSP01596//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0083M16.46|complement(1927818..1928706) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +83 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.23 T - 0.23 C - 0.31 1 cgtgtcatgt tcacgagggc gactcgtggc agacgcgctt gccacgccgg 51 cctatgcagc agggaaaggc cacaaaaaga ctctctcctg tacgactatg 101 catttcttta tccaaagaga tgaaaagtcg gtgcgcgTCA ATggcgcgtg 151 cgccgtgcac ctacccctat taatagctcc cctctgcatt gttgcgagct 201 CTAGCTCACC ACAGCCACAC TTCTGATCAC TGCTCACTCA GCTAATTAAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00433 Mean Expected Number 0.003 -strand -33 : -44 aGGGGTAGGTGC AC RSP00595 Mean Expected Number 0.001 -strand +51 : +43 GCTTAATTA AC RSP01020 Mean Expected Number 0.008 +strand -81 : -75 ATGAAAA AC RSP01108 Mean Expected Number 0.008 +strand +43 : +49 TAATTAA AC RSP01209 Mean Expected Number 0.004 -strand -122 : -131 CTTTTTGTGG AC RSP01708 Mean Expected Number 0.002 +strand -34 : -25 CTATTAATAG AC RSP01708 Mean Expected Number 0.002 -strand -25 : -34 CTATTAATAG Totally 7 motifs of 6 different REs have been found Description of REs found 413. Group TF: AtMYB84 /AC: RSP00433//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB84 BS /TF: AtMYB84 571. Group RE: Box II EE1 /AC: RSP00595//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE1 /TF: unknown 945. Group TF: GAPF /AC: RSP01020//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 2 /TF: GAPF 1026. Group RE: rAT-1 /AC: RSP01108//OS: Spinacia oleracea /GENE: rps22/RE: rAT-1 /TF: unknown 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.9|complement(1951983..1952716) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +30 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.25 T - 0.21 C - 0.21 1 taaaagaatt ccatatggca aattttaaag acggtaaagc acaattcgag 51 gattagctcc agaatcccag atcatctcca agtgagcaac agtatctcag 101 ggctaccaac cagctgaaaa attaagtgag agagaatact agtactacta 151 gctagctgct aggagtagta tataactgta ctgtcctagc tgagatcggc 201 AGCAGGAGCG ACCTGGAGGC TGGAGGATAG ATGGCCAGGA CGACGCTCTA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00011 Mean Expected Number 0.008 -strand -144 : -153 GCTAATCCTC AC RSP00503 Mean Expected Number 0.003 +strand -53 : -46 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -46 : -53 CTAGCTAG AC RSP00914 Mean Expected Number 0.003 -strand -125 : -134 GATGATCTGG AC RSP00915 Mean Expected Number 0.003 -strand -125 : -134 GATGATCTGG Totally 5 motifs of 4 different REs have been found Description of REs found 11. Group RE: C2b-BS /AC: RSP00011//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: C2b-BS /TF: unknown 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 845. Group RE: B2 /Group TF: Opaque-2 /AC: RSP00914//OS: Zea mays /GENE: b-32/RE: B2 /TF: Opaque-2 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.10|complement(1954649..1964254) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +127 bp |Promoter: TATA Nucleotide Frequencies: A - 0.36 G - 0.18 T - 0.25 C - 0.22 1 gaaaaagaag gaatagtcac tagtgattca tacggcatga atgacataac 51 gctgtcgaca attgacctgc accactagtt tatttacatc gcgattagaa 101 gattaaaact gtccttgtct ccctcctcac aagtcagaga cgatgctgac 151 ttccccatta tttctgctga taaaaaaaaa gtctaacaaa tcggaaagac 201 TAGTCAAGAA AAACAAGGCA ATGGCAATAG CATTTCTCGA GCATTAGACC 251 T Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.15|complement(1974225..1979286) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +139 bp |Promoter: TATA Nucleotide Frequencies: A - 0.26 G - 0.24 T - 0.24 C - 0.25 1 cctggctaga atttgtcgag ccatgttcta agggtcggtc aatgataata 51 tggtccatta acttctacct ttacctatcg tttcaggcaa actcaccaca 101 gaggatggag agagctagct taggtgcgaa caaaaacagg gagcgaatga 151 attcacggtc aaagtatatg gccgcgagtt gtgaccgaag cagcagcagc 201 GGTGGTTCGC TCTCTTCATC TCTCCAAAGT CCACTCCACC CTCCGCTTGC 251 A Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.38-1|2045546..2049272 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +49 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.20 T - 0.27 C - 0.25 1 attcaggtgt ggagtcccca ccggtgttcc ctcaaaaaaa aaaaaaaaaa 51 agaggcgacg gcgacttttc cacttgtgtt gattaaaatg acgtctaact 101 gatcggaaaa aggtcaagca aaacaagGCA ATggcaatgt tatttctcaa 151 gctagacctt ttcctcccct tccagttttc tgcttttctc cactcctcca 201 TGTGTAGTAG CCTGCAGGCA GCTGCTAGCT CCACCATTTG AGTGGCTAGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00445 Mean Expected Number 0.007 +strand -155 : -146 AAAAAAGAGg AC RSP01654 Mean Expected Number 0.007 +strand -114 : -105 AATGACGTCT AC RSP01751 Mean Expected Number 0.001 +strand -132 : -124 TCCACTTGT Totally 3 motifs of 3 different REs have been found Description of REs found 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 1557. Group TF: AREB2/ABF4 /AC: RSP01751//OS: Arabidopsis thaliana /GENE: COX5b-1/RE: distalB-like /TF: AREB2/ABF4 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.39|2050384..2054438 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +17 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.18 T - 0.24 C - 0.33 1 ctccttaccg atcttcgttt cgtttcatac tccgtactac tccagaagaa 51 gagagaatgg tccaagaaag tgaccaagca aatgacgcaa gtggtgcacg 101 aaaccaagtc aactacacac atgtaaaatt cctcgtctcc tcgatccatc 151 catcgatcgc ttcgcctata atacaacgcc tcttcctcgc cgcatcgcgc 201 CACCAACCGT CGTCGCGATG GACACGCCAT TGCTGCTGCT GCTTCCCTTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00431 Mean Expected Number 0.006 -strand +14 : +3 GACGACGGTTGG AC RSP00432 Mean Expected Number 0.001 -strand +12 : -1 CGACGGTtGGTGG AC RSP00522 Mean Expected Number 0.007 -strand -107 : -113 CCACTTG AC RSP00653 Mean Expected Number 0.000 -strand -144 : -154 TTCTCTCTtCT AC RSP01469 Mean Expected Number 0.006 -strand -75 : -84 TtACATGTGT Totally 5 motifs of 5 different REs have been found Description of REs found 411. Group TF: AtMYB77 /AC: RSP00431//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB77 BS /TF: AtMYB77 412. Group TF: AtMYB15 /AC: RSP00432//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: AtMYB15 BS /TF: AtMYB15 498. Group TF: DPBF-1; DPBF-2 /AC: RSP00522//OS: Daucus carota /GENE: Dc3/RE: E2-core /TF: DPBF-1; DPBF-2 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 1339. Group TF: Opaque-2 (O2) /AC: RSP01469//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z1 /TF: Opaque-2 (O2) ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.40|2056110..2059028 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +135 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.17 T - 0.21 C - 0.37 1 cataaacgac accgtccatg ggtgcccagc cagctcccac cgcccaaatt 51 aaggccggtc cacccatcgt tctcatgacc tgccaacccc atcccagccc 101 tacacgtgtc catcctcaac cacgcgtcgg cacctccaac gcacttctgg 151 aaggaagcca aaacggcagc ttattaatag cgtagccgtt acctgcttta 201 TATGGTCTTC TCAATTAAAC TCCACTAAAC CTCCCTATGG CCTATGCCAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00144 Mean Expected Number 0.009 -strand -177 : -182 CACCCA AC RSP00340 Mean Expected Number 0.010 +strand -100 : -91 TaCACGTGTC AC RSP01032 Mean Expected Number 0.006 +strand -157 : -148 CCAAATTAAG AC RSP01256 Mean Expected Number 0.003 +strand -99 : -92 ACACGTGT AC RSP01256 Mean Expected Number 0.003 -strand -92 : -99 ACACGTGT AC RSP01529 Mean Expected Number 0.000 -strand -43 : -53 GCTtCCTTCCA AC RSP01710 Mean Expected Number 0.005 -strand +5 : -5 CCATATAAAG Totally 7 motifs of 6 different REs have been found Description of REs found 140. Group TF: SEF3 /AC: RSP00144//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: SEF3 BS 1 /TF: SEF3 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 957. Group TF: FLC /AC: RSP01032//OS: Arabidopsis thaliana /GENE: SOC1/RE: CArG box /TF: FLC 1159. Group TF: GBF1 /AC: RSP01256//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS3 /TF: GBF1 1376. Group RE: Box I /AC: RSP01529//OS: Pisum sativum /GENE: PsCHS3/RE: Box I /TF: unknown ||Identical REs AC: RSP01530 RSP01531 1518. Group TF: RIN /AC: RSP01710//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Intermediate /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0443D08.45|complement(2071597..2074705) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +63 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.25 T - 0.22 C - 0.27 1 gggttgggaa catgttcatg cgaacacacc tgttcacgaa cagtatacag 51 tacttggctg tagcgggcat cttgtcctgg catgtggggc ccagtagcag 101 tgacggggac agatcacgtg ggcccacatg tcagtgtacc atgtcaaacc 151 tgcgcaccaa ctcctactct ataaaggaaa aactcgtggt cgtcttcctc 201 CTCGAGCCAT TCCACAAAAT TCGGCAAAAT CCAGTGCTCC AGTCAGTGGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00064 Mean Expected Number 0.007 +strand -152 : -143 AGTACtTGGC AC RSP00195 Mean Expected Number 0.002 +strand -70 : -60 TCaGTGTACCA AC RSP00471 Mean Expected Number 0.002 +strand -119 : -109 aTGTGGGGCCC AC RSP00640 Mean Expected Number 0.004 +strand -87 : -80 TCACGTGG AC RSP01597 Mean Expected Number 0.002 +strand -138 : -128 GcGGGCATCTT Totally 5 motifs of 5 different REs have been found Description of REs found 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 188. Group RE: Box II /AC: RSP00195//OS: Oryza sativa /GENE: Gt2/RE: Box II /TF: unknown 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 616. Group RE: G-box /Group TF: GBF /AC: RSP00640//OS: Zea mays /GENE: GRF1/RE: G-box /TF: GBF ||Identical REs AC: RSP00641 1418. Group RE: Box II* /AC: RSP01597//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box II* /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.3|complement(<2081690..2084006) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.20 T - 0.25 C - 0.31 1 agaaggtctg tcatctaaaa taaaacagaa atggttgagc ctttcctttt 51 ggttaacgga ggaataggga aagaaaaccg ctccaggtga gccgccgtgc 101 ggcagctaga tcacagggcc gcaaACAATa attcgcgata tttccttcaa 151 gtgggcccca ccaccttcgt cttccccctt tcctcagcct cctccgcgtt 201 TATATTCCCC GTCCACTCCG CCAAAAGCCC CTCTTCCGAT CTTCTTCTTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00522 Mean Expected Number 0.008 -strand -47 : -53 CCACTTG AC RSP00755 Mean Expected Number 0.007 +strand -141 : -135 AGGAATA Totally 2 motifs of 2 different REs have been found Description of REs found 498. Group TF: DPBF-1; DPBF-2 /AC: RSP00522//OS: Daucus carota /GENE: Dc3/RE: E2-core /TF: DPBF-1; DPBF-2 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.7|2093993..2097496 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1547 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.24 T - 0.25 C - 0.24 1 atgtcaaaaa agaaaaagaa aaagaaagat aagagagaga ctctttgcat 51 tggtaggctt agttggccca gattgtaagc agacctagtt atattgtggg 101 cttggtttca gcccatacga aaggagaagg ccatgatgat gcggaattcc 151 cagcccatgt cgccaccgct ttaggcgcag ccgaccggaa ttcactctct 201 CACGATTCCC GATGCTCGCG AAGTTTCTTT TCTCCGTTTC TCGCCTCGTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00227 Mean Expected Number 0.001 +strand -175 : -167 AAGATAAGA AC RSP00445 Mean Expected Number 0.006 +strand -195 : -186 AAAAAAGAaA AC RSP00864 Mean Expected Number 0.001 +strand -169 : -161 AGAGAGAGA AC RSP00915 Mean Expected Number 0.003 +strand -66 : -57 GATGATGCGG AC RSP01030 Mean Expected Number 0.004 -strand +28 : +21 AGAAACTT Totally 5 motifs of 5 different REs have been found Description of REs found 220. Group TF: GT-1 /AC: RSP00227//OS: Pisum sativum /GENE: rbcS-3A/RE: BOX III* /TF: GT-1 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 955. Group TF: AEF /AC: RSP01030//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 1 /TF: AEF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.10|complement(2105763..2106481) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +44 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.19 T - 0.24 C - 0.31 1 cacgagaccc cggttaacca cgcgtgtgtg aaccgcacac tcctttccct 51 ttcctccgct aattaattcg cccaactaaa ctactcacct gcgtccactg 101 cgatcgatcg cttaagatgt cagctatata tatactccaa gctcggtgag 151 ccagcatcac caccaaccag agctaacata gcagtagcta gctagatcga 201 TCGATCGATC GTCTCTCCTT GTAGGCTAGC TGCTATACGA GAGCATGTGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00200 Mean Expected Number 0.006 -strand -133 : -142 aATTAATTAG AC RSP00503 Mean Expected Number 0.003 +strand -13 : -6 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -6 : -13 CTAGCTAG AC RSP01080 Mean Expected Number 0.001 +strand -118 : -107 ACTCACCTgCGT AC RSP01237 Mean Expected Number 0.003 +strand -77 : -68 CTaTATATAT Totally 5 motifs of 4 different REs have been found Description of REs found 193. Group TF: GmHdl56; GmHdl57 /AC: RSP00200//OS: Glycine max /GENE: vspB/RE: PRD motif 1 /TF: GmHdl56; GmHdl57 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 998. Group TF: DcMYB1 /AC: RSP01080//OS: Daucus carota /GENE: DcPAL1/RE: box-L2 /TF: DcMYB1 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.14|2117290..2119122 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +31 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.18 T - 0.30 C - 0.29 1 ttgctcagtt tgttaggttt ggttaatttt tctttttaac ctgtcgccat 51 ggatggatga attcatggat ttcattgaga gcagctggag aagaaagaag 101 aagagtgacg tgatccattc attcgttcgt tcaccttgac tgaccactgc 151 aacttcgtct cctctcccct taaattcccc ttcactctcc tcactccatc 201 CAGCTCACCA CCAGCAGCAG CATCAGCAGC AATGCAGCCT CCCATCCTCC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00230 Mean Expected Number 0.004 -strand -177 : -186 AACCaAACCT AC RSP00416 Mean Expected Number 0.007 -strand -142 : -148 CATCCAT AC RSP00416 Mean Expected Number 0.007 -strand -146 : -152 CATCCAT AC RSP01008 Mean Expected Number 0.009 -strand -183 : -189 ACCTAAC AC RSP01654 Mean Expected Number 0.005 +strand -97 : -88 AGTGACGTGA Totally 5 motifs of 4 different REs have been found Description of REs found 223. Group TF: PcMYB1 /AC: RSP00230//OS: Petroselinum crispum /GENE: CHS-1/RE: MRECHS /TF: PcMYB1 398. Group RE: Box-1 /AC: RSP00416//OS: Hordeum vulgare /GENE: EPB-1/RE: Box-1 /TF: unknown 933. Group TF: PtMYB1; PtMYB4 /AC: RSP01008//OS: Pinus sylvestris /GENE: PsGS1b/RE: GS1b AC box 3 (AC-III) /TF: PtMYB1; PtMYB4 ||Identical REs AC: RSP01455 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.18-1|2128235..2134095 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +54 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.18 G - 0.15 T - 0.19 C - 0.48 1 acatcgccgc cattactgtt gccctctcct tcccggcgcg gccactccgt 51 ccgccgccgc cgggggcgaa cccgaacgcc tctccaccgt ccgatccgcc 101 agccggatca gatccaacac ctaccaacct accttggcac cttctccctc 151 tcgtctcctt cctcctcacc tcgcccacta cacctccacc tccggagctc 201 ACAACACAAA TCGATTTCTC CCAAACCCCC CCTAAACTCC CCACCGAATC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00651 Mean Expected Number 0.001 +strand -82 : -72 ACCTACCAACC AC RSP01505 Mean Expected Number 0.002 -strand -105 : -113 GATCGGACG Totally 2 motifs of 2 different REs have been found Description of REs found 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.19-1|2134602..2135341 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.20 T - 0.14 C - 0.39 1 caaaatacaa agaataattc taagcccaac gagcccaact gcgcttccca 51 actatcaaat ctgcaccatc cattcctcat cggatgcctt cacgccgcca 101 cgtagcggag agcaaagcaa aaccctagct agagccacac ccagaggtat 151 agattcccca ccccgccgcc tccacgcatt ccttcgccca ccaaaaccct 201 AGCCGCGCCG CCGCCGCCGA CGACCAGGTA AGGAAGGAGA TCCGCCGCCG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00042 Mean Expected Number 0.006 +strand -185 : -179 AATTCTA AC RSP00043 Mean Expected Number 0.006 -strand -97 : -104 TACGTGGC AC RSP00048 Mean Expected Number 0.001 -strand -95 : -106 gCTACGTGGCGG AC RSP00073 Mean Expected Number 0.010 +strand -104 : -95 GCCACGTaGC AC RSP00073 Mean Expected Number 0.010 -strand -95 : -104 GCtACGTGGC AC RSP00189 Mean Expected Number 0.006 +strand -104 : -95 gCCACGTAGC AC RSP00447 Mean Expected Number 0.001 +strand -90 : -81 AGCAAAGCAA AC RSP00503 Mean Expected Number 0.002 +strand -76 : -69 CTAGCTAG AC RSP00503 Mean Expected Number 0.002 -strand -69 : -76 CTAGCTAG AC RSP01109 Mean Expected Number 0.001 +strand -187 : -180 ATAATTCT AC RSP01259 Mean Expected Number 0.006 -strand -96 : -103 CTACGTGG Totally 11 motifs of 9 different REs have been found Description of REs found 41. Group RE: Motif h /AC: RSP00042//OS: Pisum sativum /GENE: PSPAL2/RE: Motif h /TF: unknown 42. Group TF: TAF-1 /AC: RSP00043//OS: Oryza sativa /GENE: rab16A-D/RE: Motif I core /TF: TAF-1 47. Group RE: ABRE A2; ABRE2 /AC: RSP00048//OS: Hordeum vulgare /GENE: HVA1 gene/RE: ABRE A2; ABRE2 /TF: unknown 72. Group TF: TAF-1 /AC: RSP00073//OS: Nicotiana tabacum /GENE: Synthetic OLIGO/RE: PA /TF: TAF-1 ||Identical REs AC: RSP00274 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 1027. Group RE: rAT-2 /AC: RSP01109//OS: Spinacia oleracea /GENE: rps22/RE: rAT-2 /TF: unknown 1161. Group TF: GBF1 /AC: RSP01259//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS6 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.32|2199079..2200589 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +127 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.13 T - 0.29 C - 0.26 1 ctaggctcaa gatagataga cgtcgtctct actactccta ctagaaaaca 51 tatctttgtc caagcaaatt aacaaaatca aatatagcaa gaacacgttt 101 aattttgtac acatgctgcg tttgggttgg tccaaataaa atacaaagac 151 cagtgtctat atatacagag cacacgccca cagcaactat cactcttcat 201 CATCATCTTC TTTGGCTTCT CCCTCTTCAC TGCCCTAATT ACAACCCATT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01237 Mean Expected Number 0.006 -strand -33 : -42 CTgTATATAT AC RSP01454 Mean Expected Number 0.002 -strand -70 : -76 ACCAACC Totally 2 motifs of 2 different REs have been found Description of REs found 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown 1325. Group RE: AC-II /Group TF: PtMYB4 /AC: RSP01454//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-II /TF: PtMYB4 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0480E02.34|complement(2212464..2218077) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +3565 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.17 T - 0.35 C - 0.19 1 aacagctact aagataaaag taccattatt ctcaactctc aaccattgtt 51 caagtgttca tgactaacat cttgcgcatc ttctttgtta catgataaat 101 ttctccatgg taaacaacga ctataaaaaa atgtgtacat gaactcatct 151 taagtctggg atctggtgtt gttagctatt ttatactaat ggagatttct 201 TTCTTAAGGT AAACGGAGAC CATGGAGGGC TTTTCTTTTG TATGGTCCAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00860 Mean Expected Number 0.005 -strand +4 : -5 AGAAAGAAA AC RSP01013 Mean Expected Number 0.004 +strand -15 : -6 CtAATGGAGA Totally 2 motifs of 2 different REs have been found Description of REs found 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 938. Group TF: GAPF /AC: RSP01013//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 1 /TF: GAPF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.7|2242533..2247237 |SUPPORT|15 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.28 T - 0.20 C - 0.28 1 agatcggacg gctgacgttc tcccgaatta taattcgaag gaggggccgt 51 aaacaggaaa cactaataag gcgaggtctc aagtgcaaaa caggatccgg 101 tactcgtcac tcctcgatct ggaccgtcca agcctgatcg gacggctgga 151 ggagatccca gcctgtgtac taagtactgg acgcggtgca gttcgcgggc 201 TACCCTTCCA CTTCCACTCG CTGGCGATAG CACCGCACCG GAGCATATGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00097 Mean Expected Number 0.004 -strand -74 : -81 ACGGTCCA AC RSP01505 Mean Expected Number 0.001 +strand -199 : -191 GATCGGACG AC RSP01505 Mean Expected Number 0.001 +strand -65 : -57 GATCGGACG Totally 3 motifs of 2 different REs have been found Description of REs found 95. Group RE: 9-mer box /AC: RSP00097//OS: Zea mays /GENE: GapC4/RE: 9-mer box /TF: unknown 1362. Group RE: NonaLS /AC: RSP01505//OS: Triticum aestivum /GENE: H1 (TH315)/RE: NonaLS /TF: unknown ||Identical REs AC: RSP01506 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.8|complement(2247640..2251875) |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +58 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.35 G - 0.22 T - 0.22 C - 0.21 1 taataaaaat attaattata aaaaagtttt atataagacg gatagtgaaa 51 cgttggatac taaagcacat gatttgtttt ttggaaggga gaagtactta 101 actttgcaca aaactggcca gcacgaagat caaagcaaaa acaaaacccc 151 aggaaggcag agaggccaag aactggagcc tgagacggag agggcaaagc 201 GCTTGGTGTC CACTTCGCTC ACCACACTTC CCCTCTTTCC CGCCTGCGTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00015 Mean Expected Number 0.001 +strand +36 : +43 TTTCCCGC AC RSP00125 Mean Expected Number 0.002 -strand -188 : -199 AATATTTTTATT AC RSP00135 Mean Expected Number 0.001 -strand -188 : -199 AATATTTTTATt AC RSP00301 Mean Expected Number 0.009 -strand -93 : -99 TGCAAAG AC RSP00442 Mean Expected Number 0.004 +strand -102 : -93 TAACTTTGCA AC RSP00683 Mean Expected Number 0.003 -strand +18 : +9 GCgAAGTGGA Totally 6 motifs of 6 different REs have been found Description of REs found 14. Group TF: E2F1 /AC: RSP00015//OS: Arabidopsis thaliana /GENE: AtCDC6/RE: E2F1-BE /TF: E2F1 ||Identical REs AC: RSP00165 RSP00298 123. Group RE: AT-1 (3) /AC: RSP00125//OS: Nicotiana plumbaginifolia /GENE: cab-E/RE: AT-1 (3) /TF: unknown ||Identical REs AC: RSP00133 RSP00788 131. Group RE: AT-1 (4) /AC: RSP00135//OS: Nicotiana plumbaginifolia /GENE: cab-E/RE: AT-1 (4) /TF: unknown 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 422. Group TF: Dof1 /AC: RSP00442//OS: Zea mays /GENE: cyPPDK1/RE: box b /TF: Dof1 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.10|2258302..2263034 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +246 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.12 T - 0.23 C - 0.33 1 aaaaagtgca ggttgcattt acccctattc aaaaaattca aagtcccaca 51 gggccccaga cccagagtgt ggccagacca gattaaacac acacaacaac 101 agtccatctg cagttcaaat ctgggtatta aaaacccccc aaaattaatc 151 cccccatcca atctctcact ctcatctcca ccaaattcaa acttcactct 201 CATCTTCATC CTCAGCTCAG CTCAGCTCAG CTCAAGCTCA AAAGCCTTTT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00596 Mean Expected Number 0.007 -strand -128 : -133 GCCACA AC RSP00642 Mean Expected Number 0.003 -strand -180 : -187 TAAATGCA Totally 2 motifs of 2 different REs have been found Description of REs found 572. Group RE: Box II EE2 /AC: RSP00596//OS: Lycopersicon esculentum /GENE: rbcS3A/RE: Box II EE2 /TF: unknown 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.11|complement(2263083..2267853) |SUPPORT|13 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +59 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.29 T - 0.25 C - 0.26 1 ctcttcatct ctctctctcc ggcgagcggc ggcggcggcg gtggaaccct 51 attcttgtcg gagtcgagga agatatatat ttagctattg acggaaatgc 101 ccctcttgta gcttcggctt tgagattcgt gcaggggtgg gatcctggcc 151 gcaggaaaga tttttttttc tatttccctc cgaatccgaa gcgaggtgag 201 GAGGAGGAGA TAAGGCCGCG CGCTCTCCAC CACCACGGCC GCGAATGCAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00629 Mean Expected Number 0.003 -strand -36 : -43 AAAAATCT AC RSP00864 Mean Expected Number 0.001 -strand -183 : -191 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand -185 : -193 AGAGAGAGA AC RSP00865 Mean Expected Number 0.001 -strand -181 : -189 GGAGAGAGA AC RSP00934 Mean Expected Number 0.004 +strand -124 : -115 ATATTTAGcT Totally 5 motifs of 4 different REs have been found Description of REs found 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 863. Group RE: AT-2b /AC: RSP00934//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2b /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.12|2267964..2279997 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +76 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.26 T - 0.20 C - 0.29 1 cggcggagga ctgcgacggc gagcaactca tggcgggtaa ttgcattcgc 51 ggccgtggtg gtggagagcg cgcggcctta tctcctcctc ctcacctcgc 101 ttcggattcg gagggaaata gaaaaaaaaa tctttcctgc ggccaggatc 151 ccacccctgc acgaatctca aagccgaagc tacaagaggg gcatttccgt 201 CAATAGCTAA ATATATATCT TCCTCGACTC CGACAAGAAT AGGGTTCCAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00629 Mean Expected Number 0.003 +strand -75 : -68 AAAAATCT AC RSP00934 Mean Expected Number 0.004 -strand +14 : +5 ATATTTAGcT Totally 2 motifs of 2 different REs have been found Description of REs found 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 863. Group RE: AT-2b /AC: RSP00934//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2b /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.13|2272040..2275662 |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +115 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.14 T - 0.25 C - 0.39 1 aagaagaaga aaaaaaaaag gcatatgcct tgcaaagttc ccagcttggt 51 tcccttccct ccaatattct ccacccctcc catggaatat cccccacaat 101 tccctactcc ccaactccac actCCAATct cttcctcctc ttcttcttct 151 tcctcgcctc gcttatatac gcggcgtgtc gagctcctcc tcctcctctt 201 CCTTGCTCCA CCACAACACC GTCGACTCGA GGCGCACGCA AACGCCGGTA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.005 -strand -25 : -31 CGCCGCG AC RSP00301 Mean Expected Number 0.005 +strand -170 : -164 TGCAAAG AC RSP00442 Mean Expected Number 0.001 -strand -161 : -170 gAACTTTGCA Totally 3 motifs of 3 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 422. Group TF: Dof1 /AC: RSP00442//OS: Zea mays /GENE: cyPPDK1/RE: box b /TF: Dof1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.14|complement(2278715..2281579) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +833 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.29 T - 0.19 C - 0.20 1 ggtattggcc aagtagcatg tagtggaggt aaaagcaaag caaggggggg 51 aggaagagaa gagaagaaga gcaagcccaa gtgtgcatgc gtgtatgcgc 101 acgcacgcac atatatgcgg cctagctagc taccaggcat catacgggta 151 ttaggtgtaa taatatatat atagtgtaaa agtcggccac aagctgagat 201 GCAAGGCCCA ATCACCAGCT GCCACTCTCA AGAACCTGAC TTTGGATCGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00029 Mean Expected Number 0.008 +strand -26 : -19 TGTAAAAG AC RSP00447 Mean Expected Number 0.001 +strand -167 : -158 AGCAAAGCAA AC RSP00503 Mean Expected Number 0.003 +strand -79 : -72 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -72 : -79 CTAGCTAG AC RSP00985 Mean Expected Number 0.007 -strand +41 : +32 AGTcAGGTTC AC RSP01237 Mean Expected Number 0.004 -strand -25 : -34 CaCTATATAT AC RSP01237 Mean Expected Number 0.004 -strand -27 : -36 CTaTATATAT Totally 7 motifs of 5 different REs have been found Description of REs found 28. Group RE: P-box 1 /AC: RSP00029//OS: Triticum aestivum /GENE: LMW-glutenin/RE: P-box 1 /TF: unknown 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 906. Group TF: PBP (Myb305) /AC: RSP00985//OS: Antirrhinum majus /GENE: gPAL2/RE: P-box /TF: PBP (Myb305) 1142. Group RE: -23 Z-BAC+ /AC: RSP01237//OS: Phaseolus vulgaris /GENE: BAC/RE: -23 Z-BAC+ /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.17-2|2291809..2294897 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +103 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.22 T - 0.29 C - 0.25 1 agaaggccaa agcggctaag ctttggccaa agcagccttc tcttcttctc 51 tagtgggaaa gtgagataag aagcagccat cagaagagca ctcccttgtt 101 ttttgaccaa aactttgctg ctcactgtcc tagctggaga gaatccagcg 151 atacacgcat gtcttcttct tcagctcggt cttggttgcc gacctcattt 201 GCAGATTTCT GCACATGAGG CATCTCTCTC TCGAAGTATC GTGTTTTGAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.002 -strand +31 : +23 AGAGAGAGA Totally 1 motifs of 1 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.29|complement(2346870..2350305) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +149 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.13 T - 0.29 C - 0.26 1 tatgtttaac tcaaaatttt ccttcagttt ttactcaaat ttgtgccaca 51 tcacaaaatt ttttttaaaa aaacataaac atgtacttac tcgtactaca 101 tacACAATaa tggaaaaaaa attatcatta ttaaaataag gtagggtaaa 151 acaaacgtga ggaggtggat gacactacgc gcccaacctt cccccccccc 201 TCTCTCTCTC TGCTTCGAAT TCCTCACCTC ACCTCACCTC CAGGCGGCGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00438 Mean Expected Number 0.004 +strand +43 : +48 GGCGGC AC RSP00438 Mean Expected Number 0.004 +strand +46 : +51 GGCGGC AC RSP00807 Mean Expected Number 0.004 -strand +51 : +46 GCCGCC AC RSP00807 Mean Expected Number 0.004 -strand +48 : +43 GCCGCC AC RSP00847 Mean Expected Number 0.000 -strand -33 : -42 CCACCTCcTC AC RSP00864 Mean Expected Number 0.002 -strand +11 : +3 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +9 : +1 AGAGAGAGA Totally 7 motifs of 4 different REs have been found Description of REs found 418. Group RE: PR-box /AC: RSP00438//OS: Arabidopsis thaliana /GENE: PR-1/RE: PR-box /TF: unknown 760. Group RE: GCC box /Group TF: Pti4 /AC: RSP00807//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: GCC box /TF: Pti4 ||Identical REs AC: RSP00809 RSP00811 RSP00814 RSP00921 RSP01328 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.31|complement(2354673..2357239) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +66 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.14 T - 0.25 C - 0.27 1 aaaaaggaac gggtctaata agttatggcg acagaactat ttttcttcct 51 ctccaagaag cgaagaatat tgcttataga tcgaatgaac atactgacca 101 agttttgaca gaatgacagg tggggcccat gcccctacct tttttttaaa 151 aaaaaaattc ccttcttaaa acaacacaaa ttctcgcctc cccatcttcc 201 AGAAAAAAAC TCCTCCTAAA CCCCCGAAAA CCCTAACCTT TCGTCCGCGC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00279 Mean Expected Number 0.005 -strand +36 : +28 TTAGGGTTT AC RSP00304 Mean Expected Number 0.004 +strand -87 : -80 TGACAGGT AC RSP00369 Mean Expected Number 0.005 +strand +28 : +36 AAACCCTAA AC RSP00439 Mean Expected Number 0.009 -strand -131 : -138 ATATTCTT AC RSP00297 Mean Expected Number 0.000 +strand -77 : +35 GGCCCA-- ** bp --ACCCTAA Totally 5 motifs of 5 different REs have been found Description of REs found 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 419. Group RE: -624-box /AC: RSP00439//OS: Arabidopsis thaliana /GENE: PR-1/RE: -624-box /TF: unknown 925. Group TF: At-TCP20 /AC: RSP00297//OS: Arabidopsis thaliana /GENE: PCNA/RE: Box II/telo-box (motifs 2 & 3) /TF: At-TCP20 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.39|complement(2371274..2373564) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +23 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.19 T - 0.27 C - 0.27 1 gttgtatcaa atcatagtgc tagaccattt ggagaaggag aattaatttc 51 acaagcacaa gaaacccata cgcaagttct gttgattttt tgtaaaaacg 101 aaatcgttga aagaggacag gaggcaagta gtgtcagcga cagatgggtc 151 ccactaaacg gtaggtataa gcgtcatcca aaacccctct tcccttttct 201 TATCCCCTCC CCTCTCCTCT CTTCTCTCCT TCGCTTCGCC ACCGCGTTCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00735 Mean Expected Number 0.005 -strand -111 : -118 AAAAATCA AC RSP00943 Mean Expected Number 0.004 +strand -157 : -147 TaATTTCACAA AC RSP01453 Mean Expected Number 0.007 -strand -35 : -41 ACCTACC AC RSP01596 Mean Expected Number 0.004 -strand -147 : -157 TTGTGAAATtA Totally 4 motifs of 4 different REs have been found Description of REs found 698. Group TF: DET1; CCA1 /AC: RSP00735//OS: Arabidopsis thaliana /GENE: CAB2/RE: CCA1 BS /TF: DET1; CCA1 872. Group TF: GBF /AC: RSP00943//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box III /TF: GBF 1324. Group RE: AC-I /Group TF: PtMYB4 /AC: RSP01453//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-I /TF: PtMYB4 1417. Group RE: Box III /AC: RSP01596//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box III /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.40|complement(2374124..2374787) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +137 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.17 T - 0.31 C - 0.25 1 catcttctcc aattgatgtg gctctctcat ttgaccattt ccttgtgcta 51 gctagctagt agcttagctg agcaaagcta agccagttgt tatccactaa 101 tcagcATTGA ttagtttagt caaaaaaaaa atctcaaggc tcaccttatt 151 atactaatct gcagttgtgc ccttaaatac ccacacgcct ctctttcttc 201 CTCTTTATCC TTTGCAGTTG CACCACCAAA CAGAGACAGA GGTAGAGAGG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00243 Mean Expected Number 0.003 +strand -34 : -27 GTGCCCTT AC RSP00447 Mean Expected Number 0.003 +strand -130 : -121 AGCAAAGCtA AC RSP00503 Mean Expected Number 0.003 +strand -153 : -146 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 +strand -149 : -142 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -142 : -149 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -146 : -153 CTAGCTAG AC RSP00629 Mean Expected Number 0.009 +strand -74 : -67 AAAAATCT AC RSP00861 Mean Expected Number 0.003 -strand -3 : -11 AGAAAGAGA AC RSP01058 Mean Expected Number 0.007 -strand -102 : -109 TAGTGGAT AC RSP01640 Mean Expected Number 0.003 -strand +41 : +32 CTcTGTCTCT Totally 10 motifs of 7 different REs have been found Description of REs found 236. Group TF: MNF1; MNB1a; MNB1b /AC: RSP00243//OS: Zea mays /GENE: PEPC/RE: MNF1 BS core /TF: MNF1; MNB1a; MNB1b 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 978. Group TF: GT-3a /AC: RSP01058//OS: Brassica napus /GENE: extA/RE: GT-3a Box III /TF: GT-3a 1460. Group RE: ARE /AC: RSP01640//OS: Nicotiana tabacum /GENE: Beta-glucanase/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0019D06.41|complement(2375627..2379388) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +404 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.20 T - 0.20 C - 0.40 1 accaaaagac cggtaggtag accccacctg tcagtgaaag caggcgacgg 51 cgaccgacat cccccaaatt cccccatctc cccgtctcgg aattcgggtt 101 gtgctccact aaatccctcg ctaatggcgt gctaatccca ccaccaccct 151 tgcattgcac gcggccgtat aaaatcccgt gccaccgtat cattcactcc 201 TCCCGTCCCT ATCGCGTCGG ATCGCCACCC ACCTCGCCGC CGCTGCTTGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.008 -strand -168 : -175 TGACAGGT AC RSP01453 Mean Expected Number 0.003 -strand -183 : -189 ACCTACC AC RSP01472 Mean Expected Number 0.000 -strand -180 : -190 TCTACCTACCg Totally 3 motifs of 3 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 1324. Group RE: AC-I /Group TF: PtMYB4 /AC: RSP01453//OS: Pinus taeda /GENE: Synthetic OLIGO/RE: AC-I /TF: PtMYB4 1341. Group RE: Box-I /AC: RSP01472//OS: Pisum sativum /GENE: PsCHS1/RE: Box-I /TF: unknown ||Identical REs AC: RSP01528 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0024G09.30|complement(2380355..2382397) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +67 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.39 G - 0.19 T - 0.20 C - 0.22 1 tagtagcaag aaagtgaacc atttccattt tttaataaaa aaataaaacc 51 tgaatcatat cagaatggct ggaaaaattc cttttatttt ctcctccttt 101 atactaggaa agaacagccg acgtggcgat caacgATTGG tcgactgagc 151 aagcaaccca cgaacagata agacggataa acacaccgtc gctaaagaag 201 AAACACAAAG AAACCAACTC CGACGACCAC CGGAGTCGGA GAGCATCAAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00208 Mean Expected Number 0.000 -strand -74 : -85 GCCACGTCgGCT AC RSP00248 Mean Expected Number 0.002 -strand -74 : -83 GCCACGTCgG AC RSP00986 Mean Expected Number 0.001 -strand -75 : -82 CCACGTCG AC RSP01034 Mean Expected Number 0.006 +strand -80 : -74 ACGTGGC Totally 4 motifs of 4 different REs have been found Description of REs found 201. Group TF: MAT2 (ROM2) /AC: RSP00208//OS: French Phaseolus vulgaris /GENE: DLEC2/RE: DLEC2,A /TF: MAT2 (ROM2) 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 907. Group RE: G-box /Group TF: GBP /AC: RSP00986//OS: Antirrhinum majus /GENE: gPAL2/RE: G-box /TF: GBP 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0024G09.31|2383175..2385399 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +91 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.11 T - 0.34 C - 0.22 1 atcactattc tcctttacct acttttactt atcaaccaat cacacatttc 51 ctccgattat tctcacctat tttttattaa taaccgtacc aacctaaaaa 101 aaatgtctac attttgggat aagggaaACA ATttggcaaa aagatctatg 151 agcactcatc tgtaaaaata aataattcat tagggtgtaa tttgtaaatt 201 GTCTTGAGTC TTTACGAACA AATCCCTATC CTGCATACCG CCATCGTCTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00377 Mean Expected Number 0.008 +strand -167 : -158 AACCAATCaC AC RSP01303 Mean Expected Number 0.001 -strand -12 : -21 TAcACCCTAA AC RSP01305 Mean Expected Number 0.000 -strand -12 : -21 TaCACCCTAA AC RSP01475 Mean Expected Number 0.001 -strand -84 : -92 CCAAAATGT AC RSP01642 Mean Expected Number 0.007 +strand -100 : -91 AAATGTCTaC Totally 5 motifs of 5 different REs have been found Description of REs found 362. Group RE: LS5 /AC: RSP00377//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS5 /TF: unknown 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown 1198. Group RE: Telo box /AC: RSP01305//OS: Nicotiana tabacum /GENE: Thio h2/RE: Telo box /TF: unknown 1343. Group RE: GCAA-like motif /AC: RSP01475//OS: Oryza sativa /GENE: GluA-3/RE: GCAA-like motif /TF: unknown 1462. Group RE: ARE /AC: RSP01642//OS: Nicotiana tabacum /GENE: WIPK/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0024G09.32|complement(2385407..2387286) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +80 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.18 T - 0.26 C - 0.29 1 atgatgtatg tccttacatt tttcagctgc tcgtggcaaa aacatatgaa 51 cctcgtttat gatctgggat ggctccaaga aaagcatggc caccctccaa 101 ccaccaaaca ccccctagaa taggttggca acttaaccgc tccaccagaa 151 tttagccctt gtcaccacta taactcagaa attggttccc tcagggttgc 201 CAACTTTAGG ATAGAGTCCA TTTCTTGCCT GATCAGCTCC TCCCAAAGCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00036 Mean Expected Number 0.009 +strand -96 : -89 CAAACACC AC RSP01209 Mean Expected Number 0.007 -strand -117 : -126 CTTTTCTTGG Totally 2 motifs of 2 different REs have been found Description of REs found 35. Group TF: ABI3 /AC: RSP00036//OS: Brassica napus /GENE: napA/RE: ABRE Bp /TF: ABI3 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0024G09.35|2400078..2402749 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +116 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.18 G - 0.27 T - 0.18 C - 0.38 1 cgtatacacg aatcagtaat aaaccgcgta ggagtccacc acatcaaata 51 ccgggcccac atgtcggtca gaccgcaggt aggaccagcc aggcaagcgg 101 ttctccttcc ctggctgaca tgtgggcccg cacgccactc gcgcaccggg 151 ccgtggtgat gggcccgagt ccgactcgaa cccgatctcc tctcctctct 201 CTCTTCTCGT CGTGCGCCTC CTCCCCGCGG CGACGGCTTC CGCGAGCCGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00095 Mean Expected Number 0.003 +strand -79 : -71 GTGGGCCCG AC RSP00095 Mean Expected Number 0.006 -strand -141 : -149 GTGGGCCCG AC RSP00864 Mean Expected Number 0.001 -strand +4 : -5 AGAGAGAGA Totally 3 motifs of 2 different REs have been found Description of REs found 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0024G09.36|2403277..2404853 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +83 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.18 T - 0.33 C - 0.30 1 aactcaatta atcatacgtt aatatcacat cggttgatga taatgcctac 51 cacctgaata atctctcccc tttgggaagg ctctctcaag tctcaaccca 101 aggactcgaa ctggctggtc ccacctgtcA TTGGctttaa tatggtcgac 151 gcatcgtcct gaaggtgtct gcttgctttt ctttctttct ttttttttct 201 CTCGCTTCCA AGTTACGCCC GCCGTTAAAC CCTAGCTCCT TCCCCGGCGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00304 Mean Expected Number 0.008 -strand -71 : -78 TGACAGGT AC RSP00444 Mean Expected Number 0.000 -strand -6 : -19 AAaAAAGAAAGAAA AC RSP00444 Mean Expected Number 0.000 -strand -10 : -23 AAGAAAGAAAGAAA AC RSP00860 Mean Expected Number 0.009 -strand -11 : -19 AGAAAGAAA AC RSP00860 Mean Expected Number 0.009 -strand -15 : -23 AGAAAGAAA AC RSP00881 Mean Expected Number 0.006 -strand -160 : -169 ATCAtCAACC Totally 6 motifs of 4 different REs have been found Description of REs found 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 424. Group TF: Dof1 /AC: RSP00444//OS: Zea mays /GENE: cyPPDK1/RE: box d /TF: Dof1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 817. Group TF: Dof family /AC: RSP00881//OS: Hordeum vulgare /GENE: Al21/RE: M2 /TF: Dof family ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0024G09.37|2411073..2411874 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +81 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.19 T - 0.29 C - 0.26 1 tgtggtctaa gtaaacaggt cctgtccaag ttgatggtga acgttttggg 51 ttttagacga aatttgatgg tgaacgaagt tgatggtgaa cgttttactt 101 aaaaacgttc accatcaact aggacaggag agaaagaatc cgcccgcacc 151 caccgttccc ttcgttatat atacccttcg acacccccct cctcctcttc 201 AGATCTCTCT CTCCTTCCTA GCAAGCTCGA TTTCTTAGAC CATCAAAGAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00621 Mean Expected Number 0.002 +strand -15 : -7 CCCCTCCTC AC RSP00653 Mean Expected Number 0.005 +strand +5 : +15 cTCTCTCTCCT AC RSP00864 Mean Expected Number 0.002 -strand +12 : +4 AGAGAGAGA AC RSP00865 Mean Expected Number 0.002 -strand +14 : +6 GGAGAGAGA Totally 4 motifs of 4 different REs have been found Description of REs found 597. Group RE: C-rich Q /AC: RSP00621//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich Q /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0416D03.4|2450543..2453297 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +2194 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.14 G - 0.29 T - 0.31 C - 0.26 1 tccatgcata tcggcgccgc tcgccgtcgc cgccgacgct gaatagttct 51 ggaagtttgc cttgtcggcc gtcgtgtcct tctggtgcta aaagcccatc 101 tttttctcct tttttttttc ttttcctttt tttttggggg gcaactgtta 151 gaagagaggg aagggtgggc catattaagt ggggcccaca tgccgtatca 201 TATCCATGAC CTTTGTCCTT GCGTTGCCGG CGGCGGCGGC GGCGGCGGCT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00282 Mean Expected Number 0.010 +strand +1 : +7 TATCCAT AC RSP00295 Mean Expected Number 0.000 +strand -35 : -13 TGGGCC-- ** bp --GGCCCA AC RSP00295 Mean Expected Number 0.000 -strand -13 : -35 TGGGCC-- ** bp --GGCCCA AC RSP00349 Mean Expected Number 0.001 +strand -200 : -192 TCCATGCAT AC RSP00967 Mean Expected Number 0.007 +strand -111 : -106 AAAAGC AC RSP01040 Mean Expected Number 0.007 -strand -106 : -111 GCTTTT AC RSP01710 Mean Expected Number 0.006 +strand -31 : -22 CCATATTAAG Totally 7 motifs of 6 different REs have been found Description of REs found 273. Group RE: Amylase-element /AC: RSP00282//OS: Oryza sativa /GENE: Amy3D/RE: Amylase-element /TF: unknown ||Identical REs AC: RSP00675 286. Group TF: At-TCP20 /AC: RSP00295//OS: Arabidopsis thaliana /GENE: PCNA/RE: Box II ("CC", comp) /TF: At-TCP20 ||Identical REs AC: RSP00297 334. Group TF: VP1 (VIVAPAROUS1) /AC: RSP00349//OS: Zea mays, Zea mays /GENE: C1/RE: Sph-core /TF: VP1 (VIVAPAROUS1) 890. Group RE: D2 /AC: RSP00967//OS: Hordeum vulgare /GENE: ITR1/RE: D2 /TF: SAD; BPBF; 964. Group RE: Dof BS2 /Group TF: Dof family /AC: RSP01040//OS: Petroselinum crispum /GENE: Icy/RE: Dof BS2 /TF: Dof family 1518. Group TF: RIN /AC: RSP01710//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC Intermediate /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0416D03.28|complement(2527692..2528192) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +186 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.26 T - 0.14 C - 0.27 1 gaagccaaca aacacgacga ccaaaagaaa aaaaaagaaa ttgaaaaaaa 51 aacactatgg tgaccacggc gcgaagacct cggtgatgac gggcagacgg 101 cgatgtcggA CAATgtcgtt gtaggctgac tctaactacc atatactcta 151 acatatcagt tgaacatatt taccaggacg gtgtagccgc cgatcccggc 201 GATGGCAGCG AGCGGCACGA CGGAGGCCCA GAGCACGGCC CTCCCCAACG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00948 Mean Expected Number 0.006 -strand -27 : -33 GGTAAAT Totally 1 motifs of 1 different REs have been found Description of REs found 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0416D03.42|complement(2576367..2580378) |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +106 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.16 T - 0.15 C - 0.41 1 aacagacaag aacaaacgac aaacgcactg aataagcaca ggccatcata 51 aacccccatg gagtagtacg aagcatcagc tcgtcaggtc aaagctccct 101 gacatgtggg ccctacagac caccgacagg tgggacccac ccgtcatcat 151 catgaccgca ccaactcaac tctcactccc cctcacctcc ctcccccttc 201 CACCGTACAC CCCCAAAACC CCCCTGCCTT CTCTCGCCGA TTCCGCCACC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00383 Mean Expected Number 0.008 +strand -114 : -108 GGTCAAA AC RSP01641 Mean Expected Number 0.004 -strand -190 : -199 TCTTGTCTgT Totally 2 motifs of 2 different REs have been found Description of REs found 368. Group TF: WRKY1 /AC: RSP00383//OS: Petroselinum crispum /GENE: WRKY1/RE: WA /TF: WRKY1 1461. Group RE: ARE /AC: RSP01641//OS: Nicotiana tabacum /GENE: P-450/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0416D03.43|complement(2581788..2584349) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +811 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.16 T - 0.35 C - 0.20 1 gcaagatgga gccatagatt catagtaatt ctttctattt tattcctttt 51 taattcacct tgtggtaaca gccaatgtaa aatttctgct gtatttcata 101 ctcttctgag taacctgagc aagtgagcag cacactactc tgaTCAATta 151 tcggtgcatg tctgtccatt tcgattatca gagaatgcga aaagtatatc 201 ACTATAAGCC ATCATATCAC TTGAAACACT TTGGTAAGTC AATAATTCAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00016 Mean Expected Number 0.007 -strand -41 : -47 CATGCAC Totally 1 motifs of 1 different REs have been found Description of REs found 15. Group RE: RY /AC: RSP00016//OS: Glycine max /GENE: beta-conglycinin/RE: RY /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0416D03.44|complement(2586637..2590407) |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +88 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.18 T - 0.26 C - 0.31 1 atgtactagt ttcttttgct tgaaaaaata aaagaagcag ataatttcta 51 gagaagtcca gagaataaaa agattggtgg tgggagtggg acccacctgt 101 cATTGTcgga ggagcctgcc tcgcctcatg tgatcccatc ggaggccaca 151 cctctgctcc ccctatatta tcctgtccat ggtgtttttc ttcctcctcc 201 ACAAAAACCA AAATCCAATC TCCAGCTCTC TTCCCCCCCC CCCCCCCCCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00122 Mean Expected Number 0.003 -strand -115 : -121 CTCCCAC AC RSP00304 Mean Expected Number 0.009 -strand -99 : -106 TGACAGGT AC RSP01250 Mean Expected Number 0.009 +strand +10 : +19 AAAATcCAAT Totally 3 motifs of 3 different REs have been found Description of REs found 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0434B04.12|complement(2610474..2619993) |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +3919 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.23 T - 0.25 C - 0.31 1 atgcatcaaa aatggcattg gtgtaattat cttctcttta catatactgc 51 atacgtcaag tcagaggaac gtggtggctg acatgtgagc cccaccgctc 101 acgggcccac ctgtcagtga ccacgtcagg tgcgaggatc cgctttccca 151 gtagaggctc cagtaggcag gttaggtcag gtcaggtacg gacgcatccc 201 CTCGATTCCC CTCTCCCCTC ACTTTCTCTC TCTCTCTCTC TCTCGACGCG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00018 Mean Expected Number 0.007 -strand -188 : -194 ATTTTTG AC RSP00095 Mean Expected Number 0.002 -strand -91 : -99 GTGGGCCCG AC RSP00214 Mean Expected Number 0.006 -strand -73 : -80 TGACGTGG AC RSP00215 Mean Expected Number 0.006 +strand -80 : -73 CCACGTCA AC RSP00230 Mean Expected Number 0.004 -strand -23 : -32 gACCTAACCT AC RSP00248 Mean Expected Number 0.009 +strand -81 : -72 aCCACGTCAG AC RSP00303 Mean Expected Number 0.001 -strand -89 : -100 AGGTGGGCCCGT AC RSP00304 Mean Expected Number 0.008 -strand -85 : -92 TGACAGGT AC RSP00864 Mean Expected Number 0.002 -strand +43 : +35 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +41 : +33 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +39 : +31 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +37 : +29 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +35 : +27 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 -strand +33 : +25 AGAGAGAGA AC RSP01115 Mean Expected Number 0.007 +strand -194 : -188 CAAAAAT AC RSP01174 Mean Expected Number 0.007 +strand +10 : +20 CCTCTCCCcTC AC RSP01283 Mean Expected Number 0.000 -strand +44 : +28 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 -strand +42 : +26 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 -strand +40 : +24 GAGAGAGAGAGAGAGAA AC RSP01660 Mean Expected Number 0.000 -strand -141 : -152 CTTGACGTATgC Totally 20 motifs of 13 different REs have been found Description of REs found 17. Group TF: SEF4 /AC: RSP00018//OS: Glycine max /GENE: beta-conglycinin/RE: SEF4 /TF: SEF4 93. Group TF: GCBP-2 /AC: RSP00095//OS: Zea mays /GENE: GapC4/RE: GCBP-2 BS /TF: GCBP-2 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 223. Group TF: PcMYB1 /AC: RSP00230//OS: Petroselinum crispum /GENE: CHS-1/RE: MRECHS /TF: PcMYB1 241. Group TF: REB /AC: RSP00248//OS: Oryza sativa /GENE: alpha-globulin/RE: REB2 /TF: REB 290. Group TF: PCF1; PCF2 /AC: RSP00303//OS: Oryza sativa /GENE: PCNA/RE: IIa /TF: PCF1; PCF2 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1034. Group RE: CCAAT box-like motif 2 /AC: RSP01115//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 2 /TF: unknown 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown 1478. Group TF: STF1/HY5 /AC: RSP01660//OS: Arabidopsis thaliana /GENE: CKX5/6 (At1g75450)/RE: C/A-box /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0434B04.16|2629419..2634631 |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +20 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.25 T - 0.17 C - 0.27 1 aacttatttc tctttttaaa acaagcccag tgccaagata ttttgagacg 51 gacgtcacaa gcccatagaa aatgaagcat cggcccatac tggcccatcc 101 agacgaggat gaaggggata ttctcgtagt atcacacact tcacaccacg 151 tcaccacgcc ctctctgctc agcagattaa acaagacaaa aaaaaaacaa 201 CGGCGGGGCG GGGCGCCGAC ATGGACGGCG GCGGCGGGGG CGATCCGGGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00214 Mean Expected Number 0.005 -strand -48 : -55 TGACGTGG AC RSP00215 Mean Expected Number 0.005 +strand -55 : -48 CCACGTCA AC RSP00445 Mean Expected Number 0.000 -strand -183 : -192 tAAAAAGAGA AC RSP00654 Mean Expected Number 0.009 +strand -68 : -59 CACaCACTTC AC RSP00701 Mean Expected Number 0.004 -strand +49 : +42 CCCGGATC AC RSP01326 Mean Expected Number 0.007 -strand -153 : -159 TCTCAAA AC RSP01280 Mean Expected Number 0.002 -strand -46 : -56 GGTGACGTGGt Totally 7 motifs of 7 different REs have been found Description of REs found 207. Group TF: TGA1; GBF1 /AC: RSP00214//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: TGA1; GBF1 ||Identical REs AC: RSP01257 RSP01474 208. Group TF: HBP-11(17); HBP-1b(c38) /AC: RSP00215//OS: Triticum aestivum /GENE: H3/RE: Hex /TF: HBP-11(17); HBP-1b(c38) 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 628. Group RE: CT-B /AC: RSP00654//OS: Spinacia oleracea /GENE: PetH/RE: CT-B /TF: unknown 667. Group RE: Oct (d) /AC: RSP00701//OS: Triticum aestivum /GENE: H3/RE: Oct (d) /TF: unknown 1089. Group TF: ABF-2 /AC: RSP01326//OS: Pisum sativum /GENE: AB80/RE: AB1 heptamer /TF: ABF-2 ||Identical REs AC: RSP01326 1179. Group TF: OBF4; OBF5 /AC: RSP01280//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: Hex motif /TF: OBF4; OBF5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0434B04.17|complement(2637802..2641467) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.21 T - 0.19 C - 0.29 1 aaactcgagc attacatgag tgacttaaat tgaacttttt ccgcgtgaga 51 actagcaagt gggctgggcc gtgtccaccg tgccgctagc gggccggtcc 101 gcagaagaca aaacaccggg ccatgtcgac acggcctact ttgtcagttc 151 catcagacac aaagccacaa caaaagtcta aacctctagc tacccaaacc 201 AAACCCTAAT TTCTCTTCTC AAAAAAAAAA AAAAAATCCA GCGGCGGCGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00279 Mean Expected Number 0.004 -strand +9 : +1 TTAGGGTTT AC RSP00369 Mean Expected Number 0.004 +strand +1 : +9 AAACCCTAA AC RSP01004 Mean Expected Number 0.007 +strand -178 : -169 ACTTAAATtG AC RSP01250 Mean Expected Number 0.003 -strand -163 : -172 AAAgTTCAAT AC RSP01303 Mean Expected Number 0.006 +strand -1 : +9 cAAACCCTAA AC RSP01472 Mean Expected Number 0.003 +strand -16 : -6 TCTAgCTACCC AC RSP01621 Mean Expected Number 0.007 -strand -21 : -30 TAgACTTTTG Totally 7 motifs of 7 different REs have been found Description of REs found 270. Group RE: inverted Telo box /AC: RSP00279//OS: Arabidopsis thaliana /GENE: A-p40/RE: inverted Telo box /TF: unknown ||Identical REs AC: RSP00448 354. Group RE: telo-box /AC: RSP00369//OS: Arabidopsis thaliana /GENE: eEF1AA1/RE: telo-box /TF: unknown 929. Group TF: DEF/GLO /AC: RSP01004//OS: Antirrhinum majus /GENE: DEFH125/RE: CArG2 /TF: DEF/GLO 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C 1196. Group RE: Telo box /AC: RSP01303//OS: Arabidopsis thaliana /GENE: A1 EF-1alpha/RE: Telo box /TF: unknown 1341. Group RE: Box-I /AC: RSP01472//OS: Pisum sativum /GENE: PsCHS1/RE: Box-I /TF: unknown ||Identical REs AC: RSP01528 1441. Group TF: GmDof4; GmDof22 /AC: RSP01621//OS: Glycine max /GENE: Synthetic OLIGO/RE: E4 /TF: GmDof4; GmDof22 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0434B04.21|2649449..2700984 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +20 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.25 T - 0.28 C - 0.25 1 ttttttttta taataatggc taaaatttgg cttggaaagt cacttggaga 51 ggctgttgga tatgcggtgc agctatattt gagggagtca aagtggactt 101 acttccgatt caaaagccat ggcggagcat gggccgtttc actcgggcca 151 atgaggagga ggacccggcc tatgtagggt ttccttcctc tttctctgtc 201 TACTCGCACT CGCCGCCGCT GCCGTTCCCC ATCCCAAGTC CCAGACCAAA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00378 Mean Expected Number 0.009 -strand -109 : -115 TTTGACT AC RSP01134 Mean Expected Number 0.007 +strand +38 : +47 GTcCCAGACC Totally 2 motifs of 2 different REs have been found Description of REs found 363. Group TF: WRKY1 /AC: RSP00378//OS: Petroselinum crispum /GENE: WRKY1/RE: WB /TF: WRKY1 1052. Group TF: CTF2 /AC: RSP01134//OS: Nectria haematococca /GENE: Cutinase/RE: CTF2 BS /TF: CTF2 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0434B04.34|complement(2695930..2700295) |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +429 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.23 T - 0.39 C - 0.14 1 tgtggaaaca tttccacacg gtttaaatac gttgtccgtg ggaatcagtg 51 tttttcttca ctgaagtgcc tgcccctgtg aagatttcat tttcttgtca 101 cctaattatt gattaggaAT TGAaattcta actaacaagg atatgtatgg 151 atatatggtt taattggtgt cttaagaaat ggtttagttg ctgttggtgg 201 GTGTTTGTCT GCATGTTTTC AGAAAGAGGT GCTTGTGTCA GCATCATTTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00808 Mean Expected Number 0.006 -strand -65 : -71 GTTAGTT Totally 1 motifs of 1 different REs have been found Description of REs found 761. Group TF: Pti4 /AC: RSP00808//OS: Arabidopsis thaliana /GENE: PDF1.2/RE: Myb1 /TF: Pti4 ||Identical REs AC: RSP00810 RSP00812 RSP00813 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0434B04.35-1|complement(2704511..2708224) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +86 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.27 T - 0.18 C - 0.35 1 gaaagcaatc ggtgatcaaa cggtgtgttt ttgcacactg aattttactt 51 ttgggggtcc atggaccggg tccatacaat caagagggcc ggatacgtcg 101 cataactccg gtgggtccaa cggcccagcg gcccgtgggc cccacacctt 151 cttgcccccg cgggatcaaa tacacctcct ccggccactc cccgatcccc 201 ACCTCGTCTC CACCGCACGA GCAGCAGCAG CAGCAGCGGC GGCCGCAGCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00339 Mean Expected Number 0.009 +strand -174 : -168 GTTTTTG AC RSP00471 Mean Expected Number 0.008 -strand -54 : -64 GTGTGGGGCCC AC RSP01250 Mean Expected Number 0.001 -strand -155 : -164 AAAATTCAgT Totally 3 motifs of 3 different REs have been found Description of REs found 324. Group TF: SEF4 /AC: RSP00339//OS: Glycine max /GENE: beta-conglicinin alfa'/RE: SEF4 BScons /TF: SEF4 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 1154. Group TF: CBF-C /AC: RSP01250//OS: Arabidopsis thaliana /GENE: AtpC/RE: CBF-C BS /TF: CBF-C ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.5|2714637..2718005 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +62 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.24 T - 0.27 C - 0.23 1 atacttgtga ttgagaacag agagagaaat gagagatttt tttttactga 51 acctgcgtgt ctgaactctt ctgaagataa aattgaaagt tgcagtactg 101 aactgaattt gcagcagatc acatggatga tATTGGcggg agagccggct 151 cagtcagctg cagctgccat aactgccacc gccaccccca catccactcc 201 GATTCATTGC GAATTCAGTT TGATCAGTGG TTGGTCGGTT GGCCAGCCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00629 Mean Expected Number 0.006 -strand -160 : -167 AAAAATCT AC RSP00651 Mean Expected Number 0.002 -strand +39 : +29 ACCgACCAACC AC RSP00864 Mean Expected Number 0.001 +strand -182 : -174 AGAGAGAGA AC RSP00987 Mean Expected Number 0.006 +strand -40 : -31 CAGCTgCCAT AC RSP00988 Mean Expected Number 0.001 -strand -59 : -70 CTCCCGCCAAtA AC RSP00989 Mean Expected Number 0.001 -strand -58 : -66 TCTCCCGCC AC RSP01470 Mean Expected Number 0.008 -strand -71 : -80 TCATcCATGT AC RSP01602 Mean Expected Number 0.005 -strand -185 : -192 TCTCAATC Totally 8 motifs of 8 different REs have been found Description of REs found 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 908. Group RE: H-box-like motif /AC: RSP00987//OS: Antirrhinum majus /GENE: CHS/RE: H-box-like motif /TF: unknown 909. Group TF: E2F/DP /AC: RSP00988//OS: Zea mays /GENE: RBR3/RE: E2F/DP I /TF: E2F/DP 910. Group TF: E2F/DP /AC: RSP00989//OS: Zea mays /GENE: RBR3/RE: E2F/DP IV /TF: E2F/DP 1340. Group TF: Opaque-2 (O2) /AC: RSP01470//OS: Zea mays /GENE: alpha-22kDa zein/RE: Z2 /TF: Opaque-2 (O2) 1423. Group RE: Inr /AC: RSP01602//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.10|complement(2728198..2736811) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +3487 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.17 T - 0.33 C - 0.22 1 catttccatt ctagtagtaa cctttacttc tttattcagg aaatggtagc 51 aacctgagcc gtagcttcga taagaaatca gattccatag ctcttgagta 101 gttATTGTta aagggtatat gtgtcttttc atctcttgta tacattatat 151 gtggtccttg accctaagtc aatagtacac agcaaattcc ccaaatttat 201 CTATCACTGG TATCAGAGCT CATGGGCTGA ACCCTATGTC ACACCCTGAA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00872 Mean Expected Number 0.009 -strand +45 : +36 gGTGTGACAT Totally 1 motifs of 1 different REs have been found Description of REs found 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.12|2739307..2744241 |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +353 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.30 G - 0.18 T - 0.35 C - 0.17 1 gaatgagaaa gagaagttgt atacttgtaa tcacgtgcta tcttttcgct 51 gttgcaatga aatttcctga tcacatgttc acatgaatca tatcggcagt 101 ttggcaggca gtttcagtgG CAATaagttc aactgtgtgc tgctcaacca 151 tttccttttc gaacaaatct atatatgttt tatctgttct tgagaatata 201 GTAAAGGAAC TTCTTTTCTG AAGACTGATT AAAAAAACAT GACCTTTGAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00861 Mean Expected Number 0.001 +strand -195 : -187 AGAAAGAGA AC RSP00966 Mean Expected Number 0.001 -strand -162 : -171 aGCACGTGAT AC RSP00978 Mean Expected Number 0.003 +strand -171 : -162 ATCACGTGcT Totally 3 motifs of 3 different REs have been found Description of REs found 797. Group TF: BPC1 /AC: RSP00861//OS: Arabidopsis thaliana /GENE: STK/RE: GA-2 /TF: BPC1 889. Group RE: G-box /Group TF: GBF /AC: RSP00966//OS: Antirrhinum majus /GENE: pallida/RE: G-box /TF: GBF 900. Group RE: G-box /AC: RSP00978//OS: Glycine max /GENE: vspA/RE: G-box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.15|2748946..2758356 |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.22 T - 0.30 C - 0.22 1 acatggacga aattggcggg gtagctggca gttttagtag cattaactgc 51 caactgtccg ctgctaatct gatttgatcc aaattatgtg gttattaatc 101 aaatcccata gccccataaa tacataatcc ccaaccggta agatgctcaa 151 acttgtatct tggtgcttct gatgttgcga tagtgtgatg cttgtacatc 201 TTGGAGGAGT AGAGTATCCC GGTCAAAGCC ATCAGCCATC TCGACGTTTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01435 Mean Expected Number 0.003 +strand -73 : -64 TCCCCAACCg Totally 1 motifs of 1 different REs have been found Description of REs found 1308. Group TF: RNFG2 /AC: RSP01435//OS: Oryza sativa /GENE: RSs1/RE: BoxII /TF: RNFG2 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.17|2762580..2765404 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +739 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.19 G - 0.14 T - 0.31 C - 0.35 1 taatacttta aattagtgtc taaatatagg gactaaagtt aactccctgg 51 atccaataca ctaccccaat atctctaaaa ttactggaca cggttgcatt 101 ctgcgacccg caaacgactt ttggatccgt aacccgttga cacccgcgac 151 ccctgttttc gcttttcttt gggccctcct ctctcctctc tctcttcctc 201 CATTGTTCCC CTCCTCCCCT TCTCTCCCCT CTCCTCCTCG CTTCCGGCGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01351 Mean Expected Number 0.004 +strand -32 : -22 tTGGGCCCTCC AC RSP01476 Mean Expected Number 0.004 -strand -189 : -196 TTTAAAGT AC RSP01708 Mean Expected Number 0.003 +strand -181 : -172 CTAAATATAG AC RSP01708 Mean Expected Number 0.003 -strand -172 : -181 CTATATTTAG Totally 4 motifs of 3 different REs have been found Description of REs found 1233. Group TF: CPRF1 /AC: RSP01351//OS: Arabidopsis thaliana /GENE: APX1/RE: DNase I footprint /TF: CPRF1 1344. Group RE: E motif /AC: RSP01476//OS: Oryza sativa /GENE: GluA-3/RE: E motif /TF: unknown 1516. Group TF: RIN /AC: RSP01708//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [MEF2] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.18-1|2766941..2770963 |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +156 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.19 T - 0.24 C - 0.28 1 atcataatag actctatatt ataatagaaa atattacata cagttttagt 51 ttcatttagg acagagggag tattacgtac actgtagtag tgagccgctt 101 tgatgaagtg gcgaagtgga gttgtgcacc gagtccacag caaaagagcg 151 cggaaaggag gaagaagata aagcatcccc cacctccgcc tcttcccctc 201 CAACGACTAC CTCTTCTTCC TCCTCTCGCA CCACCACCAC TCACCACCCC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00683 Mean Expected Number 0.005 +strand -90 : -81 GCgAAGTGGA AC RSP00847 Mean Expected Number 0.002 -strand -90 : -99 CCACtTCATC AC RSP00868 Mean Expected Number 0.001 -strand -175 : -186 TATTATAaTATA AC RSP00915 Mean Expected Number 0.001 +strand -99 : -90 GATGAAGTGG AC RSP00950 Mean Expected Number 0.006 +strand +40 : +50 CTCACCAcCCC Totally 5 motifs of 5 different REs have been found Description of REs found 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 789. Group RE: NON /AC: RSP00847//OS: Zea mays /GENE: H3C4/RE: NON /TF: unknown 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown 846. Group TF: Opaque-2 /AC: RSP00915//OS: Zea mays /GENE: b-32/RE: B3 /TF: Opaque-2 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.21|2788220..2792659 |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +51 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.29 T - 0.14 C - 0.33 1 cttctcatcc atttgcaata tcaaaatcac ggtgatgcct atcctgccac 51 caccgctgaa ctcgcggtta ctcgccagcg tcgccggccc gccacgtgta 101 cggctctgAT TGGaccgccc taccacgagt cagaagaggg gagaggagca 151 aagagaacaa cgacgagacg aatcgttgga gaagcgaagc gacgctactc 201 GACCCAGCGT CCACGGCGAG CGCCCCCCGC CGGCGACGGC GACGGCGAGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00002 Mean Expected Number 0.001 -strand -102 : -110 ACACGTGGC AC RSP00175 Mean Expected Number 0.007 -strand -103 : -110 CACGTGGC AC RSP00204 Mean Expected Number 0.006 -strand -101 : -110 tACACGTGGC AC RSP00231 Mean Expected Number 0.004 -strand -88 : -94 CCAATCA AC RSP00416 Mean Expected Number 0.010 +strand -195 : -189 CATCCAT AC RSP00682 Mean Expected Number 0.008 +strand -110 : -101 GCCACGTGtA AC RSP00783 Mean Expected Number 0.000 -strand -101 : -110 TACACGTGGC AC RSP01174 Mean Expected Number 0.006 -strand -55 : -65 CCTCTCCCcTC AC RSP01255 Mean Expected Number 0.003 -strand -102 : -109 ACACGTGG Totally 9 motifs of 9 different REs have been found Description of REs found 2. Group RE: ABRE-3 /AC: RSP00002//OS: Brassica napus /GENE: Oleosin/RE: ABRE-3 /TF: unknown 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 197. Group TF: ABI5 /AC: RSP00204//OS: Arabidopsis thaliana /GENE: AtEm6/RE: ABRE/6.2 /TF: ABI5 ||Identical REs AC: RSP01151 224. Group RE: CCAAT box 1 /AC: RSP00231//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CCAAT box 1 /TF: unknown 398. Group RE: Box-1 /AC: RSP00416//OS: Hordeum vulgare /GENE: EPB-1/RE: Box-1 /TF: unknown 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 738. Group TF: G-box binding TF /AC: RSP00783//OS: Nicotiana tabacum /GENE: OLIGO-GUS/RE: G-box 7 /TF: G-box binding TF 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a 1158. Group TF: GBF1 /AC: RSP01255//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS2 /TF: GBF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.22|2797317..2800503 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +233 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.14 T - 0.27 C - 0.36 1 gtaaattaca aaacccaaac gtataaaatt ctcttaaaat ttggatgaat 51 ccaggtcgat tcgattcttt ctgtgacgat tccaaattcc tttctgtctc 101 gtcttcttcc taatccttcc tgcatcgatt ctaactccgc gaccaactct 151 gcaccggcgc ccccaaccat aaataaccac ctcctcctcc ccttccgcct 201 CGCTCCCGCC TCCCGCGCCC GCGCATTGAA CAACTCGTCG ATCTGTCCGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00862 Mean Expected Number 0.005 -strand -106 : -114 AGAAAGGAA AC RSP01071 Mean Expected Number 0.008 +strand -185 : -176 CAAACGTAtA Totally 2 motifs of 2 different REs have been found Description of REs found 798. Group TF: BPC1 /AC: RSP00862//OS: Arabidopsis thaliana /GENE: STK/RE: GA-3 /TF: BPC1 989. Group TF: PvAlf /AC: RSP01071//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em1c /TF: PvAlf ||Identical REs AC: RSP01153 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.26|2807114..2811819 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1028 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.17 G - 0.25 T - 0.28 C - 0.30 1 aactttgttg ctcagcctgt cagataatgg gccatatctc gtgcttgcct 51 cgaatagttt gggcctttac acgggcccaa atgtatctct cttggttgta 101 gcccgttgca aatcatgggc tgcgcgctaa ccttcttgtg ggcctccttc 151 tggtattgtg ggcccaccaa aatgctaatc caccgcaagg tccattcact 201 GTTGGACAGA TCGCTCACGC GCGCGCTTCC GCCGGGGTCT CGTGCTCACC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01114 Mean Expected Number 0.005 +strand -34 : -28 CCAAAAT Totally 1 motifs of 1 different REs have been found Description of REs found 1033. Group RE: CCAAT box-like motif 1 /AC: RSP01114//OS: Agrobacterium tumefaciens /GENE: ags/RE: CCAAT box-like motif 1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0009G03.36|2836735..2840314 |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +46 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.42 G - 0.14 T - 0.22 C - 0.22 1 tccagataca tatcctgaac ggaaggtatt tagaacaaac aaacaaaggg 51 agtactatat tataaagtca aacgaagtgt tccagaaatg gaaaaaagga 101 attaaaagaa tGCAATcaac aaactgtcat catctccaaa tttgcttcaa 151 agaccatcta tactctccat ataatacgga cagccattgg tactaagata 201 TAGCACTACC ACTCTCACAA ACCAATCAAG AAACACAATA CGTCCCATGA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00868 Mean Expected Number 0.003 +strand -148 : -137 TAcTATATTATA Totally 1 motifs of 1 different REs have been found Description of REs found 804. Group RE: TA-rich motif /AC: RSP00868//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: TA-rich motif /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0030H07.31|complement(2889722..2891509) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +49 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.22 T - 0.27 C - 0.25 1 ggcacctttg ccgatgacat ccgctcggct ttctacatcc atcgttccga 51 cattcagatc acaaaattcc atccagaaga tttcttcctc actttcgtta 101 atcatagcga tcgtgaggag gttctgcaag aaccaagATT GGtgacccga 151 agcggaagag tgtatcattt caatccttgg aatgaaaggc gaaatgctga 201 AGTTGTTGAC ATTCGCTACC ACGCCCGAGT CTGCATTGAA GGTATCCCGA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00941 Mean Expected Number 0.005 +strand -33 : -26 TTTCAATC AC RSP01594 Mean Expected Number 0.005 -strand -26 : -33 GATTGAAA Totally 2 motifs of 2 different REs have been found Description of REs found 870. Group TF: GBF /AC: RSP00941//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box I /TF: GBF 1416. Group RE: Box I /AC: RSP01594//OS: Pisum sativum /GENE: rbcS-3.6/RE: Box I /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0030H07.45|2922737..2925567 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1491 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.29 T - 0.22 C - 0.29 1 actttttgta aaaaacgaac cgtttagtag tttgaaaagc gtgcgcgagg 51 aaatcgtgta gcagaggatg ggaacagcca cggccgaaca cagcctgtca 101 acgtgcagct cctccgataa catgggccgg tatctgtaaa tgggccgaaa 151 ggggggtccc gctttacagg tcgtggtctg ctcgtcgtct tcgactcttc 201 ATCGCCACTC GCCTCCCTCC TCCTCTCAGG CCGGCGGCTG CGGCAGCGGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00394 Mean Expected Number 0.009 -strand -33 : -39 TGTAAAG AC RSP00866 Mean Expected Number 0.004 -strand -95 : -102 GCACGTTG AC RSP00874 Mean Expected Number 0.010 +strand -57 : -47 GCCgAAAGGGG AC RSP01019 Mean Expected Number 0.009 -strand +2 : -5 ATGAAGA Totally 4 motifs of 4 different REs have been found Description of REs found 377. Group TF: PBF-1 /AC: RSP00394//OS: Zea mays /GENE: gamma-27kDa zein/RE: P-box (s) /TF: PBF-1 ||Identical REs AC: RSP00396 RSP00429 RSP01402 802. Group RE: G-box /AC: RSP00866//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: G-box /TF: unknown 810. Group TF: Dof3 /AC: RSP00874//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof3 BSopt /TF: Dof3 944. Group TF: GAPF /AC: RSP01019//OS: Arabidopsis thaliana /GENE: GapB/RE: Gap box 1 /TF: GAPF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0030H07.46|2927604..2929688 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1111 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.31 G - 0.21 T - 0.22 C - 0.27 1 taaagatgca atgaaaaaat atagataaaa tcatatcata acgtaatttt 51 attttgatgc taaccgcaca attacgcggg ccctgaaaca gcacacgaag 101 tcaggaaacg tcaacgtgca gcacctccgg caactccgat tacggcggca 151 tcggggcggg ccggtatttg taaatggcca aaggaagcaa accattaggc 201 TACTACTACT ACTACCCGTG CTCATCCATC ATCGTCCTCG ACTCCTCGCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00866 Mean Expected Number 0.004 -strand -82 : -89 GCACGTTG AC RSP00918 Mean Expected Number 0.007 -strand -86 : -95 GTTGACGTTT AC RSP01086 Mean Expected Number 0.009 -strand -87 : -96 TTgACGTTTC AC RSP01501 Mean Expected Number 0.005 +strand -47 : -41 GGGCGGG AC RSP01511 Mean Expected Number 0.003 +strand -56 : -49 GCGGCATC Totally 5 motifs of 5 different REs have been found Description of REs found 802. Group RE: G-box /AC: RSP00866//OS: Nicotiana tabacum /GENE: NiPMT1a/RE: G-box /TF: unknown 849. Group TF: Opaque-2 /AC: RSP00918//OS: Zea mays /GENE: O2/RE: B5-like motif /TF: Opaque-2 1004. Group TF: bZIP TF /AC: RSP01086//OS: Helianthus annuus /GENE: sHSP/RE: bZIP BS /TF: bZIP TF 1361. Group RE: GC-box /AC: RSP01501//OS: Triticum aestivum /GENE: H1 (TH315)/RE: GC-box /TF: unknown ||Identical REs AC: RSP01502 1365. Group RE: OLS /AC: RSP01511//OS: Triticum aestivum /GENE: H1 (TH315)/RE: OLS /TF: unknown ||Identical REs AC: RSP01512 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0030H07.55|complement(2953968..2955243) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +32 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.18 T - 0.26 C - 0.22 1 ccgttctgaa aagtaacact ccttccatct ttttctcaaa aaaaaaagag 51 aaaaatatct actaagtctt gacagccaaa gtcatggttt ggcgatcaag 101 gcaacgacta ggattaggaa gcttcgtgtc aaccgattaa ttatctaatt 151 aattaattag cccatctgct tacttaaacg aaacaaccgt gtttaattag 201 GCACTAAGCG TTGGCACACT GAAGAAGTAA CCATGTCCGG GCACGCCGCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.004 +strand +44 : +50 CGCCGCG AC RSP00331 Mean Expected Number 0.007 +strand +27 : +35 GTAACCATG AC RSP00445 Mean Expected Number 0.001 +strand -159 : -150 AAAAAAGAGA AC RSP00681 Mean Expected Number 0.003 -strand -58 : -66 TAATTAATC AC RSP01056 Mean Expected Number 0.004 -strand -181 : -191 AgTGTTACTTT AC RSP01757 Mean Expected Number 0.002 -strand -128 : -135 GTCAAGAC Totally 6 motifs of 6 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 976. Group TF: GT-3a /AC: RSP01056//OS: Arabidopsis thaliana /GENE: cab2/RE: GT-3a Box III (3) /TF: GT-3a 1562. Group TF: B /AC: RSP01757//OS: Glycine max /GENE: a2/RE: BBS /TF: B ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.18|complement(2967932..2973811) |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +541 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.32 G - 0.24 T - 0.31 C - 0.13 1 tacccaaagt gccatttctg gactaaagag gaattctgac attatgaggt 51 agttataaat ctactaacaa gcatctagac tcttattggg ggagaaaggg 101 ggggggggtc ctatgcattt atttaggaat ttatatactt cttgtggaca 151 atttgaaact taaatacttt tgttactcta atatgtttat gtcgcttcag 201 AATAGATGCT GAAGCTGTAG AGTTGTGGAA GAAACTAAAT GAGAAGGAGA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00642 Mean Expected Number 0.008 -strand -80 : -87 TAAATGCA Totally 1 motifs of 1 different REs have been found Description of REs found 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.20|2979343..2982896 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +728 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.31 C - 0.24 1 ctcctgtaat ctgttgctca ggatacgcat gccgaattgc cagccatgtg 51 tagatgaccg cactgctgct ccaagaaaaa tctctgaagt ttgtagtatc 101 ttGCAATaat aacacggcat cagtttctga gtgtatcttg tcagtattaa 151 ttccagtcag ccatgaattc ccttttgttt tcagagtaca ggacactgac 201 TGCATTTCTT TTCATACCCT CGAGAGGAAA AGGCCACCAT GCTTCCGATT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00254 Mean Expected Number 0.008 -strand +33 : +27 CCTTTTC AC RSP00629 Mean Expected Number 0.006 +strand -125 : -118 AAAAATCT Totally 2 motifs of 2 different REs have been found Description of REs found 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.21|complement(2983131..2986083) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +359 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.17 T - 0.26 C - 0.27 1 taaaaaaaaa tctaaaaacg aaaaaaattc aacagtagca gagtaattgc 51 taatgggcct ttcgtcttag atgggcctcc aaatcaatat gactagtccg 101 gaacgagtac tactgtgatt agaaatctcg gcccatagaa agcccatata 151 tagccaacag cccagcgtaa ttaattgacc tcggtctcct tgctccccta 201 TCTTTACCCT AGTCGATCTC CCCGTCGCTT CGGTCTCGAC TCCTCGTCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00057 Mean Expected Number 0.010 +strand +41 : +50 TCCtCGTCTC AC RSP00888 Mean Expected Number 0.003 +strand -195 : -187 AAAAATCTA Totally 2 motifs of 2 different REs have been found Description of REs found 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 820. Group TF: CCA1 /AC: RSP00888//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: CCA1 motif (2) /TF: CCA1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.25|complement(3000662..3002530) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +72 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.21 T - 0.27 C - 0.31 1 tacgcgcgca ttgccgtctc catgcaacct cgccaactgt acgcgctaaa 51 ccgcgcctaa ttcttaggcc actccagccc tcctcctcct cctcctcatc 101 ttcgatcgtc gtcaacctcc aaacccacaa agggatcttc ggtttctttc 151 ttggctttgc ataggtatat atatgtgcca tgtgtgcgtc tgctcgattc 201 GATTTGGGGA CTGGAGTTGT GTTGATGGAT AGGAACACGA ACAACAACAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00282 Mean Expected Number 0.007 -strand +31 : +25 TATCCAT AC RSP00313 Mean Expected Number 0.001 -strand -17 : -27 CACATGGCACa AC RSP00860 Mean Expected Number 0.003 -strand -50 : -58 AGAAAGAAA AC RSP01214 Mean Expected Number 0.003 -strand -68 : -77 CCTTTGTGGG Totally 4 motifs of 4 different REs have been found Description of REs found 273. Group RE: Amylase-element /AC: RSP00282//OS: Oryza sativa /GENE: Amy3D/RE: Amylase-element /TF: unknown ||Identical REs AC: RSP00675 299. Group RE: G-box /Group TF: GBF (CG-1) /AC: RSP00313//OS: Pisum sativum /GENE: rbcS-3A/RE: G-box /TF: GBF (CG-1) 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 1122. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01214//OS: Brassica oleracea /GENE: BoCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.27|complement(3010717..3011553) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +60 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.23 T - 0.23 C - 0.28 1 cttgccggtg aagacacggg aaattaccgg ccctctgtgt cactgacaac 51 ttgcgtaccc gcagtttcaa atttttttaa ccgcgagtat gcacattttt 101 cactcggccc cgaggtgaat aatctgttta caaccgtggg ccacacgtct 151 cttccaggct ggctgatgct aaagtactac tccgcgaagc gaagcattcc 201 AGAAACAAAC TGTCTAAGTC GAAGTGTCGA ACACCCACCG AGCGAGCGAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00110 Mean Expected Number 0.005 +strand -59 : -52 CACACGTC AC RSP01017 Mean Expected Number 0.004 +strand +1 : +8 AGAAACAA AC RSP01599 Mean Expected Number 0.003 +strand -136 : -129 TTTCAAAT Totally 3 motifs of 3 different REs have been found Description of REs found 108. Group RE: ACGT motif /AC: RSP00110//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: ACGT motif /TF: unknown 942. Group TF: AEF /AC: RSP01017//OS: Arabidopsis thaliana /GENE: GapA/RE: AE box 2 /TF: AEF 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.40|3034491..3035510 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +3 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.27 T - 0.19 C - 0.29 1 tcgccggcat aagtaacagg gggtaaatca atttcctgcg gcttctcacg 51 caaggaaccc aaattactat ccactgtaat taatatcctc gcaaaaatcc 101 gccgccgccg ccgcatccat acaagtagcc tctttcttcc acacgcggag 151 gcggtgcgtc caccgccatt acacaaaggg agagagctcg gggggtcgtt 201 GGAATGGAGA AACCGCAGCG CGAGCAGATG GCGCTGATGG TGCCGGAACT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00979 Mean Expected Number 0.008 +strand -84 : -75 CCATACAAgT AC RSP01108 Mean Expected Number 0.007 +strand -124 : -118 TAATTAA Totally 2 motifs of 2 different REs have been found Description of REs found 901. Group RE: Box I /AC: RSP00979//OS: Glycine max /GENE: vspA/RE: Box I /TF: unknown 1026. Group RE: rAT-1 /AC: RSP01108//OS: Spinacia oleracea /GENE: rps22/RE: rAT-1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.42|complement(3038282..3041150) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +150 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.31 T - 0.19 C - 0.24 1 aaaatacgga ggtgaaagcg cgtggagacc gagaagaaga tggcttcgca 51 gcgaagagat caagggagag aggcgagagg tggaagaggg tgaaagcgtg 101 cgactcccaa agagcgtcgt ctgctttaga aagcgtattt tctaggaaga 151 agacgtattc cagtgagttg gttttgaaag gcccagccgg cccagcccaa 201 GTAGGGTTGT TCTTCCCTAC TATCTCTCCC ACCTCCACCG CCTCCGGCCG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00122 Mean Expected Number 0.009 +strand +26 : +32 CTCCCAC AC RSP00357 Mean Expected Number 0.004 -strand -31 : -38 CAACTCAC AC RSP00565 Mean Expected Number 0.005 +strand -66 : -60 GTATTTT AC RSP00716 Mean Expected Number 0.000 -strand -25 : -33 CAAAACCAA AC RSP01702 Mean Expected Number 0.003 +strand -51 : -42 AAgACGTATT Totally 5 motifs of 5 different REs have been found Description of REs found 120. Group RE: Box C /AC: RSP00122//OS: Pisum sativum /GENE: AS1/RE: Box C /TF: unknown 342. Group RE: CARE1 /AC: RSP00357//OS: Oryza sativa /GENE: Rep-1/RE: CARE1 /TF: unknown 541. Group RE: AT-rich G /AC: RSP00565//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich G /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 1511. Group RE: ACGT1 /AC: RSP01702//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.43|3041289..3043930 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +147 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.19 G - 0.25 T - 0.24 C - 0.31 1 tcgccggaga ggcggccgga ggcggtggag gtgggagaga tagtagggaa 51 gaacaaccct acttgggctg ggccggctgg gcctttcaaa accaactcac 101 tggaatacgt cttcttccta gaaaatacgc tttctaaagc agacgacgct 151 ctttgggagt cgcacgcttt caccctcttc cacctctcgc ctctctccct 201 TGATCTCTTC GCTGCGAAGC CATCTTCTTC TCGGTCTCCA CGCGCTTTCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00357 Mean Expected Number 0.004 +strand -108 : -101 CAACTCAC AC RSP00565 Mean Expected Number 0.005 -strand -73 : -79 GTATTTT AC RSP00716 Mean Expected Number 0.000 +strand -114 : -106 CAAAACCAA AC RSP01702 Mean Expected Number 0.003 -strand -88 : -97 AAgACGTATT Totally 4 motifs of 4 different REs have been found Description of REs found 342. Group RE: CARE1 /AC: RSP00357//OS: Oryza sativa /GENE: Rep-1/RE: CARE1 /TF: unknown 541. Group RE: AT-rich G /AC: RSP00565//OS: Lycopersicon esculentum /GENE: rbcS3B/RE: AT-rich G /TF: unknown 681. Group RE: GT motif /AC: RSP00716//OS: Arabidopsis thaliana /GENE: Adh/RE: GT motif /TF: unknown 1511. Group RE: ACGT1 /AC: RSP01702//OS: Arabidopsis thaliana /GENE: XERO2/RE: ACGT1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.44|3044230..3048996 |SUPPORT|11 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +48 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.20 T - 0.26 C - 0.27 1 aacggttttg aattcagtga attcaaataa accgagatag aatgcgtgtg 51 ccagtttagt cgcgaaacat tcagaattca tcgaaaattg ctaaaaattt 101 aaaatcaaac acgatgtact ctacttcagt atcaagttgg gccacacggg 151 tgaggcctac tcactagccg cctcaaatcc ggcccagtct accgccttgc 201 GTGCTCGTTT ACTCCTCCGT CGATTTCCAC TTTCGCCAAA CCTCGCGGCC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00837 Mean Expected Number 0.007 -strand +26 : +17 AaATCGACGG AC RSP01075 Mean Expected Number 0.004 -strand -51 : -60 CCCGtGTGGC AC RSP01767 Mean Expected Number 0.002 +strand -109 : -101 TAAAAATTT Totally 3 motifs of 3 different REs have been found Description of REs found 782. Group RE: NON /AC: RSP00837//OS: Arabidopsis thaliana /GENE: H4A748/RE: NON /TF: unknown 993. Group TF: CpbZIP1; CpbZIP2 (short) /AC: RSP01075//OS: Craterostigma plantagineum (Scrophulariaceae) /GENE: CpC2/RE: ABRE II /TF: CpbZIP1; CpbZIP2 (short) 1570. Group RE: AT-rich element /AC: RSP01767//OS: Zea mays /GENE: Bz1/RE: AT-rich element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.45|complement(3049043..3049953) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +31 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.21 T - 0.25 C - 0.30 1 atgaaagaga cttggttttt aatcctttat ctgaaaaaca tagggcctgc 51 accttaattg tggctttgaa atcgcatttg aatatggaga aacacaagaa 101 aagggagTCA ATggcatcag acggctccca gctcatccga cggcgaatcg 151 ggtagatcag ctcgctctct agccttcgca cgccaagcag ctcagcttcc 201 GCTTCCGCTT CCGCTCTCTT CTCCGCACCT CATGGCGTCC CTCCTCTCCC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00254 Mean Expected Number 0.007 -strand -97 : -103 CCTTTTC AC RSP00385 Mean Expected Number 0.003 -strand -129 : -136 ATTTCAAA AC RSP01003 Mean Expected Number 0.008 -strand -140 : -149 ACAATTAAGG AC RSP01497 Mean Expected Number 0.008 -strand -57 : -66 GCCGTCGGAT AC RSP01497 Mean Expected Number 0.008 -strand -76 : -85 GCCGTCtGAT AC RSP01600 Mean Expected Number 0.003 -strand -130 : -137 TTTCAAAG Totally 6 motifs of 5 different REs have been found Description of REs found 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 370. Group RE: ERE-core /AC: RSP00385//OS: Dianthus caryophillus /GENE: GST1/RE: ERE-core /TF: unknown ||Identical REs AC: RSP00893 928. Group TF: DEF/GLO /AC: RSP01003//OS: Antirrhinum majus /GENE: DEFH125/RE: CArG1 /TF: DEF/GLO 1359. Group RE: CS5 /AC: RSP01497//OS: Triticum aestivum /GENE: H1 (TH315)/RE: CS5 /TF: unknown ||Identical REs AC: RSP01498 1421. Group RE: Inr /AC: RSP01600//OS: Spinacia oleracea /GENE: RPS22/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0011G08.46|3051282..3054000 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.20 T - 0.16 C - 0.39 1 agggcaaaca aatcgacatg agaactttga aaaggggaac acacagtgag 51 ctgccactgc caggccggcg agtggcgacg ctgcaagacc gcgaaccatt 101 cagccaacaa ccaccccatg cgctgcacgc gtccccaacg gaaattccgt 151 atcaatcatc tccctcccca accctcccct tctccctcgc ggagtcgcac 201 CACTGACTTC CCACACAGAC TGCTCCGAGC TCTCCATTCC CGCGACCCAT 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00254 Mean Expected Number 0.008 -strand -166 : -172 CCTTTTC AC RSP01600 Mean Expected Number 0.001 -strand -169 : -176 TTTCAAAG Totally 2 motifs of 2 different REs have been found Description of REs found 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 1421. Group RE: Inr /AC: RSP01600//OS: Spinacia oleracea /GENE: RPS22/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.2|complement(3055366..3056520) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +42 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.17 T - 0.31 C - 0.26 1 tggcatcttc tggatgcaca ccaaattcat catctcgaac cagattccat 51 gctcaaaagc ttgctggaaa aggagctttt atttcctcct gcttttctcc 101 accgctaatc ttgatgccat cttgcttgat gaaattttct actccaggca 151 tggcaggcga aaaggccaat aaaagcgtaa attctttctc catttcagct 201 CAGAAAAAAA CTGGCTCAGC TGTTCTGGTC TTGAGCTCTT CTTCCTCAAC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00254 Mean Expected Number 0.006 -strand -36 : -42 CCTTTTC AC RSP00254 Mean Expected Number 0.006 -strand -128 : -134 CCTTTTC AC RSP00331 Mean Expected Number 0.007 +strand -158 : -150 GATTCCATG AC RSP01013 Mean Expected Number 0.010 -strand -5 : -14 gAAATGGAGA AC RSP01209 Mean Expected Number 0.004 -strand -26 : -35 CTTTTATTGG Totally 5 motifs of 4 different REs have been found Description of REs found 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 317. Group TF: S1F /AC: RSP00331//OS: Spinacia oleracea; Pisum sativum; Arabidopsis thaliana; /GENE: prs 1 and RPL21 (spinach), rbcS-3a (pea, tomato, Arabidopsis),/RE: S1, consensus /TF: S1F 938. Group TF: GAPF /AC: RSP01013//OS: Arabidopsis thaliana /GENE: GapA/RE: Gap box 1 /TF: GAPF 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.5|complement(3064752..3068040) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +153 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.41 G - 0.16 T - 0.27 C - 0.16 1 aatatgccta tcaaaaataa aattttcaga tttgaaaata tgactatcaa 51 aaatagatgg agggagtatg atataatgtg aaaaaatata tataataatg 101 ctagccgtgt aatctgtact aatttaaata aaatgctagg aggaaactag 151 ggacatccac tcgaccaata aaaagtttgc cccgcaactc acatcgatcc 201 CAATGGAAGC TTTATTGCTA TAAACTTGAA ATCTCCCTCC AAGTAGAGAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00280 Mean Expected Number 0.005 +strand +38 : +47 TCCAaGTAGA AC RSP00357 Mean Expected Number 0.003 +strand -16 : -9 CAACTCAC Totally 2 motifs of 2 different REs have been found Description of REs found 271. Group TF: Opaque-1 /AC: RSP00280//OS: Zea mays /GENE: alpha-22kDa zein/RE: O2-box /TF: Opaque-1 342. Group RE: CARE1 /AC: RSP00357//OS: Oryza sativa /GENE: Rep-1/RE: CARE1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.9|complement(3082254..3087690) |SUPPORT|13 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +81 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.37 G - 0.19 T - 0.22 C - 0.22 1 taaggataag ggaattaata tatacaacgt gtcgaaattt tgagtcaatt 51 tgccaactat ggataaaaaa ttacaaattc aaaaagaaac ttgttgcccg 101 acagatcagc ccacacaaag tttgaaggct aaaagcCCAA Tctggggggc 151 gcaagaattc cagcccaagt tataaaaatc acgaaatatc ttggatctga 201 CAGTCTGACA GCAAAAGGCC ACACTCCTCA CAAATCTCGT GCGCGCCACC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00039 Mean Expected Number 0.009 -strand -120 : -130 TGAATTTGTaA AC RSP00188 Mean Expected Number 0.003 +strand -177 : -168 aCAACGTGTC AC RSP00933 Mean Expected Number 0.003 -strand -124 : -136 TTTgTAATTTTTT AC RSP01030 Mean Expected Number 0.009 +strand -116 : -109 AGAAACTT AC RSP01035 Mean Expected Number 0.008 +strand -174 : -168 ACGTGTC Totally 5 motifs of 5 different REs have been found Description of REs found 38. Group TF: GT-1 related TFs /AC: RSP00039//OS: Lycopersicon esculentum /GENE: LAT56; LAT59;/RE: 56/59 box /TF: GT-1 related TFs 182. Group TF: ABI5 /AC: RSP00188//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.2 /TF: ABI5 862. Group RE: AT-2a /AC: RSP00933//OS: Pinus sylvestris /GENE: GS1a/RE: AT-2a /TF: unknown 955. Group TF: AEF /AC: RSP01030//OS: Arabidopsis thaliana /GENE: GapB/RE: AE box 1 /TF: AEF 960. Group TF: ABI3; ABI5; AREB1 /AC: RSP01035//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 3 /TF: ABI3; ABI5; AREB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.16|complement(3104919..3110743) |SUPPORT|13 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +126 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.22 T - 0.24 C - 0.34 1 cgtaatgtct ccctgacagg tgggccacct ttgggctttc ccgtgggcgc 51 acagcggtaa atgcaggggt cctccaccat gcgggcccca cacatatccg 101 gtttcttctc agcctatgac atgtggggcc cacccgaacc agaacgtatt 151 tgtgtctccg tacataaagc tgcaaaggca agcgagagag tcggagatat 201 CACTACTACT ACTCCTCTTT CCCACTCCTC TCGCTTCCTT CCTCCTCCTC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00301 Mean Expected Number 0.007 +strand -30 : -24 TGCAAAG AC RSP00304 Mean Expected Number 0.005 +strand -187 : -180 TGACAGGT AC RSP00460 Mean Expected Number 0.003 -strand -76 : -85 cACATGTCAT AC RSP00471 Mean Expected Number 0.002 +strand -80 : -70 aTGTGGGGCCC AC RSP00471 Mean Expected Number 0.004 -strand -108 : -118 GTGTGGGGCCC AC RSP00642 Mean Expected Number 0.002 +strand -143 : -136 TAAATGCA AC RSP00873 Mean Expected Number 0.010 +strand -39 : -29 ACATAAAGCTG AC RSP00948 Mean Expected Number 0.005 +strand -145 : -139 GGTAAAT AC RSP01202 Mean Expected Number 0.004 -strand -167 : -174 CCAAAGGT AC RSP01642 Mean Expected Number 0.005 +strand -198 : -189 tAATGTCTCC Totally 10 motifs of 9 different REs have been found Description of REs found 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 291. Group TF: KN1/KIP /AC: RSP00304//OS: Zea mays /GENE: Synthetic OLIGO/RE: KN1/KIP BS /TF: KN1/KIP 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 449. Group TF: Alfin1 /AC: RSP00471//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS1 /TF: Alfin1 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 809. Group TF: Dof2 /AC: RSP00873//OS: Zea mays /GENE: Synthetic oligonucleotids/RE: Dof2 BSopt /TF: Dof2 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 1113. Group TF: NIT2 /AC: RSP01202//OS: Chlorella vulgaris /GENE: NR/RE: NIT2 BS III /TF: NIT2 1462. Group RE: ARE /AC: RSP01642//OS: Nicotiana tabacum /GENE: WIPK/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.22|complement(3121153..3122135) |SUPPORT| 2 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +133 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.16 G - 0.31 T - 0.18 C - 0.35 1 ccgccgcgtg tttacccgtg gtctctgaac ccgcgcgcgc gtgccacccg 51 cgcatggcca ccacgccgcc ctgctgctgc tgcctcggtt aaacggccgc 101 ggctacgtga gtacgtagca gcggcgcatg cgcgcggcgt ggtgcgtatc 151 gtgctcatcg catcggcctc cgtataagta gcggtgccga gccgcgcaaa 201 GCGGAGGCAT CGATCCATCG CTAGCTTATC TCAATCTCGC CACGAGGAAA 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00054 Mean Expected Number 0.009 +strand +24 : +30 GCTTATC AC RSP00064 Mean Expected Number 0.007 +strand -91 : -82 AGTACGTaGC AC RSP01602 Mean Expected Number 0.002 +strand +29 : +36 TCTCAATC Totally 3 motifs of 3 different REs have been found Description of REs found 53. Group RE: C2a-BS /AC: RSP00054//OS: Oryza sativa tungro bacillform virus (RTBV; plant pararetrovirus) /GENE: RTBV promoter/RE: C2a-BS /TF: unknown 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 1423. Group RE: Inr /AC: RSP01602//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0041E11.27|complement(3140403..3143615) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +191 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.22 C - 0.25 1 ctgttacggc agctgcacgg taagctcgcc tcctagtcct agcctcctag 51 gctcctagcc agtcattcat tccatctgtc tgaaatcagg gataaaaatg 101 gggacagaaa aaatgaagaa aaaaaagGCA ATagattcag gcttgccata 151 gtactgccat tgatgtatat atacacagta cacaaggtac acctcgaagc 201 TAGTTCTCCG ATAAACTAAA CCACACCAAG ACACCAAGTT GATCGTCGGC 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01604 Mean Expected Number 0.005 -strand -22 : -29 ACTGTGTA Totally 1 motifs of 1 different REs have been found Description of REs found 1425. Group TF: SPF1 /AC: RSP01604//OS: Ipomoea batatas /GENE: Sporamin; beta-amylase/RE: SP8a /TF: SPF1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: B1189A09.21|3254746..3255691 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +124 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.21 T - 0.36 C - 0.16 1 tctggttcga atcattgtgc cacatagaac gatggaatcg caaaaaacga 51 tgattgttag tatacactat atgtatggtg tttatccacc tacggacatg 101 atatatgtgt atgtgtgtac tcgtaattag tgagaattta aattcatttt 151 ctgttgataa gaatgcagcc ttctgctttg catagttttg tatatgtgat 201 TATCAGGTCT AGTGGCGCCA TCTATAAGCA ATGTGCTCTT TGCGCTAACC 251 T Any Motif not found ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: B1189A09.47|complement(3325374..3328766) |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +25 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.26 T - 0.18 C - 0.33 1 tttaaattta tttgaatttg acgcggttac cgcggtttac cccttaccgt 51 acccccgcgg taagcgcgat aaccgcggta accgcgcggt ttaccgcggt 101 aaatgcaacc ctggagaaga ctacgcggcc caccatcacg gcCCAATcga 151 tgaacccccc ggaatcccta aaccaacagc aagaggaagt ctctcctgct 201 CAAGCGGCGC GACGCGAGTA GCAGACGCGG CGGCGCGACG CCATGTCGTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00179 Mean Expected Number 0.003 +strand -200 : -194 TTTAAAT AC RSP00642 Mean Expected Number 0.002 +strand -101 : -94 TAAATGCA AC RSP00948 Mean Expected Number 0.007 +strand -103 : -97 GGTAAAT Totally 3 motifs of 3 different REs have been found Description of REs found 173. Group RE: AT-rich motif /AC: RSP00179//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: AT-rich motif /TF: unknown 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 877. Group TF: GT-2 /AC: RSP00948//OS: Oryza sativa /GENE: PHYA/RE: GT3-bx /TF: GT-2 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: B1189A09.48|complement(3329754..3332842) |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +82 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.26 T - 0.27 C - 0.26 1 tcgtgctcgc gcgaatctta aagcagttcc cccgtttctg acccggattc 51 ttactcgaac ccccttggaa atccacttat tctgcgatta gtccttatgt 101 agtaaacttt ttcactttgg tccttacgag aatagataat acgtaagggg 151 tgtatttgaa aaagtgccgt gctagtgacg tgtcttgcct gcctccacca 201 CTAGCGAGCG AGCGAGCGAT TCACGGTGGC CGCGGGCGAC GGAGGCGAGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00574 Mean Expected Number 0.005 -strand -117 : -124 CAGAATAA AC RSP00870 Mean Expected Number 0.006 +strand -44 : -35 TGaAAAAGTG AC RSP01258 Mean Expected Number 0.004 +strand -25 : -18 TGACGTGT AC RSP01599 Mean Expected Number 0.003 -strand -40 : -47 TTTCAAAT AC RSP01601 Mean Expected Number 0.005 +strand -91 : -84 TTTCACTT AC RSP01654 Mean Expected Number 0.008 +strand -27 : -18 AGTGACGTGT Totally 6 motifs of 6 different REs have been found Description of REs found 550. Group RE: AT-rich K /AC: RSP00574//OS: Lycopersicon esculentum /GENE: rbcS1/RE: AT-rich K /TF: unknown 806. Group RE: EM2 /AC: RSP00870//OS: Triticum aestivum /GENE: LMWG-1D1/RE: EM2 /TF: unknown 1160. Group TF: GBF1 /AC: RSP01258//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: GBF1 BS5 /TF: GBF1 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown 1472. Group TF: STF1/HY5 /AC: RSP01654//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: STF1/HY5 BS (cons) /TF: STF1/HY5 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.20|3394241..3397289 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.21 T - 0.20 C - 0.34 1 tccggaccgt ccagccaggg caccgcccgg atccaatcac cgccctccac 51 gtggcaaatc tcgcttcgac tcgacagctt aacagctttt cctccctcgt 101 gaagagagct ccgattccga aacggctaaa accgctttca cactgcctct 151 ttcgcgcaga tccatacaaa accaccggaa aagttttcaa atcccgaagc 201 GGATTCGCGC ACGGAAACCC ACAGTCGATT CTCCGGTGAG AGGATTGTTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00175 Mean Expected Number 0.005 +strand -153 : -146 CACGTGGC AC RSP00189 Mean Expected Number 0.006 +strand -155 : -146 TCCACGTgGC AC RSP00340 Mean Expected Number 0.009 +strand -155 : -146 TCCACGTGgC AC RSP00682 Mean Expected Number 0.006 -strand -146 : -155 GCCACGTGGA AC RSP00683 Mean Expected Number 0.009 -strand -146 : -155 GCCAcGTGGA AC RSP00701 Mean Expected Number 0.007 +strand -175 : -168 CCCGGATC AC RSP00718 Mean Expected Number 0.005 +strand -154 : -147 CCACGTGG AC RSP00718 Mean Expected Number 0.005 -strand -147 : -154 CCACGTGG AC RSP00784 Mean Expected Number 0.000 +strand -155 : -146 TCCACGTGGC AC RSP00938 Mean Expected Number 0.001 -strand -145 : -156 TGCCACGTGGAg AC RSP00940 Mean Expected Number 0.004 +strand +29 : +38 TTCTcCGGTG AC RSP01599 Mean Expected Number 0.002 +strand -16 : -9 TTTCAAAT Totally 12 motifs of 11 different REs have been found Description of REs found 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 183. Group TF: ABI5 /AC: RSP00189//OS: Arabidopsis thaliana /GENE: AtEm1/RE: ABRE/1.3 /TF: ABI5 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 651. Group TF: GBF3 /AC: RSP00682//OS: Arabidopsis thaliana /GENE: Adh/RE: -214 G-box (core) /TF: GBF3 652. Group TF: GBF3 /AC: RSP00683//OS: Arabidopsis thaliana /GENE: Adh/RE: -190 half G-box (core) /TF: GBF3 667. Group RE: Oct (d) /AC: RSP00701//OS: Triticum aestivum /GENE: H3/RE: Oct (d) /TF: unknown 683. Group TF: GBF /AC: RSP00718//OS: Arabidopsis thaliana /GENE: Adh/RE: G-box-1 /TF: GBF ||Identical REs AC: RSP01254 739. Group TF: G-box binding TF /AC: RSP00784//OS: Nicotiana tabacum /GENE: OLIGO-GUS/RE: G-box 8 /TF: G-box binding TF 867. Group TF: GBF /AC: RSP00938//OS: Arabidopsis thaliana /GENE: RbcS-1A/RE: G box-2 /TF: GBF 869. Group TF: GBF /AC: RSP00940//OS: Lycopersicon esculentum /GENE: RbcS-3.6/RE: box II* /TF: GBF 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.21|complement(3398001..3398851) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +415 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.20 T - 0.23 C - 0.24 1 gttacagcct tagaatccac ctgaagaaac tagcacacat ttttcagaca 51 ttcaactacc acagcattgc taaaggatat gccaattgca aagagagtga 101 ggcctcacgg ggagcgtgtg cagctcatac ttaacacctt gaggtttggg 151 cgtcaacgac attatccaat taaatccatg gcttgatacc ttcttctgca 201 ACAGCAAAGT AAAACGACCA AGAAATCGAA TTTAGGACAC CAAGACATTG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01094 Mean Expected Number 0.001 -strand -29 : -40 TAATTGGATAAt AC RSP01103 Mean Expected Number 0.002 -strand -54 : -61 AAACCTCA Totally 2 motifs of 2 different REs have been found Description of REs found 1012. Group TF: GT-1 /AC: RSP01094//OS: Pisum sativum /GENE: GS2/RE: GT-1 box /TF: GT-1 1021. Group RE: AC1 /AC: RSP01103//OS: Spinacia oleracea /GENE: rps22/RE: AC1 /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.23|complement(3411668..3412746) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +77 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.18 T - 0.24 C - 0.29 1 tacctcggat ctgagtgagt gaagaggtga gcagcagtag tatagcaata 51 gcaagcggat taattatatt aagaggacgt gcaaattaat taactaatta 101 attaaacacc caactaatct ccactaataa aaccgtatta ctcccggcca 151 ctgacaccgc agcgcagcat aagaagaagc cactcgccgc cgcgctctct 201 CGTCTTCCTC CTCACTCTCT CCAGCTTCCC TCTCCTCGAG CTCGAGATCT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00200 Mean Expected Number 0.009 -strand -98 : -107 aATTAATTAG AC RSP00653 Mean Expected Number 0.003 +strand +26 : +36 TTCcCTCTCCT AC RSP00681 Mean Expected Number 0.001 -strand -135 : -143 TAATTAATC AC RSP00842 Mean Expected Number 0.003 +strand -197 : -190 CTCGGATC Totally 4 motifs of 4 different REs have been found Description of REs found 193. Group TF: GmHdl56; GmHdl57 /AC: RSP00200//OS: Glycine max /GENE: vspB/RE: PRD motif 1 /TF: GmHdl56; GmHdl57 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 650. Group RE: Box 4 /AC: RSP00681//OS: Pisum sativum /GENE: PSPAL2/RE: Box 4 /TF: unknown 787. Group RE: dOCT /AC: RSP00842//OS: Zea mays /GENE: H3C4/RE: dOCT /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.24|3419174..3422302 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +980 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.34 G - 0.15 T - 0.33 C - 0.18 1 ctattaggaa ggaactgaag tgtttacaac aacctgttgt gtgaatcttt 51 tatctgattt ttctttttct tatctcttca tcataactcc aaaatcgaat 101 aaaaaccaaa aactaactta ggaagaggca aacataattc tgtctaaaat 151 tttgggggac aaaaaaaaac tatctccttt ctttttgaaa aaaaaaaatc 201 TACTTTCTCA TCCACTCCTG TCGTTGTTCA GCTTAGCTTG GAAGGGAGGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00405 Mean Expected Number 0.006 -strand -108 : -115 TTTGGAGT AC RSP00888 Mean Expected Number 0.007 +strand -7 : +2 AAAAATCTA Totally 2 motifs of 2 different REs have been found Description of REs found 387. Group RE: adjb /AC: RSP00405//OS: Nicotiana tabacum /GENE: RNP2/RE: adjb /TF: unknown 820. Group TF: CCA1 /AC: RSP00888//OS: Arabidopsis thaliana /GENE: AtAOX1a/RE: CCA1 motif (2) /TF: CCA1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.25|complement(3422596..3426376) |SUPPORT|14 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +78 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.27 T - 0.12 C - 0.39 1 cccggcagca gcgcgcaccc gcagacgggc cgcactcccg tgccgaatgc 51 taggacggcc cattaggccc aatagacgca ccaaggtcca agtaccagga 101 gaggcgcgcA TTGGcgggaa gagggggaga aaacggcggg aagcgccgcc 151 gccagtggcg cgaaaacccc acccgctata actcctctcc ctcctcacct 201 CACCACTTCT CCCGCCATTG CTCCGCTCCC CAATCTCCCC AACGAGAGAG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00299 Mean Expected Number 0.000 -strand -80 : -91 cTTCCCGCCAAT AC RSP00989 Mean Expected Number 0.003 +strand +8 : +16 TCTCCCGCC Totally 2 motifs of 2 different REs have been found Description of REs found 288. Group TF: E2F /AC: RSP00299//OS: Nicotiana benthamiana /GENE: PCNA/RE: E2F-2 /TF: E2F 910. Group TF: E2F/DP /AC: RSP00989//OS: Zea mays /GENE: RBR3/RE: E2F/DP IV /TF: E2F/DP ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.33|3442021..3443290 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +225 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.19 T - 0.35 C - 0.23 1 gtgactgtga cgcctgtcag tgtggactgt gtcatacatt agcagccgct 51 gacccctgca ttaataaacc agcaccttat cttgctcatc tttatttcta 101 gtttgaggca gtctcgcgac tcagtctaag ctcagtcttc ttttttcttc 151 ttctttgttt gacggaacaa aaatctcagg catgatatga tattctgatc 201 TGTTCATGAG TTCATCTGTA TCTCAGTGTA CATGCATTTG CAAAGCAAAA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00143 Mean Expected Number 0.004 +strand -192 : -183 GACGCcTGTC AC RSP00301 Mean Expected Number 0.009 +strand +39 : +45 TGCAAAG AC RSP00447 Mean Expected Number 0.002 +strand +39 : +48 tGCAAAGCAA AC RSP00629 Mean Expected Number 0.005 +strand -32 : -25 AAAAATCT Totally 4 motifs of 4 different REs have been found Description of REs found 139. Group TF: TRAB1 /AC: RSP00143//OS: Oryza sativa /GENE: Osem/RE: CE3 /TF: TRAB1 289. Group RE: PROL box /AC: RSP00301//OS: Oryza sativa /GENE: GluB-1/RE: PROL box /TF: unknown ||Identical REs AC: RSP00882 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.34|complement(3443742..3446982) |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +374 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.36 G - 0.16 T - 0.19 C - 0.28 1 ttgcaataat caaatcaatt aaatgcatcc cccaaattat cactaatcac 51 ccccttcaaa agtcactaat ttacaaattt acaaatcagt ccattctcac 101 atcaccactc accaacccga agcgaccaac caagaaaagg aggaaaaaaa 151 aagatcccat ttttatataa aagcccctgt ctccgtctcc gatcagctgc 201 AGGAGAGGCG AGGAGGCGAA GCAGCAGCAG CTGAAGCGAG CCGAGCCGAT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00642 Mean Expected Number 0.007 +strand -181 : -174 TAAATGCA AC RSP00713 Mean Expected Number 0.007 -strand -2 : -8 CAGCTGA AC RSP00950 Mean Expected Number 0.009 +strand -93 : -83 CTCACCAACCC AC RSP01083 Mean Expected Number 0.002 +strand -94 : -83 aCTCACCAACCC AC RSP01458 Mean Expected Number 0.000 +strand -132 : -120 ATTTAcAAATTTA Totally 5 motifs of 5 different REs have been found Description of REs found 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 679. Group TF: MYC /AC: RSP00713//OS: Hordeum vulgare /GENE: HvLTP2/RE: MYC RS /TF: MYC 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 1001. Group TF: DcMYB1 /AC: RSP01083//OS: Daucus carota /GENE: DcPAL1/RE: box-L5 /TF: DcMYB1 1328. Group RE: AT-rich ELS /AC: RSP01458//OS: Glycine max /GENE: BiP9/RE: AT-rich ELS /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.40|complement(3470648..3473852) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +1107 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.21 G - 0.17 T - 0.41 C - 0.21 1 ccatgtgcca ctatttattt cttgtctatt ttgtttccat ccttttgctt 51 ttatctctcg ttttcctttt tttttggaga gattggtaac aatacaccgt 101 actttcttcc ccatgtgtta acaaaaaggt tcatactctc tctctctctc 151 tgcttcaagt tttcttcttt aaaagcagga gtagatcttg gatccttcga 201 GTAGTAATAC ACATAGTAGT AGGAGTAGGT GGGCTGTAGT CATCTCTGCT 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00079 Mean Expected Number 0.002 -strand +33 : +24 CCCACCTACt AC RSP00092 Mean Expected Number 0.008 +strand -82 : -76 TAACAAA AC RSP00234 Mean Expected Number 0.001 -strand -25 : -34 GCTTTTAAAG AC RSP00748 Mean Expected Number 0.000 +strand -120 : -109 GAtTGGTAACAA AC RSP00864 Mean Expected Number 0.006 -strand -50 : -58 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand -52 : -60 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand -54 : -62 AGAGAGAGA AC RSP00864 Mean Expected Number 0.006 -strand -56 : -64 AGAGAGAGA AC RSP01283 Mean Expected Number 0.000 -strand -51 : -67 GAGAGAGAGAGAGAGtA Totally 9 motifs of 6 different REs have been found Description of REs found 78. Group RE: AC-I /AC: RSP00079//OS: Phaseolus vulgaris /GENE: PAL2/RE: AC-I /TF: unknown ||Identical REs AC: RSP00420 90. Group TF: GAmyb /AC: RSP00092//OS: Hordeum vulgare /GENE: Amy pHV19/RE: TAACAAA box /TF: GAmyb ||Identical REs AC: RSP00393 RSP01051 227. Group RE: CArG Box 2 /AC: RSP00234//OS: Arabidopsis thaliana /GENE: AGAMAOUS (AG)/RE: CArG Box 2 /TF: unknown 710. Group TF: GT-1 /AC: RSP00748//OS: Arabidopsis thaliana /GENE: Pc/RE: PCbox1 /TF: GT-1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.41|complement(3475339..3475783) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +98 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.23 T - 0.23 C - 0.30 1 gaaaaatata cccaggcagc cacgctcttc aactcgatcc taaccgcacg 51 tgtagatcca acggtcaata caggtccgag attcggatcg ctaccaatga 101 tagcgatcca acggttggca acggttgcta ccattatatg gggcctttta 151 tgcaaaatta cacctcgatg acatgtgggg tcaccggcct agtgggtccc 201 ACCTGTAAGT CTCTCTTTCC GTCACAAGGG CATCGCCTCT GCGCCGCCGT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00049 Mean Expected Number 0.009 +strand -156 : -147 CGCACGTGTa AC RSP00460 Mean Expected Number 0.004 -strand -24 : -33 cACATGTCAT AC RSP00759 Mean Expected Number 0.010 +strand -68 : -62 ATTATAT AC RSP00817 Mean Expected Number 0.004 -strand -147 : -156 TACACGTGCg AC RSP00913 Mean Expected Number 0.002 +strand -34 : -25 GATGACATGT AC RSP00974 Mean Expected Number 0.003 -strand -147 : -156 TACACGTGCG AC RSP00997 Mean Expected Number 0.002 +strand -34 : -25 GATGACATGT AC RSP01744 Mean Expected Number 0.000 -strand -131 : -142 tATTGACCGTTG Totally 8 motifs of 8 different REs have been found Description of REs found 48. Group RE: G-box /AC: RSP00049//OS: Hordeum vulgare /GENE: HVA22/RE: G-box /TF: unknown 438. Group TF: O2 /AC: RSP00460//OS: coix /GENE: alpha-coixin/RE: O2d /TF: O2 721. Group RE: submotif D /AC: RSP00759//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif D /TF: unknown 763. Group TF: ACE-binding TF /AC: RSP00817//OS: Arabidopsis thaliana /GENE: CFI/RE: ACE-core (AtCFI) /TF: ACE-binding TF 844. Group TF: Opaque-2 /AC: RSP00913//OS: Zea mays /GENE: b-32/RE: B1 /TF: Opaque-2 897. Group RE: G-box /AC: RSP00974//OS: Glycine max /GENE: vspB/RE: G-box /TF: unknown ||Identical REs AC: RSP00981 918. Group TF: Opaque-2 (O2) /AC: RSP00997//OS: Zea mays /GENE: cyPPDK1/RE: O2 BS-2 /TF: Opaque-2 (O2) 1551. Group TF: WRKY11 /AC: RSP01744//OS: Arabidopsis thaliana /GENE: AtCMPG1 (At3g02840)/RE: WRKY11 BS /TF: WRKY11 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.42|complement(3476225..3481384) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +2973 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.13 T - 0.29 C - 0.34 1 aataaagtta ataaactaaa ttctattatc taataaccgt tttgatctaa 51 tccacctgct cccgtcgcgt aaacgcgtcc agctcatcgt cgccggcgcc 101 tcgtttcacc agtcacgcca tctaccccac cgaggGCAAT cttgtcattt 151 cactcacaac catctcctcc tctttaataa cagcgcactc cactctctct 201 CTCTCTCACC TCCCTGACAC TAAACTGGTT TCATTAAGGC CGTTTTGATC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00864 Mean Expected Number 0.007 -strand +6 : -3 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand +4 : -5 AGAGAGAGA AC RSP00864 Mean Expected Number 0.007 -strand +2 : -7 AGAGAGAGA AC RSP01598 Mean Expected Number 0.006 +strand -58 : -51 TGTCATTT Totally 4 motifs of 2 different REs have been found Description of REs found 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1419. Group RE: Inr /AC: RSP01598//OS: Spinacia oleracea /GENE: RPL21/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0701D05.44|complement(3486150..3488793) |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +858 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.18 T - 0.34 C - 0.24 1 gtttcttgac tcttgtgtct aaaccggctg taagtttaca gcctgctcct 51 cctctctctc cactcttctt tcctccactt cagcatttag ccggctctaa 101 tgcatccatg tgagtacttg caggtgtgta acgtcaaaat ATTGAttttt 151 ttgtactaac aataatatta tatttactag tggtggtagt agtagtaaca 201 GTATGATGCT AACCGGAAGC TCACGGCTTA TACAGGAGCA ACTTCCCCCA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00865 Mean Expected Number 0.002 -strand -140 : -148 GGAGAGAGA Totally 1 motifs of 1 different REs have been found Description of REs found 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1276_B06.17|complement(3490213..3493361) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +47 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.28 G - 0.17 T - 0.30 C - 0.25 1 tatgtagttt tatgataaat ttagtgttaa ttctatagtt ttgtgataca 51 tcgctttaaa tatctcgtcc gtgataattt gatacatagt attgtggaat 101 ttactttaaa aaaaagaaaa gaaaaggaaa acgaatttgc ccctagtcca 151 agccgctctc cagtgagagt ctaaccaaaa ccaccgtcgt ccgtcctctt 201 CCCCTTCGTC TCCTCCGCCG CCGCGAACCC GATCTCGATC CCCTCCCATG 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00142 Mean Expected Number 0.005 +strand +19 : +25 CGCCGCG AC RSP00254 Mean Expected Number 0.007 -strand -74 : -80 CCTTTTC AC RSP00445 Mean Expected Number 0.005 +strand -91 : -82 AAAAAAGAaA AC RSP01167 Mean Expected Number 0.003 +strand -144 : -136 TAAATATCT Totally 4 motifs of 4 different REs have been found Description of REs found 138. Group RE: GC-rich motif /AC: RSP00142//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: GC-rich motif /TF: unknown 247. Group RE: Py box /AC: RSP00254//OS: Hordeum vulgare /GENE: Amy pHV19/RE: Py box /TF: unknown ||Identical REs AC: RSP00676 425. Group TF: Dof1 /AC: RSP00445//OS: Zea mays /GENE: cyPPDK1/RE: box e /TF: Dof1 1079. Group RE: TATA box /Group TF: HMG proteins /AC: RSP01167//OS: Zea mays /GENE: pMS1/RE: TATA box /TF: HMG proteins ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1276_B06.18|3497895..3501577 |SUPPORT| 8 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +292 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.45 G - 0.14 T - 0.12 C - 0.29 1 cgacaaattt cacacgcttt caaattaaaa gagagaaaac ccgtaccgat 51 ccaactatta aatgatgcac aaataaataa acgagcgcgc acacacagtg 101 acacaaacct aaccaacccc aaccaaccgc gcgcacgcaa cgcaagcaac 151 gagtcgacga cgatatccaa accccccgac cacgcccgaa aaagaaataa 201 TAATAAACAA AAACATTAGA CCCCCAAAAA AAAATCTGAG AAAGAAGCGA 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01599 Mean Expected Number 0.001 +strand -183 : -176 TTTCAAAT Totally 1 motifs of 1 different REs have been found Description of REs found 1420. Group RE: Inr /AC: RSP01599//OS: Spinacia oleracea /GENE: RPS1/RE: Inr /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1276_B06.19|3502560..3507145 |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +960 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.16 T - 0.23 C - 0.33 1 ccgtaatgac gaggaaacga taaaaacggt aacaaaaaac ataaacaaca 51 tataactatt agcactacaa tatatactgt cataacaaac caaaaaaaga 101 agaaaacatt tgtgccttcc ttgccgactg cccgactccc ccgtccgaag 151 cccgactccg acccatcccg tcgtcctcgt cgtcgtcctc ctcctttgct 201 TGCTTTGCCT GCCTCGCTTC GCTCGCATCA CGTGGCTCCG CCTCCTCGTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00175 Mean Expected Number 0.002 +strand +29 : +36 CACGTGGC AC RSP00447 Mean Expected Number 0.002 -strand +9 : -1 gGCAAAGCAA AC RSP00640 Mean Expected Number 0.002 +strand +28 : +35 TCACGTGG AC RSP00966 Mean Expected Number 0.003 -strand +36 : +27 GcCACGTGAT AC RSP01032 Mean Expected Number 0.009 +strand -111 : -102 CCAAAAAAAG AC RSP01034 Mean Expected Number 0.007 +strand +30 : +36 ACGTGGC AC RSP01209 Mean Expected Number 0.009 -strand -102 : -111 CTTTTTTTGG Totally 7 motifs of 7 different REs have been found Description of REs found 169. Group RE: ABRE /Group TF: ABF /AC: RSP00175//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: ABRE /TF: ABF ||Identical REs AC: RSP00723 RSP01570 427. Group TF: Dof1 /AC: RSP00447//OS: Zea mays /GENE: pepcZm2A/RE: box b /TF: Dof1 616. Group RE: G-box /Group TF: GBF /AC: RSP00640//OS: Zea mays /GENE: GRF1/RE: G-box /TF: GBF ||Identical REs AC: RSP00641 889. Group RE: G-box /Group TF: GBF /AC: RSP00966//OS: Antirrhinum majus /GENE: pallida/RE: G-box /TF: GBF 957. Group TF: FLC /AC: RSP01032//OS: Arabidopsis thaliana /GENE: SOC1/RE: CArG box /TF: FLC 959. Group TF: ABI3; ABI5; AREB1 /AC: RSP01034//OS: Arabidopsis thaliana /GENE: RD29B/RE: ABRE 1/2 /TF: ABI3; ABI5; AREB1 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1276_B06.29|complement(3547853..3549948) |SUPPORT| 4 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +962 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.20 G - 0.13 T - 0.39 C - 0.28 1 aatgatgatg agatgaggaa ggcactgtgg tagatattct tacgagtagt 51 ggcaatgtca ccctcacact ttttcttgta ctgccattaa tcccgatttg 101 tccttattta tctgtttact ttctccctcg ctctctctct ctctcccccc 151 atgtcttttt tgcaacacca taatattctt caactctcac tccatcattc 201 AATACTGGGC CTTGCTTTTT CATATTTTGT TGCCTCTACA TCTCACCTTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00756 Mean Expected Number 0.009 +strand -138 : -131 CTCACACT AC RSP00865 Mean Expected Number 0.010 -strand -55 : -63 GGAGAGAGA Totally 2 motifs of 2 different REs have been found Description of REs found 718. Group RE: submotif B /AC: RSP00756//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif B /TF: unknown 801. Group TF: BPC1 /AC: RSP00865//OS: Arabidopsis thaliana /GENE: STK/RE: GA-6 /TF: BPC1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1276_B06.30|complement(3556611..3571082) |SUPPORT|24 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +74 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.30 T - 0.20 C - 0.26 1 cggcggtcag ttgagggagt caaagtgatc ttattccgct ctctgatgcg 51 tccgaagaga ggcccacctg agttgggcct agtgggctta gttgcttgcg 101 agacttagaa gtgggcccta aaaggccacg cggaATTGAa cgctacagaa 151 accaattccg gccacgttct cttcttctcc ccgcagccca cagtgtccgc 201 GAGAGAGAGA GAGAGAGAGA GAGAGAGAGT AGACTAGAGA CGCCTCCGCC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00064 Mean Expected Number 0.007 -strand -31 : -40 AGaACGTGGC AC RSP00377 Mean Expected Number 0.003 +strand -51 : -42 AACCAATtCC AC RSP00821 Mean Expected Number 0.005 +strand -40 : -31 GCCACGTTCT AC RSP00864 Mean Expected Number 0.002 +strand +2 : +10 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +4 : +12 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +6 : +14 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +8 : +16 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +10 : +18 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +12 : +20 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +14 : +22 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +16 : +24 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +18 : +26 AGAGAGAGA AC RSP00864 Mean Expected Number 0.002 +strand +20 : +28 AGAGAGAGA AC RSP01214 Mean Expected Number 0.006 -strand -76 : -85 CCTTTTAGGG AC RSP01283 Mean Expected Number 0.000 +strand +1 : +17 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +3 : +19 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +5 : +21 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +7 : +23 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +9 : +25 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +11 : +27 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +13 : +29 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand +15 : +31 GAGAGAGAGAGAGAGtA Totally 22 motifs of 6 different REs have been found Description of REs found 63. Group RE: Motif I /AC: RSP00064//OS: Oryza sativa /GENE: rab16B/RE: Motif I /TF: unknown 362. Group RE: LS5 /AC: RSP00377//OS: Lemna gibba /GENE: Lhcb2 (cabAB19)/RE: LS5 /TF: unknown 767. Group TF: ACE-binding TF /AC: RSP00821//OS: Arabidopsis thaliana /GENE: FLS/RE: ACE-core (AtFLS) /TF: ACE-binding TF 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 1122. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01214//OS: Brassica oleracea /GENE: BoCRC/RE: EM1 /TF: MADS box TFs 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OJ1276_B06.36|complement(3588629..3592957) |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +147 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.26 G - 0.23 T - 0.25 C - 0.27 1 agggggtcga gatatccggt tttgtggttt agggtcacgg attagatttc 51 gatcactttt gagaatcacg aaatgaactt attccaaata aaaataaatt 101 caggtatagg atgggccttg aATTGAgccc gctaattccg ggcccatcaa 151 ggcccactca gatcaggccc aattaagagg aggcaggcaa acccaaccga 201 CTCGCACTCG TCGTCGTCGT CCCCATCTGG ATCCCTCCCT CTTCTCCTCC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00140 Mean Expected Number 0.000 -strand -102 : -114 AtTTATTTTTATT AC RSP00894 Mean Expected Number 0.004 -strand -77 : -84 AATTCAAG AC RSP01045 Mean Expected Number 0.001 +strand -61 : -50 GGgCCCATCAAG AC RSP01692 Mean Expected Number 0.004 +strand -153 : -146 TTCGATCA Totally 4 motifs of 4 different REs have been found Description of REs found 136. Group RE: AT-1 (2) /Group TF: AT-1 /AC: RSP00140//OS: Pisum sativum /GENE: rbcS-3.6/RE: AT-1 (2) /TF: AT-1 825. Group TF: Dof family /AC: RSP00894//OS: Solanum melongena /GENE: SmCP/RE: ERE 2 /TF: Dof family 969. Group RE: box E /AC: RSP01045//OS: Petroselinum crispum /GENE: CCoAOMT/RE: box E /TF: unknown 1509. Group RE: CARE J /AC: RSP01692//OS: Arabidopsis thaliana /GENE: AOX1a/RE: CARE J /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.10|complement(3630092..3635961) |SUPPORT| 7 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +137 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.27 G - 0.22 T - 0.29 C - 0.21 1 ctgccatatt tatgccggta tggtttagta taggtcgaac atgtccgtaa 51 atatatacac ggtattgctg tatttatttt ggtgtggttg agagtctagt 101 ctaaatcgaa ctactttgtc cttgaccatg tggaggcaga gagctttgca 151 ttgctatctc cactatattt atagcctcaa gtcaaggagt tcaagggagg 201 AAGAGGACAA CCCACTCCAA CTCCAACCCG CAAGCATCCA AACTGAGCTG 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP01296 Mean Expected Number 0.002 -strand -27 : -35 CTATAAATA AC RSP01639 Mean Expected Number 0.010 -strand +12 : +3 GGTTGTCCTC Totally 2 motifs of 2 different REs have been found Description of REs found 1192. Group RE: TATA box /Group TF: TBF /AC: RSP01296//OS: Avena fatua /GENE: Amy2/D/RE: TATA box /TF: TBF 1459. Group RE: ARE /AC: RSP01639//OS: Nicotiana tabacum /GENE: PR-Q; ACS2/RE: ARE /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.14|3649074..3653281 |SUPPORT| 6 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +541 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.33 G - 0.25 T - 0.25 C - 0.17 1 gggtaaaatg gtcattttta tagaaaatac acggtcaact aacggtcaac 51 tgacgggagg ggtatgcaag ggatcaaaat caaattttgg gggtatataa 101 ggaagtaagc aaaattcagg ggtatagaag ggattaggaa aaatttcagg 151 ggtatataag ggattttctc aataaaaaga aaaggaaaat aagtgttgcc 201 CGTGTTCTCA GCTTCCTCCA CTAGTCTACC GCCGCTGCCT CCTCCTCGTC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00960 Mean Expected Number 0.003 +strand -165 : -158 CAACTAAC AC RSP01174 Mean Expected Number 0.003 -strand -139 : -149 CCcCTCCCGTC Totally 2 motifs of 2 different REs have been found Description of REs found 885. Group TF: HvGAMYB /AC: RSP00960//OS: Hordeum vulgare /GENE: ITR1/RE: MYB BS /TF: HvGAMYB 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.17|3658490..3661001 |SUPPORT| 3 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +117 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.10 G - 0.29 T - 0.16 C - 0.44 1 cccgcgccgc cctcatccgc gacgcgtccg tgctcctcga atcggccata 51 gccaagcact cctcctcgtc gcccgcttct gccttcttgg acgccttctt 101 cgcggcctac gaggacagcg gcacggccgc gacgacccgt ggactccacc 151 tcctggtgca cgcctacgcg cgcgcgcgcc tcccggagga ggcgctcgag 201 GCCTGCCGCT ACCTGGCGCA GCGCGGGGTG GTCCCCTCCC TGCCCGCCTT 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00340 Mean Expected Number 0.003 -strand -58 : -67 TCCACGgGTC Totally 1 motifs of 1 different REs have been found Description of REs found 325. Group TF: SGBF-1; SGBF-2 /AC: RSP00340//OS: Glycine max /GENE: GmAux28/RE: B1-core /TF: SGBF-1; SGBF-2 ||Identical REs AC: RSP00965 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.18|complement(3661844..3662849) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +360 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.23 G - 0.31 T - 0.18 C - 0.28 1 ccaagagagc acgtcatgtg attgtgcgag atctagctag ctatacggag 51 ttgtgtgaca gtcgagagag agagagagag agaggccgag accggtcaag 101 cggccgcaca tcatatggcc tcgccacggc gcacggcggc gaccgggtgg 151 ccggcgaaac gatcactcat tgcgcctttc cgtcgcgcgg cttgtccgcc 201 TCTCGCGTCA AATCGACCCG AATTATTATC GCTCGCTAAA GCGCACAAGT 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00399 Mean Expected Number 0.005 +strand -192 : -185 GCACGTCA AC RSP00503 Mean Expected Number 0.003 +strand -168 : -161 CTAGCTAG AC RSP00503 Mean Expected Number 0.003 -strand -161 : -168 CTAGCTAG AC RSP00864 Mean Expected Number 0.001 +strand -136 : -128 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -134 : -126 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -132 : -124 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -130 : -122 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -128 : -120 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 +strand -126 : -118 AGAGAGAGA AC RSP00872 Mean Expected Number 0.004 +strand -149 : -140 TGTGTGACAg AC RSP01174 Mean Expected Number 0.002 +strand -2 : +9 CCTCTCgCGTC AC RSP01283 Mean Expected Number 0.000 +strand -137 : -121 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -135 : -119 GAGAGAGAGAGAGAGAg AC RSP01283 Mean Expected Number 0.000 +strand -133 : -117 GAGAGAGAGAGAGAGAg Totally 14 motifs of 6 different REs have been found Description of REs found 381. Group TF: AP1-like leucine zipper TF /AC: RSP00399//OS: Nicotiana tabacum /GENE: RNP2/RE: ATF /TF: AP1-like leucine zipper TF ||Identical REs AC: RSP00884 479. Group TF: RITA-1 /AC: RSP00503//OS: Nicotiana tabacum /GENE: Ntltp1/RE: D1 box /TF: RITA-1 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 808. Group RE: GLM2 /AC: RSP00872//OS: Triticum aestivum /GENE: LMWG-1D1/RE: GLM2 /TF: unknown 1085. Group TF: Zmhox1a /AC: RSP01174//OS: Zea mays /GENE: Sh/RE: Zmhox1a BS 1 /TF: Zmhox1a 1180. Group RE: GAGA element /AC: RSP01283//OS: OS: Glycine max /GENE: gsa1/RE: GAGA element /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.19-2|complement(3664327..3669588) |SUPPORT|12 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +35 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.10 G - 0.37 T - 0.36 C - 0.17 1 ctctctctct ctacttctct ctgcctctgc ttgctctgct ctgtatctgt 51 gaccatctcg cttcgtcatc tcgtcgtcgt ttgtgttctt ggattgggtt 101 gggttgggtt ggtgaggtgg ggagatggtt tggtgaggag ttgtgtgttg 151 ctgcagctgc agctgctctg ctggtgtggg ggtggaattg tgttgggttt 201 CTTTGGTTGA GGAGAGAGGA GGGCGAATCT GTGGGATGAG GATGCGGTGG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00197 Mean Expected Number 0.002 -strand -48 : -61 cAGCAACACACAAC AC RSP00653 Mean Expected Number 0.000 -strand +20 : +10 TcCTCTCTCCT AC RSP00864 Mean Expected Number 0.001 -strand -189 : -197 AGAGAGAGA AC RSP00864 Mean Expected Number 0.001 -strand -191 : -199 AGAGAGAGA AC RSP00950 Mean Expected Number 0.001 -strand -85 : -95 CTCACCAACCC AC RSP01073 Mean Expected Number 0.003 -strand -168 : -176 CAAGCAGAG AC RSP01083 Mean Expected Number 0.003 -strand -84 : -95 cCTCACCAACCC Totally 7 motifs of 6 different REs have been found Description of REs found 190. Group RE: Box BP-1 /AC: RSP00197//OS: Oryza sativa /GENE: Gt3/RE: Box BP-1 /TF: unknown 627. Group RE: CT-LB /AC: RSP00653//OS: Spinacia oleracea /GENE: petH/RE: CT-LB /TF: unknown 800. Group TF: BPC1 /AC: RSP00864//OS: Arabidopsis thaliana /GENE: STK/RE: GA-5 /TF: BPC1 879. Group RE: CTCACCAACCC motif /AC: RSP00950//OS: Petroselinum crispum /GENE: 4CL-1/RE: CTCACCAACCC motif /TF: unknown 991. Group TF: PvAlf /AC: RSP01073//OS: Arachis hypogea; Phaseolus vulgaris /GENE: Em/RE: Em2b /TF: PvAlf 1001. Group TF: DcMYB1 /AC: RSP01083//OS: Daucus carota /GENE: DcPAL1/RE: box-L5 /TF: DcMYB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.21-1|complement(3679748..3684209) |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +19 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.18 G - 0.25 T - 0.25 C - 0.32 1 ggccatcgta cgtgggcctt gcagcgggcc gcgacgccgt tcacagcgag 51 caccgccagg agtcgcggga tttttttttt ttcatttccc ctctcttact 101 agtagtacta atttcttgcA TTGCaacttg caagcccctc cctttcccat 151 ccccaccaaa tggtagttta aattgtttcg ccacggccat cgcagggtgg 201 GAGGCGCAAC GCAAGCGCGA TGGGCTACGG CTTCTCCACC AAGCTCACGG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00179 Mean Expected Number 0.006 +strand -34 : -28 TTTAAAT AC RSP00601 Mean Expected Number 0.002 +strand -50 : -42 CCCCACCAA AC RSP01276 Mean Expected Number 0.003 +strand -193 : -186 GTACGTGG AC RSP01577 Mean Expected Number 0.005 -strand -20 : -29 GCgAAACAAT Totally 4 motifs of 4 different REs have been found Description of REs found 173. Group RE: AT-rich motif /AC: RSP00179//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: AT-rich motif /TF: unknown 577. Group RE: C-rich R /AC: RSP00601//OS: Lycopersicon esculentum /GENE: rbcS2/RE: C-rich R /TF: unknown 1175. Group RE: Box III /AC: RSP01276//OS: Petroselinum crispum /GENE: CHS/RE: Box III /TF: unknown 1406. Group RE: ICEr2 /Group TF: STK /AC: RSP01577//OS: Solanum tuberosum /GENE: PAT21/RE: ICEr2 /TF: STK ||Identical REs AC: RSP01578 RSP01579 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.26|complement(3692957..3696521) |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +807 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.30 T - 0.22 C - 0.25 1 gatcggttac tcgcaaagac aaatccgtac aagcaaaaaa acgagtgaga 51 gccatcagtc gaagctgtcc gagtcagtga gagcgaggcg tcgctggatc 101 cacctgggct caccacgtct ccagattcca gatcacccgc ccgcgcgtgg 151 ctggatggag ctccaagatt aaccgagctg agccgcgatg tgtggagatt 201 GGATGGTTGG CTTCTTCTCG GTTTGTTCGT TCCTTGTGGT CGAGAGTGAG 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00057 Mean Expected Number 0.006 +strand -89 : -80 aCCACGTCTC AC RSP00878 Mean Expected Number 0.004 -strand -94 : -101 CCAGGTGG AC RSP00947 Mean Expected Number 0.009 -strand -27 : -33 GGTTAAT AC RSP01081 Mean Expected Number 0.001 -strand +11 : -1 gCCAACCATCCA Totally 4 motifs of 4 different REs have been found Description of REs found 56. Group TF: ABF /AC: RSP00057//OS: Zea mays /GENE: rab28/RE: ABRE B /TF: ABF 814. Group TF: RPCF-1 /AC: RSP00878//OS: Arabidopsis thaliana /GENE: PCNA/RE: Site I /TF: RPCF-1 876. Group TF: GT-2 /AC: RSP00947//OS: Oryza sativa /GENE: PHYA/RE: GT1-bx /TF: GT-2 999. Group TF: DcMYB1 /AC: RSP01081//OS: Daucus carota /GENE: DcPAL1/RE: box-L3 /TF: DcMYB1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.29|3708014..3710455 |SUPPORT| 9 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +223 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.35 G - 0.20 T - 0.29 C - 0.16 1 agtgaaacat aaaatactat tcatatttta ttatctaata ataataaaaa 51 ttaataaaaa tattaaataa gacaacggtc aaacaatata cattgaaatt 101 tataattgcg tgtaatatag gatggaggga gtaaccagca atgcaCCAAT 151 gcatactgca taggcaggtc ttcaaatctg agtggcgttc gtgctccctc 201 CTCTTTGTGT TTGATTATTC GTTCCGGTGT GCGCGAAAGC GGGGAAGGAG 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00022 Mean Expected Number 0.006 -strand -167 : -175 ATAATAAAA AC RSP00125 Mean Expected Number 0.005 -strand -137 : -148 AATATTTTTATT AC RSP00130 Mean Expected Number 0.000 +strand -164 : -145 AATAATAATAAaAATtAATA AC RSP00135 Mean Expected Number 0.003 -strand -137 : -148 AATATTTTTATt Totally 4 motifs of 4 different REs have been found Description of REs found 21. Group TF: PCF1 /AC: RSP00022//OS: Pisum sativum /GENE: petE/RE: A/T-rich BOX1 /TF: PCF1 123. Group RE: AT-1 (3) /AC: RSP00125//OS: Nicotiana plumbaginifolia /GENE: cab-E/RE: AT-1 (3) /TF: unknown ||Identical REs AC: RSP00133 RSP00788 128. Group RE: C2 /AC: RSP00130//OS: Glycine max /GENE: GmAux28/RE: C2 /TF: unknown 131. Group RE: AT-1 (4) /AC: RSP00135//OS: Nicotiana plumbaginifolia /GENE: cab-E/RE: AT-1 (4) /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: P0583G08.31|complement(3716940..3719947) |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +210 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.22 G - 0.28 T - 0.20 C - 0.31 1 ggggttggac gcttggagtc ctgcactgac ctgcctcgct gtggttggtt 51 ggttggtttg gttccccacc cccccccccc cccccccgcc ctcccaatgg 101 tgggacccaa cagtgcattt aaagacctta aactgtcgtt ggATTGCgga 151 aagcgagagg aaagaaagaa aaacgaaggg gaagcgaggt gaggaaaggc 201 AGCGCAGCGC ACTCTGTCAA ATCCGTGCAA TCTCCGCCAT CTCCCTCTCA 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00179 Mean Expected Number 0.004 -strand -78 : -84 TTTAAAT AC RSP00444 Mean Expected Number 0.000 +strand -43 : -30 AgGAAAGAAAGAAA AC RSP00642 Mean Expected Number 0.001 -strand -80 : -87 TAAATGCA AC RSP00651 Mean Expected Number 0.001 -strand -144 : -154 ACCaACCAACC AC RSP00651 Mean Expected Number 0.001 -strand -148 : -158 ACCaACCAACC AC RSP00860 Mean Expected Number 0.000 +strand -38 : -30 AGAAAGAAA AC RSP00958 Mean Expected Number 0.005 +strand -83 : -77 TTTAAAG AC RSP01046 Mean Expected Number 0.000 -strand -55 : -63 CAATCCAAC Totally 8 motifs of 7 different REs have been found Description of REs found 173. Group RE: AT-rich motif /AC: RSP00179//OS: Phaseolus vulgaris /GENE: beta-phaseolin, or phas/RE: AT-rich motif /TF: unknown 424. Group TF: Dof1 /AC: RSP00444//OS: Zea mays /GENE: cyPPDK1/RE: box d /TF: Dof1 617. Group RE: L1-box /AC: RSP00642//OS: Arabidopsis thaliana /GENE: PDF1/RE: L1-box /TF: unknown 625. Group TF: C1 /AC: RSP00651//OS: Zea mays /GENE: a1/RE: C1 PBS/P /TF: C1 796. Group TF: BPC1 /AC: RSP00860//OS: Arabidopsis thaliana /GENE: STK/RE: GA-1 /TF: BPC1 884. Group TF: BPBF /AC: RSP00958//OS: Hordeum vulgare /GENE: Hor2/RE: PB2 /TF: BPBF 970. Group RE: NON /AC: RSP01046//OS: Nicotiana tabacum /GENE: histone genes (oligo)/RE: NON /TF: unknown ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0089K24.2|3732762..3733584 |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +45 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.14 T - 0.31 C - 0.30 1 cacagtacgt acagcgatac tcttatcttt ttttaaaaaa atgtttcctc 51 tcctctctat ttttttttaa aaaaaatctg ctgcccttgc tgcttgcgct 101 aatctccccg catcaaagaa aaaATTGAtc tgacacttgg cagttgagct 151 tctgatccag taatcagtac tgatcatctc tccgactcac cagtcaccac 201 CACTTGTCCG GTCAACTCTC CAGTGACCTC GCCATCTCCT CAGCCATGGC 251 T RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00056 Mean Expected Number 0.009 +strand -2 : +8 aCCACTTGTC AC RSP00219 Mean Expected Number 0.000 +strand -70 : -59 TGACACtTGGCA AC RSP00227 Mean Expected Number 0.005 -strand -172 : -180 AAGATAAGA AC RSP00474 Mean Expected Number 0.001 -strand +6 : -6 CAAGTGGTGgTG AC RSP00629 Mean Expected Number 0.007 +strand -129 : -122 AAAAATCT AC RSP00936 Mean Expected Number 0.000 -strand -59 : -70 TGCCAaGTGTCA Totally 6 motifs of 6 different REs have been found Description of REs found 55. Group TF: ABI3 /AC: RSP00056//OS: Brassica napus /GENE: napA/RE: ABRE Bd /TF: ABI3 212. Group TF: HY5 /AC: RSP00219//OS: Arabidopsis thaliana /GENE: RBCS-1A/RE: G box-1 /TF: HY5 220. Group TF: GT-1 /AC: RSP00227//OS: Pisum sativum /GENE: rbcS-3A/RE: BOX III* /TF: GT-1 452. Group TF: Alfin1 /AC: RSP00474//OS: Medicago sativa /GENE: MSPRP2/RE: Alfin1 BS4 /TF: Alfin1 605. Group TF: CCA1 /AC: RSP00629//OS: Arabidopsis thaliana /GENE: Lhcb1*3/RE: CCA1 BS2 /TF: CCA1 865. Group TF: GBF /AC: RSP00936//OS: Lycopersicon esculentum /GENE: RbcS-3A/RE: G box /TF: GBF ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0089K24.5|complement(3739580..3741264) |SUPPORT| 5 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +75 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.24 G - 0.22 T - 0.15 C - 0.39 1 accttcggtg tactttttcc tattccttgt caccactgcc cagcccatac 51 acggcccaaa aaaggcccaa ttccagtagg gttacgaagc gcacgggccg 101 gagccctcca gtctcgcgca gccagccatt cctcctcctg tctcccctgc 151 ccgtacgcca ccccacaagc gaagaagacg agaggaagag gaggccaagc 201 CGCACAACCC ACCACCACCA CCACCACCGA TCTGCGGAGA GCGAGCTACC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00003 Mean Expected Number 0.009 -strand -136 : -145 CCTTTTTTGG AC RSP00755 Mean Expected Number 0.004 -strand -174 : -180 AGGAATA AC RSP01033 Mean Expected Number 0.008 -strand -136 : -145 CCTTTTTTGG AC RSP01209 Mean Expected Number 0.008 -strand -137 : -146 CTTTTTTGGG AC RSP01709 Mean Expected Number 0.006 +strand -145 : -136 CCAAAAAAGG AC RSP01709 Mean Expected Number 0.006 -strand -136 : -145 CCTTTTTTGG Totally 6 motifs of 5 different REs have been found Description of REs found 3. Group TF: AGL3; MADS-box TF /AC: RSP00003//OS: Arabidopsis thaliana /GENE: Synthetic OLIGO/RE: CArG1 (AGL3) /TF: AGL3; MADS-box TF 717. Group RE: submotif A /AC: RSP00755//OS: Solanum tuberosum /GENE: S2-RNase/RE: submotif A /TF: unknown 958. Group TF: FLC /AC: RSP01033//OS: Arabidopsis thaliana /GENE: FT/RE: CArG box /TF: FLC ||Identical REs AC: RSP01204 1119. Group RE: EM1 /Group TF: MADS box TFs /AC: RSP01209//OS: Lepidium africanum /GENE: LaCRC/RE: EM1 /TF: MADS box TFs 1517. Group TF: RIN /AC: RSP01709//OS: Solanum lycopersicum /GENE: Synthetic OLIGO/RE: RIN BSC [SRF] /TF: RIN ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0089K24.17|3801473..3807522 |SUPPORT|10 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +69 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.16 G - 0.29 T - 0.17 C - 0.38 1 cggtaaaaag gatgcggcgg gtggtggttg ccatcctctc gcggtgaagt 51 gaaacgtggg gacgagacga cgagtcgacg gcggtggcgg tgtctccctc 101 ccgctgcctt gcaccgcaag gagcccccct cgccgcccgc cgcctttgac 151 cgccgcgcgc gcgcgcctac tataccacaa ccccccctaa ttggcccatc 201 TGTTGCAGAG CTACACTGAG CCACTCACTC CCCATGCCCT TGGCCGCCGC 251 A RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00383 Mean Expected Number 0.008 -strand -50 : -56 GGTCAAA AC RSP01601 Mean Expected Number 0.000 -strand -147 : -154 TTTCACTT AC RSP01755 Mean Expected Number 0.002 -strand -171 : -178 CAACCACC Totally 3 motifs of 3 different REs have been found Description of REs found 368. Group TF: WRKY1 /AC: RSP00383//OS: Petroselinum crispum /GENE: WRKY1/RE: WA /TF: WRKY1 1422. Group RE: Inr /AC: RSP01601//OS: Spinacia oleracea /GENE: PsaDb/RE: Inr /TF: unknown 1560. Group TF: C1 /AC: RSP01755//OS: Glycine max /GENE: a2/RE: C1BS1 /TF: C1 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0089K24.19|complement(3814852..3815561) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +55 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.25 G - 0.16 T - 0.33 C - 0.26 1 agaggataaa tgattctgtt gcgttgtcga tttatcaatc aattgctcag 51 atgctaattc agtgtgcggg caaaccttcc tcatccttgc ccttatctgc 101 ctgtcaccat cacctgaccc atatcccttc aacttgcaat atttCCAATt 151 tgtggatata tatgctattt agccttggtc ataccattct cttgctccct 201 TAGTCCTCAT TGCATACCAT AGAACATTCC TAGATAGAGA ACCACCGTGA 251 G RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00038 Mean Expected Number 0.001 +strand -50 : -39 TGTGGaTATATA AC RSP00093 Mean Expected Number 0.007 -strand -43 : -49 TATCCAC Totally 2 motifs of 2 different REs have been found Description of REs found 37. Group TF: GT-1 related TFs /AC: RSP00038//OS: Lycopersicon esculentum /GENE: LAT52; LAT56;/RE: 52/56 box /TF: GT-1 related TFs 91. Group RE: TATCCAC box /AC: RSP00093//OS: Hordeum vulgare /GENE: Amy pHV19/RE: TATCCAC box /TF: unknown ||Identical REs AC: RSP01050 ------------------------------------------------------------ > O.sativa (japonica), Chr 1 ( 7 contigs)|GENE: OSJNBa0089K24.20|complement(3815901..3816586) |SUPPORT| 1 exon(s)|Contig: NT_0363123.txt | -200:+51 from mRNA start|,5"-UTR: +199 bp |Taxon: Monocot |Promoter: TATA-less Nucleotide Frequencies: A - 0.29 G - 0.11 T - 0.36 C - 0.24 1 acggctaaaa gaactctaaa agcaaaacag ttatccagct tcatcatctt 51 tttacttata cttatcagct aaattattta ttttcaacca aatttgattt 101 taggtttttt ttcagcgaaa tttatttttc accatttact ttaagATTGT 151 taaaaacacg tactatatca aaattttatt tgcaaattat ttttcagcct 201 CGTTTCGTCG CCGCTTCCTC TCCCACACGG CCACGGCCAC GCCGCGACAC 251 C RE motifs found (positions are given in relation to TSS at 201; Mismatches - in lower case): AC RSP00063 Mean Expected Number 0.000 -strand +45 : +36 GCgGCGTGGC AC RSP00142 Mean Expected Number 0.001 +strand +40 : +46 CGCCGCG AC RSP00628 Mean Expected Number 0.004 -strand -50 : -57 AACAATCT AC RSP01702 Mean Expected Number 0.008 +strand -46 : -37 AACACGTAcT Totally 4 motifs of 4 different REs have been found Description of REs found 62. Group RE: Motif III /AC: RSP00063//OS: Oryza sativa /GENE: rab16B/RE: Motif III /TF: unknown 138. Group RE: GC-rich motif /AC: R