RegSite Database of Plant Regulatory Elements

Release 14, May 03, 2014

Recent sequencing of many plant genomes makes the task of identifying their regulatory elements very important, yet popular regulatory site databases such as TFD or TRANSFAC list very few plant elements. One existing database, PLACE, contains relatively few entries and limited information on each element.

Current RegSite release contains 2779 motifs and more descriptive fields than PLACE, including several fields on expression and some others.

RegSite is used by Softberry for training its NSITE-PL and TSSP programs, and also is available for licensing as a stand-alone database.

An example of RegSite entry is given below. For list of RegSite motifs, click here.

 
  Regsite DB 
  AC    RSP00001
  DT    19-05- 2002 IS
  OS    Spinach
  GS    rps1
  GF    nuclear gene rps1 coding for the spinach plastid ribisomal protein CS1
  SN    S1F_BS
  SD    Negative cis-element conserved in plastid-related genes and binding 
  spinach leaf nuclear factor S1F
  DE
  BF    S1F, spinach leaf nuclear factor
  SA    Negative; element down-regulating the promoter activity of rps1
  SL    5'-end
  SP    -243:-226
  SB    1-box
  SC    1-comp
  DI
  SQ    agaatgttaccatgaaa
  SS
  CS    gwwwccatg
  AL    See: [1]
  MA
  PT    TATA(?)
  PS    
  OR    Mature leaves
  TI
  CE    Dark-grown de-differentiated soybean suspension cells
  ON
  ES    Darkness
  EC    Transient expression in soybean cell protoplasts
  MT    Oligonucleotide-directed mutagenesis; DNAase I protection and Gel shift 
  assays
  RE    [1]
  RS    JBC
  RL    267:23515-23519 (1992)
  RA    Zhou A-X, Li Y-F, Rocipon M, Mache E
  RT    Sequence-specific interaction between S1F, a spinach nuclear factor, and 
  a negative cis-element conserved in plastid-related genes
  CT    2 TSS (Pos. 351, 391); Site position in relation to TSS 2 (pos. 391)
  //