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 3743 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) //