Plant Promoter and Regulatory Element Resources:
(Src: http://www.dna.affrc.go.jp/PLACE/)
)
- Plantpan (http://plantpan.mbc.nctu.edu.tw/seq_analysis.php): Curently have transcription factor binding site search options in following species: Arabidopsis, Barley ,Bean ,Maize ,Medicago, Pea, Petunia, Potato, Rape, Rice, Snapdragon, Soybean, Tobacco, Tomato, Wheat and others. Alongwith transcription facors, plantpan also finds Tandem repeats, CpNpG and miRNA (Arabidopsis Maize Medicago Rice)
- AGRIS (http://arabidopsis.med.ohio-state.edu/)
Currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regulatory database) and AtTFDB (Arabidopsis thaliana transcriptionfactor database). - AthaMap (http://www.athamap.de/)
A genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana. - AtProbe (http://exon.cshl.org/cgi-bin/atprobe/atprobe.pl)
The Arabidopsis thaliana promoter binding element database, an aid to find binding elements and check data against the primary literature. - DATF: Database of Arabidopsis Transcription Factors (http://datf.cbi.pku.edu.cn/)
The Database of Arabidopsis Transcription Factors (DATF) contains known and predicted Arabidopsis transcription factors with sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and Nuclear Location Signals. - DoOP: Databases of Orthologous Promoters (http://doop.abc.hu/)
A database containing orthologous clusters of promoters from Homo sapiens, Arabidopsis thaliana and other organisms. - GRASSIUS (http://grassius.org/)
A public web resource composed by a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. GRASSIUS currently contains regulatory information on maize, rice, sorghum and sugarcane. - PlantCare (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/)
Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. - PlantProm DB (http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom)
Database with annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start sites (TSS) from various plant species. - PlantTFDB: Plant Transcription Factor Database (http://plntfdb.bio.uni-potsdam.de/v2.0/)
An integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa(rice), Chlamydomonas reinhardtii and Ostreococcus tauri. - PPDB (Plant Promoter DB) (http://ppdb.gene.nagoya-u.ac.jp/cgi-bin/index.cgi)
Database that provides transcription start sites (TSS) and other structural information for Arabidopsis and rice promoters. - Transfac (http://www.gene-regulation.com/pub/databases.html#transfac)
Database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Commercial site.