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A database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well.
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An online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. AREsite2 contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs. Improvements include annotation of motifs not only in 3'UTRs but in the whole gene body including introns, additional genomes, and locally stable secondary structures from genome wide scans.
AtcisDB / Arabidopsis cis-regulatory element database
Compiles cis-regulatory information related to Arabidopsis thaliana. AtcisDB gathers data relative to transcription factor binding site information, promoter sequence and related annotations. Searches can be made by gene symbol or locus ID and displays a chart that give access to a gene description, chromosome location, promoter sequence, type and sources as well as information about the regulatory network. The totality of the database can be downloaded in zip format.
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