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AtcisDB - Arabidopsis cis-regulatory element database

AtcisDB provides a comprehensive resource for the scientific community working with gene regulatory information of Arabidopsis thaliana. AtcisDB consists of a searchable relational database, which includes many different data types, such as transcription factor binding site information, promoter sequence and related annotations. The data can be viewed using the Generic Genome Browser.

AtcisDB can be searched by Gene Symbol or Locus ID. The Gene Symbol can be any symbol used by TAIR for gene annotation (e.g., NAC, CAF, MYB etc.). The Locus ID is also the ID used by TAIR (e.g,. At1g01010, At1g01050 etc.). The search results will include the Locus ID, the Gene Model that represents that locus, and cross reference for gene annotation from MIPS, TIGR, TAIR and SALK. The cis-regulatory element annotation for each gene can also be obtained.

The binding sites are color-coded with two colors: RED and GREY. The RED color indicates experimentally validated cis-regulatory element present in a specific promoter. The GREY color indicates predicted motifs. For the complete list of binding sites used in these anlayses please click here Bindingsites List.

Frequencies for words of length 5 - 15 across the non-coding segments of the Arabidopsis genome are available for download [1].

Arabidopsis core promoters were defined as the region flanking 50 bps to each side the transcription start site (TSS), in cases when TSS have been established. Click here to download Core Promoter data [2].

1. Lichtenberg J, Yilmaz A, Welch JD, Kurz K, Liang X, Drews F, Ecker K, Lee SS, Geisler M, Grotewold E, Welch LR. The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics. 2009 Oct 8;10:463. PMID 19814816
2. Molina C, Grotewold E. Genome wide analysis of Arabidopsis core promoters. BMC Genomics. 2005 Feb 25;6:25. PMID 15733318

For details on how to use the database please read HELP.

Download promoter gene list (csv)
Download all promoter sequences (csv)
Download all promoter sequences (fasta)

AtcisDB Search Engine

Start typing to see locus id or gene symbol suggestions

(i.e. Myb, At2g30420)

Submit a list of Locus Ids