ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

Journal Article · Tue Aug 08 04:00:00 EDT 2006 · Bioinformatics, n/a, n/a, November 7, 2006, pp. 122-124

OSTI ID:899427

Loots, G; Ovcharenko, I

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA
• Sponsoring Organization: USDOE
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 899427
• Report Number(s): UCRL-JRNL-223593
• Journal Information: Bioinformatics, n/a, n/a, November 7, 2006, pp. 122-124, Journal Name: Bioinformatics, n/a, n/a, November 7, 2006, pp. 122-124
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
DNA
FUNCTIONALS
MARSUPIALS
PROMOTERS
TRANSCRIPTION FACTORS
VERTEBRATES