ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes

Bioinformatics. 2007 Jan 1;23(1):122-4. doi: 10.1093/bioinformatics/btl546. Epub 2006 Nov 7.


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, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Anura
  • Binding Sites
  • Chickens
  • Conserved Sequence*
  • Databases, Factual*
  • Dogs
  • Evolution, Molecular
  • Genome Components / genetics
  • Humans
  • Macaca mulatta
  • Mice
  • Opossums
  • Promoter Regions, Genetic / genetics*
  • Rats
  • Species Specificity
  • Takifugu
  • Transcription Factors / metabolism*
  • Zebrafish


  • Transcription Factors