The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D82-5. doi: 10.1093/nar/gkh122.


The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Computational Biology
  • DNA Primers / genetics*
  • DNA, Complementary / genetics
  • Databases, Nucleic Acid*
  • Eukaryotic Cells*
  • Expressed Sequence Tags
  • Humans
  • Internet
  • Promoter Regions, Genetic / genetics*
  • Response Elements / genetics
  • User-Computer Interface


  • DNA Primers
  • DNA, Complementary