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EcoGene, comprehensive data resource for E. coli


Kenn Rudd, Univ. of Miami Med School

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About EcoGene

The EcoGene home page

EcoGene[1] is a manually curated resource containing genomic and proteomic information about E.coli K-12 MG1655. EcoGene works with the CGSC to manage the assignment of canonical gene names for E. coli genes.

Using EcoGene



Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

Input Output
  • Gene Name (DNA, RNA, or pseudo gene)
  • Synonym
  • Gene Product
  • EcoGene number (EG) (Syntax:
  • ECK number
  • SWISS-PROT number
  • Genbank number (gi)
  • Blattner lab number (b)
  • CGSC number
  • Genomic Address
  • Gene Description
  • Primary Gene Name
  • EG number
  • ECK number
  • b number
  • Sequence
  • Gene Name Mnemonic
  • Alternate Gene Symbols
  • Sequence
  • Description
  • Protein Sequence
  • Protein length and MW
  • Gene Quality
  • Genomic Address (right end, left end, direction, and minute(%))
  • EcoMap (10 kb neighbor genes)
  • Link out
    • Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot)
    • ASAP
    • CGSC
    • GenoBase
    • RegulonDB
    • PDB Links
Title, author, or reference ID Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
Enzyme(s) and Genomic Adress Restriction Map


  • Find the neighboring genes to the initially identified set

Yes. EcoMap (10 kb neighboring genes)

  • Find/design primers for a certain gene


  • Find all the clones/KOs for those genes

Yes. Link to CGSC and GenoBase

  • Find commonalities in function in the genes that are up or down-regulated in a given experiment


  • Find genes with similar behavior across sets of different experiments (see Hughes et al 2000)


  • Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones)


  • For a gene, segment of DNA, operon/regulons, pathway , find all the available information


Usage examples

Add links to additional pages describing success stories here.

Other sites with related content


Web Services/API



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See Help:References for how to manage references in EcoliWiki.

  1. Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 28 60-4 PubMed

External Links


Discussion of EcoGene on other websites