Schema for sgdGene
  Database: sacCer2    Primary Table: sgdGene    Row Count: 6,717   Data last updated: 2009-02-10
Format description: GenePred table with proteinID field for WormBase Genes.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name R0010Wvarchar(255) values Name of gene
chrom 2micronvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 251int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1523int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 251int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1523int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 251,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1523,longblob   Exon end positions (or start positions for minus strand item)
proteinID n/avarchar(40) values Swiss-Prot protein ID

Connected Tables and Joining Fields
        sacCer2.ceBlastTab.query (via sgdGene.name)
      sacCer2.choExpDistance.query (via sgdGene.name)
      sacCer2.choExpDistance.target (via sgdGene.name)
      sacCer2.dmBlastTab.query (via sgdGene.name)
      sacCer2.drBlastTab.query (via sgdGene.name)
      sacCer2.esRegGeneToModule.gene (via sgdGene.name)
      sacCer2.esRegGeneToMotif.gene (via sgdGene.name)
      sacCer2.esRegUpstreamRegion.name (via sgdGene.name)
      sacCer2.hgBlastTab.query (via sgdGene.name)
      sacCer2.mmBlastTab.query (via sgdGene.name)
      sacCer2.rnBlastTab.query (via sgdGene.name)
      sacCer2.sgdAbundance.name (via sgdGene.name)
      sacCer2.sgdBlastTab.query (via sgdGene.name)
      sacCer2.sgdBlastTab.target (via sgdGene.name)
      sacCer2.sgdCanonical.transcript (via sgdGene.name)
      sacCer2.sgdDescription.name (via sgdGene.name)
      sacCer2.sgdIsoforms.transcript (via sgdGene.name)
      sacCer2.sgdLocalization.name (via sgdGene.name)
      sacCer2.sgdPep.name (via sgdGene.name)
      sacCer2.sgdToName.name (via sgdGene.name)
      sacCer2.sgdToPfam.name (via sgdGene.name)
      sacCer2.sgdToSwissProt.name (via sgdGene.name)
      go.goaPart.dbObjectId (via sgdGene.proteinID)
      knownGeneV39.kgProtAlias.alias (via sgdGene.proteinID)
      knownGeneV39.kgSpAlias.spID (via sgdGene.proteinID)
      knownGeneV39.kgXref.spID (via sgdGene.proteinID)
      proteome.spOldNew.acc (via sgdGene.proteinID)
      proteome.spReactomeEvent.spID (via sgdGene.proteinID)
      proteome.spReactomeId.spID (via sgdGene.proteinID)
      sacCer2.sgdCanonical.protein (via sgdGene.proteinID)
      sacCer2.sgdToSwissProt.value (via sgdGene.proteinID)
      uniProt.accToKeyword.acc (via sgdGene.proteinID)
      uniProt.accToTaxon.acc (via sgdGene.proteinID)
      uniProt.citation.acc (via sgdGene.proteinID)
      uniProt.comment.acc (via sgdGene.proteinID)
      uniProt.description.acc (via sgdGene.proteinID)
      uniProt.displayId.acc (via sgdGene.proteinID)
      uniProt.extDbRef.acc (via sgdGene.proteinID)
      uniProt.feature.acc (via sgdGene.proteinID)
      uniProt.gene.acc (via sgdGene.proteinID)
      uniProt.geneLogic.acc (via sgdGene.proteinID)
      uniProt.info.acc (via sgdGene.proteinID)
      uniProt.otherAcc.acc (via sgdGene.proteinID)
      uniProt.protein.acc (via sgdGene.proteinID)
      visiGene.gene.uniProt (via sgdGene.proteinID)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinID
585R0010W2micron+251152325115231251,1523,n/a
585R0020C2micron-188630081886300811886,3008,n/a
585R0030W2micron+327038163270381613270,3816,n/a
585R0040C2micron-530761985307619815307,6198,n/a
585YAL069WchrI+3346493346491334,649,n/a
585YAL068W-AchrI+5377925377921537,792,n/a
585YAL068CchrI-180621691806216911806,2169,P53055
585YAL067W-AchrI+247927072479270712479,2707,Q8TGK6
585YAL067CchrI-723590177235901717235,9017,P39709
585YAL066WchrI+10091104001009110400110091,10400,n/a

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.