Schema for SGD Genes - Protein-Coding Genes from Saccharomyces Genome Database
  Database: sacCer3    Primary Table: sgdGene    Row Count: 6,692   Data last updated: 2011-08-29
Format description: GenePred table with proteinID field for WormBase Genes.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name YAL069Wvarchar(255) values Name of gene
chrom chrIvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 334int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 649int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 334int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 649int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 334,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 649,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
        sacCer3.ceBlastTab.query (via sgdGene.name)
      sacCer3.choExpDistance.query (via sgdGene.name)
      sacCer3.choExpDistance.target (via sgdGene.name)
      sacCer3.dmBlastTab.query (via sgdGene.name)
      sacCer3.drBlastTab.query (via sgdGene.name)
      sacCer3.esRegGeneToModule.gene (via sgdGene.name)
      sacCer3.esRegGeneToMotif.gene (via sgdGene.name)
      sacCer3.esRegUpstreamRegion.name (via sgdGene.name)
      sacCer3.hgBlastTab.query (via sgdGene.name)
      sacCer3.mmBlastTab.query (via sgdGene.name)
      sacCer3.rnBlastTab.query (via sgdGene.name)
      sacCer3.sgdBlastTab.query (via sgdGene.name)
      sacCer3.sgdBlastTab.target (via sgdGene.name)
      sacCer3.sgdCanonical.transcript (via sgdGene.name)
      sacCer3.sgdDescription.name (via sgdGene.name)
      sacCer3.sgdIsoforms.transcript (via sgdGene.name)
      sacCer3.sgdPep.name (via sgdGene.name)
      sacCer3.sgdToName.name (via sgdGene.name)
      sacCer3.sgdToSwissProt.name (via sgdGene.name)
      go.goaPart.dbObjectId (via sgdGene.proteinID)
      proteome.spOldNew.acc (via sgdGene.proteinID)
      proteome.spReactomeEvent.spID (via sgdGene.proteinID)
      proteome.spReactomeId.spID (via sgdGene.proteinID)
      sacCer3.sgdCanonical.protein (via sgdGene.proteinID)
      sacCer3.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
585YAL069WchrI+3346493346491334,649,n/a
585YAL068W-AchrI+5377925377921537,792,n/a
585YAL068CchrI-180621691806216911806,2169,P0CE93
585YAL067W-AchrI+247927072479270712479,2707,Q8TGK6
585YAL067CchrI-723490167234901617234,9016,P39709
585YAL066WchrI+10090103991009010399110090,10399,n/a
585YAL065CchrI-11564119511156411951111564,11951,O13511
585YAL064W-BchrI+12045124261204512426112045,12426,O13512
585YAL064C-AchrI-13362137431336213743113362,13743,Q6B2U8
585YAL064WchrI+21565218502156521850121565,21850,P39711

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

SGD Genes (sgdGene) Track Description
 

Description

This track shows annotated genes and open reading frames (ORFs) of Saccharomyces cerevisiae obtained from the Saccharomyces Genome Database (SGD).

Clicking on an item in this track brings up a display that synthesizes available data on the gene from a wide variety of sources.

The data were downloaded from the SGD: saccharomyces_cerevisiae.gff (accessed 29 Aug. 2011)

This track excludes the ORFs classified as dubious by SGD.

Credits

Thanks to the SGD for providing the data used in this annotation.