Schema for rgdGene2Canonical
  Database: rn4    Primary Table: rgdGene2Canonical    Row Count: 17,428   Data last updated: 2012-03-02
Format description: Describes the canonical splice variant of a gene
On download server: MariaDB table dump directory
fieldexampleSQL type info description
chrom chrXvarchar(255) values Chromosome
chromStart 175821int(11) range Start position (0 based). Represents transcription start for + strand genes, end for - strand genes
chromEnd 179442int(11) range End position (non-inclusive). Represents transcription end for + strand genes, start for - strand genes
clusterId 1int(10) unsigned range Which cluster of transcripts this belongs to in knownIsoforms
transcript RGD:1563873varchar(255) values Corresponds to knownGene name field.
protein D4ABX0varchar(255) values Accession of the associated protein, or UCSC ID in newer tables.

Connected Tables and Joining Fields
        rn4.affyExonTissuesGsMedianDistRgdGene2.query (via rgdGene2Canonical.transcript)
      rn4.affyExonTissuesGsMedianDistRgdGene2.target (via rgdGene2Canonical.transcript)
      rn4.affyExonTissuesGsMedianRgdGene2.name (via rgdGene2Canonical.transcript)
      rn4.affyExonTissuesGsRgdGene2.name (via rgdGene2Canonical.transcript)
      rn4.ceBlastTab.query (via rgdGene2Canonical.transcript)
      rn4.dmBlastTab.query (via rgdGene2Canonical.transcript)
      rn4.drBlastTab.query (via rgdGene2Canonical.transcript)
      rn4.gnfAtlas2RgdGene2Distance.query (via rgdGene2Canonical.transcript)
      rn4.gnfAtlas2RgdGene2Distance.target (via rgdGene2Canonical.transcript)
      rn4.hgBlastTab.query (via rgdGene2Canonical.transcript)
      rn4.mmBlastTab.query (via rgdGene2Canonical.transcript)
      rn4.rgdGene2.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2BlastTab.query (via rgdGene2Canonical.transcript)
      rn4.rgdGene2BlastTab.target (via rgdGene2Canonical.transcript)
      rn4.rgdGene2Isoforms.transcript (via rgdGene2Canonical.transcript)
      rn4.rgdGene2KeggPathway.rgdId (via rgdGene2Canonical.transcript)
      rn4.rgdGene2Pep.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToDescription.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToDisplayId.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToEnsembl.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToGenbank.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToGenbankAll.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToGnfAtlas2.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToKeggEntrez.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToLocusLink.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToPDB.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToPfam.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToRAE230.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToRefSeq.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToSymbol.rgdId (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToU34A.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2ToUniProt.name (via rgdGene2Canonical.transcript)
      rn4.rgdGene2Xref.rgdGeneId (via rgdGene2Canonical.transcript)
      rn4.rgdGenePathway.geneId (via rgdGene2Canonical.transcript)
      rn4.scBlastTab.query (via rgdGene2Canonical.transcript)

Sample Rows
 
chromchromStartchromEndclusterIdtranscriptprotein
chrX1758211794421RGD:1563873D4ABX0
chrX5989516029812RGD:1560768D3ZKN9
chrX6319816324883RGD:1588662RGD:1588662
chrX111384811143674RGD:1588647RGD:1588647
chrX189528525292115RGD:1561678RGD:1561678
chrX319620433107496RGD:1561623RGD:1561623
chrX550178655024887RGD:1560720D3ZPZ8
chrX649071064914068RGD:1560124RGD:1560124
chrX674466967491169RGD:1311230Q499P3
chrX6800505683802310RGD:1564494D3ZNZ7

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