Schema for knownCanonical
  Database: mm9    Primary Table: knownCanonical    Row Count: 28,661   Data last updated: 2011-03-02
Format description: Describes the canonical splice variant of a gene
On download server: MariaDB table dump directory
fieldexampleSQL type info description
chrom chr1varchar(255) values Chromosome
chromStart 3204562int(11) range Start position (0 based). Represents transcription start for + strand genes, end for - strand genes
chromEnd 3661579int(11) range End position (non-inclusive). Represents transcription end for + strand genes, start for - strand genes
clusterId 1int(11) range Which cluster of transcripts this belongs to in knownIsoforms
transcript uc007aeu.1varchar(255) values Corresponds to knownGene name field.
protein uc007aeu.1varchar(255) values Accession of the associated protein, or UCSC ID in newer tables.

Connected Tables and Joining Fields
        knownGeneV39.knownCanonical.clusterId (via knownCanonical.clusterId)
      knownGeneV39.knownIsoforms.clusterId (via knownCanonical.clusterId)
      mm9.knownIsoforms.clusterId (via knownCanonical.clusterId)
      knownGeneV39.bioCycPathway.kgID (via knownCanonical.transcript)
      knownGeneV39.ceBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.dmBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.drBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.foldUtr3.name (via knownCanonical.transcript)
      knownGeneV39.foldUtr5.name (via knownCanonical.transcript)
      knownGeneV39.gnfAtlas2Distance.query (via knownCanonical.transcript)
      knownGeneV39.gnfAtlas2Distance.target (via knownCanonical.transcript)
      knownGeneV39.kgAlias.kgID (via knownCanonical.transcript)
      knownGeneV39.kgColor.kgID (via knownCanonical.transcript)
      knownGeneV39.kgProtAlias.kgID (via knownCanonical.transcript)
      knownGeneV39.kgSpAlias.kgID (via knownCanonical.transcript)
      knownGeneV39.kgTargetAli.qName (via knownCanonical.transcript)
      knownGeneV39.kgXref.kgID (via knownCanonical.transcript)
      knownGeneV39.knownAttrs.kgID (via knownCanonical.transcript)
      knownGeneV39.knownBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.knownBlastTab.target (via knownCanonical.transcript)
      knownGeneV39.knownCanonical.protein (via knownCanonical.transcript)
      knownGeneV39.knownCanonical.transcript (via knownCanonical.transcript)
      knownGeneV39.knownCds.name (via knownCanonical.transcript)
      knownGeneV39.knownGene.name (via knownCanonical.transcript)
      knownGeneV39.knownGeneMrna.name (via knownCanonical.transcript)
      knownGeneV39.knownGenePep.name (via knownCanonical.transcript)
      knownGeneV39.knownIsoforms.transcript (via knownCanonical.transcript)
      knownGeneV39.knownToEnsembl.name (via knownCanonical.transcript)
      knownGeneV39.knownToGnfAtlas2.name (via knownCanonical.transcript)
      knownGeneV39.knownToHprd.name (via knownCanonical.transcript)
      knownGeneV39.knownToLocusLink.name (via knownCanonical.transcript)
      knownGeneV39.knownToMrna.name (via knownCanonical.transcript)
      knownGeneV39.knownToMrnaSingle.name (via knownCanonical.transcript)
      knownGeneV39.knownToMupit.name (via knownCanonical.transcript)
      knownGeneV39.knownToPfam.name (via knownCanonical.transcript)
      knownGeneV39.knownToRefSeq.name (via knownCanonical.transcript)
      knownGeneV39.knownToSuper.gene (via knownCanonical.transcript)
      knownGeneV39.knownToTag.name (via knownCanonical.transcript)
      knownGeneV39.knownToU133.name (via knownCanonical.transcript)
      knownGeneV39.knownToU95.name (via knownCanonical.transcript)
      knownGeneV39.knownToVisiGene.name (via knownCanonical.transcript)
      knownGeneV39.knownToWikipedia.name (via knownCanonical.transcript)
      knownGeneV39.mmBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.rnBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.scBlastTab.query (via knownCanonical.transcript)
      knownGeneV39.ucscScop.ucscId (via knownCanonical.transcript)
      mm9.affyGnfU74ADistance.query (via knownCanonical.transcript)
      mm9.affyGnfU74ADistance.target (via knownCanonical.transcript)
      mm9.affyGnfU74BDistance.query (via knownCanonical.transcript)
      mm9.affyGnfU74BDistance.target (via knownCanonical.transcript)
      mm9.affyGnfU74CDistance.query (via knownCanonical.transcript)
      mm9.affyGnfU74CDistance.target (via knownCanonical.transcript)
      mm9.bioCycPathway.kgID (via knownCanonical.transcript)
      mm9.ccdsKgMap.geneId (via knownCanonical.transcript)
      mm9.ceBlastTab.query (via knownCanonical.transcript)
      mm9.dmBlastTab.query (via knownCanonical.transcript)
      mm9.drBlastTab.query (via knownCanonical.transcript)
      mm9.foldUtr3.name (via knownCanonical.transcript)
      mm9.foldUtr5.name (via knownCanonical.transcript)
      mm9.gnfAtlas2Distance.query (via knownCanonical.transcript)
      mm9.gnfAtlas2Distance.target (via knownCanonical.transcript)
      mm9.hgBlastTab.query (via knownCanonical.transcript)
      mm9.keggPathway.kgID (via knownCanonical.transcript)
      mm9.kgAlias.kgID (via knownCanonical.transcript)
      mm9.kgColor.kgID (via knownCanonical.transcript)
      mm9.kgProtAlias.kgID (via knownCanonical.transcript)
      mm9.kgProtMap2.qName (via knownCanonical.transcript)
      mm9.kgSpAlias.kgID (via knownCanonical.transcript)
      mm9.kgTargetAli.qName (via knownCanonical.transcript)
      mm9.kgTxInfo.name (via knownCanonical.transcript)
      mm9.kgXref.kgID (via knownCanonical.transcript)
      mm9.knownBlastTab.query (via knownCanonical.transcript)
      mm9.knownBlastTab.target (via knownCanonical.transcript)
      mm9.knownGene.name (via knownCanonical.transcript)
      mm9.knownGeneMrna.name (via knownCanonical.transcript)
      mm9.knownGenePep.name (via knownCanonical.transcript)
      mm9.knownIsoforms.transcript (via knownCanonical.transcript)
      mm9.knownToAllenBrain.name (via knownCanonical.transcript)
      mm9.knownToEnsembl.name (via knownCanonical.transcript)
      mm9.knownToGnfAtlas2.name (via knownCanonical.transcript)
      mm9.knownToKeggEntrez.name (via knownCanonical.transcript)
      mm9.knownToLocusLink.name (via knownCanonical.transcript)
      mm9.knownToPfam.name (via knownCanonical.transcript)
      mm9.knownToRefSeq.name (via knownCanonical.transcript)
      mm9.knownToSuper.gene (via knownCanonical.transcript)
      mm9.knownToVisiGene.name (via knownCanonical.transcript)
      mm9.rnBlastTab.query (via knownCanonical.transcript)
      mm9.scBlastTab.query (via knownCanonical.transcript)
      mm9.ucscScop.ucscId (via knownCanonical.transcript)

Sample Rows
 
chromchromStartchromEndclusterIdtranscriptprotein
chr1320456236615791uc007aeu.1uc007aeu.1
chr1363839136489852uc007aev.1uc007aev.1
chr1433358743503953uc007aex.2uc007aex.2
chr1448100844864944uc007aez.1uc007aez.1
chr1476327847758075uc007aff.2uc007aff.2
chr1479797348368166uc007afh.1uc007afh.1
chr1484777448879907uc007afi.2uc007afi.2
chr1489965650603668uc007afl.2uc007afl.2
chr1507325351526309uc007afn.1uc007afn.1
chr15159376515940210uc011whv.1uc011whv.1

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