Schema for knownCanonical
  Database: mm39    Primary Table: knownCanonical    Row Count: 78,298   Data last updated: 2024-08-15
Format description: Describes the canonical splice variant of a gene
On download server: MariaDB table dump directory
fieldexampleSQL type info description
chrom chr3varchar(255) values Chromosome
chromStart 108014595int(11) range Start position (0 based). Represents transcription start for + strand genes, end for - strand genes
chromEnd 108053462int(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 ENSMUST00000000001.5varchar(255) values Corresponds to knownGene name field.
protein ENSMUSG00000000001.5varchar(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)
      mm39.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)
      mm39.bioCycPathway.kgID (via knownCanonical.transcript)
      mm39.ceBlastTab.query (via knownCanonical.transcript)
      mm39.dmBlastTab.query (via knownCanonical.transcript)
      mm39.drBlastTab.query (via knownCanonical.transcript)
      mm39.foldUtr3.name (via knownCanonical.transcript)
      mm39.foldUtr5.name (via knownCanonical.transcript)
      mm39.hgBlastTab.query (via knownCanonical.transcript)
      mm39.kgAlias.kgID (via knownCanonical.transcript)
      mm39.kgColor.kgID (via knownCanonical.transcript)
      mm39.kgProtAlias.kgID (via knownCanonical.transcript)
      mm39.kgSpAlias.kgID (via knownCanonical.transcript)
      mm39.kgTargetAli.qName (via knownCanonical.transcript)
      mm39.kgXref.kgID (via knownCanonical.transcript)
      mm39.knownAttrs.kgID (via knownCanonical.transcript)
      mm39.knownBlastTab.query (via knownCanonical.transcript)
      mm39.knownBlastTab.target (via knownCanonical.transcript)
      mm39.knownCds.name (via knownCanonical.transcript)
      mm39.knownGene.name (via knownCanonical.transcript)
      mm39.knownGeneMrna.name (via knownCanonical.transcript)
      mm39.knownIsoforms.transcript (via knownCanonical.transcript)
      mm39.knownToEnsembl.name (via knownCanonical.transcript)
      mm39.knownToLocusLink.name (via knownCanonical.transcript)
      mm39.knownToMrna.name (via knownCanonical.transcript)
      mm39.knownToMrnaSingle.name (via knownCanonical.transcript)
      mm39.knownToMupit.name (via knownCanonical.transcript)
      mm39.knownToNextProt.name (via knownCanonical.transcript)
      mm39.knownToPfam.name (via knownCanonical.transcript)
      mm39.knownToRefSeq.name (via knownCanonical.transcript)
      mm39.knownToSuper.gene (via knownCanonical.transcript)
      mm39.knownToTag.name (via knownCanonical.transcript)
      mm39.knownToVisiGene.name (via knownCanonical.transcript)
      mm39.knownToWikipedia.name (via knownCanonical.transcript)
      mm39.rnBlastTab.query (via knownCanonical.transcript)
      mm39.scBlastTab.query (via knownCanonical.transcript)
      mm39.ucscScop.ucscId (via knownCanonical.transcript)

Sample Rows
 
chromchromStartchromEndclusterIdtranscriptprotein
chr31080145951080534621ENSMUST00000000001.5ENSMUSG00000000001.5
chrX76881506768972292ENSMUST00000000003.14ENSMUSG00000000003.16
chr1618599196186307223ENSMUST00000000028.14ENSMUSG00000000028.16
chr71421292671421339574ENSMUST00000299854.1ENSMUSG00000000031.20
chrX1599460551600386555ENSMUST00000077375.5ENSMUSG00000000037.18
chr111082861181083052226ENSMUST00000000049.6ENSMUSG00000000049.12
chr111211280781211466827ENSMUST00000103015.4ENSMUSG00000000056.8
chr617281183172891148ENSMUST00000000058.7ENSMUSG00000000058.7
chr13591148059203939ENSMUST00000000080.8ENSMUSG00000000078.8
chr412026250312038738110ENSMUST00000000087.13ENSMUSG00000000085.17

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