Schema for kgTxInfo
  Database: hg19    Primary Table: kgTxInfo    Row Count: 82,960   Data last updated: 2013-06-14
Format description: Various bits of information about a transcript from the txGraph/txCds system (aka KG3)
On download server: MariaDB table dump directory
fieldexampleSQL type info description
name uc001aaa.3varchar(255) values Name of transcript
category nearCodingvarchar(255) values coding/nearCoding/noncoding for now
sourceAcc NR_046018.2varchar(255) values Accession of genbank transcript patterned on (may be refSeq)
isRefSeq 0tinyint(3) unsigned range Is a refSeq
sourceSize 1652int(11) range Number of bases in source, excluding poly-A tail.
aliCoverage 1double range Fraction of bases in source aligning.
aliIdRatio 1double range matching/total bases in alignment
genoMapCount 1int(11) range Number of times source aligns in genome.
exonCount 3int(11) range Number of exons (excludes gaps from frame shift/stops)
orfSize 0int(11) range Size of ORF
cdsScore 310.5double range Score of best CDS according to txCdsPredict
startComplete 0tinyint(3) unsigned range Starts with ATG
endComplete 0tinyint(3) unsigned range Ends with stop codon
nonsenseMediatedDecay 0tinyint(3) unsigned range If true, is a nonsense mediated decay candidate.
retainedIntron 0tinyint(3) unsigned range True if has a retained intron compared to overlapping transcripts
bleedIntoIntron 0int(11) range If nonzero number of bases start or end of tx bleeds into intron
strangeSplice 0int(11) range Count of splice sites not gt/ag, gc/ag, or at/ac
atacIntrons 0int(11) range Count of number of at/ac introns
cdsSingleInIntron 0tinyint(3) unsigned range True if CDS is single exon and in intron of other transcript.
cdsSingleInUtr3 0tinyint(3) unsigned range True if CDS is single exon and in 3' UTR of other transcript.
selenocysteine 0tinyint(3) unsigned range If true TGA codes for selenocysteine
genomicFrameShift 0tinyint(3) unsigned range True if genomic version has frame shift we cut out
genomicStop 0tinyint(3) unsigned range True if genomic version has stop codon we cut out

Connected Tables and Joining Fields
        hg19.bioCycPathway.kgID (via kgTxInfo.name)
      hg19.ccdsKgMap.geneId (via kgTxInfo.name)
      hg19.ceBlastTab.query (via kgTxInfo.name)
      hg19.dmBlastTab.query (via kgTxInfo.name)
      hg19.drBlastTab.query (via kgTxInfo.name)
      hg19.foldUtr3.name (via kgTxInfo.name)
      hg19.foldUtr5.name (via kgTxInfo.name)
      hg19.gnfAtlas2Distance.query (via kgTxInfo.name)
      hg19.gnfAtlas2Distance.target (via kgTxInfo.name)
      hg19.gnfU95Distance.query (via kgTxInfo.name)
      hg19.gnfU95Distance.target (via kgTxInfo.name)
      hg19.humanHprdP2P.query (via kgTxInfo.name)
      hg19.humanHprdP2P.target (via kgTxInfo.name)
      hg19.humanVidalP2P.query (via kgTxInfo.name)
      hg19.humanVidalP2P.target (via kgTxInfo.name)
      hg19.humanWankerP2P.query (via kgTxInfo.name)
      hg19.humanWankerP2P.target (via kgTxInfo.name)
      hg19.keggPathway.kgID (via kgTxInfo.name)
      hg19.kgAlias.kgID (via kgTxInfo.name)
      hg19.kgColor.kgID (via kgTxInfo.name)
      hg19.kgProtAlias.kgID (via kgTxInfo.name)
      hg19.kgProtMap2.qName (via kgTxInfo.name)
      hg19.kgSpAlias.kgID (via kgTxInfo.name)
      hg19.kgTargetAli.qName (via kgTxInfo.name)
      hg19.kgXref.kgID (via kgTxInfo.name)
      hg19.knownBlastTab.query (via kgTxInfo.name)
      hg19.knownBlastTab.target (via kgTxInfo.name)
      hg19.knownCanonical.transcript (via kgTxInfo.name)
      hg19.knownGene.name (via kgTxInfo.name)
      hg19.knownGeneMrna.name (via kgTxInfo.name)
      hg19.knownGenePep.name (via kgTxInfo.name)
      hg19.knownGeneTxMrna.name (via kgTxInfo.name)
      hg19.knownGeneTxPep.name (via kgTxInfo.name)
      hg19.knownIsoforms.transcript (via kgTxInfo.name)
      hg19.knownToAllenBrain.name (via kgTxInfo.name)
      hg19.knownToEnsembl.name (via kgTxInfo.name)
      hg19.knownToGnfAtlas2.name (via kgTxInfo.name)
      hg19.knownToHInv.name (via kgTxInfo.name)
      hg19.knownToHprd.name (via kgTxInfo.name)
      hg19.knownToKeggEntrez.name (via kgTxInfo.name)
      hg19.knownToLocusLink.name (via kgTxInfo.name)
      hg19.knownToLynx.name (via kgTxInfo.name)
      hg19.knownToMupit.name (via kgTxInfo.name)
      hg19.knownToNextProt.name (via kgTxInfo.name)
      hg19.knownToPfam.name (via kgTxInfo.name)
      hg19.knownToRefSeq.name (via kgTxInfo.name)
      hg19.knownToSuper.gene (via kgTxInfo.name)
      hg19.knownToTreefam.name (via kgTxInfo.name)
      hg19.knownToU133.name (via kgTxInfo.name)
      hg19.knownToU133Plus2.name (via kgTxInfo.name)
      hg19.knownToU95.name (via kgTxInfo.name)
      hg19.knownToVisiGene.name (via kgTxInfo.name)
      hg19.knownToWikipedia.name (via kgTxInfo.name)
      hg19.mmBlastTab.query (via kgTxInfo.name)
      hg19.rnBlastTab.query (via kgTxInfo.name)
      hg19.scBlastTab.query (via kgTxInfo.name)
      hg19.ucscScop.ucscId (via kgTxInfo.name)
      knownGeneV39.bioCycPathway.kgID (via kgTxInfo.name)
      knownGeneV39.ceBlastTab.query (via kgTxInfo.name)
      knownGeneV39.dmBlastTab.query (via kgTxInfo.name)
      knownGeneV39.drBlastTab.query (via kgTxInfo.name)
      knownGeneV39.foldUtr3.name (via kgTxInfo.name)
      knownGeneV39.foldUtr5.name (via kgTxInfo.name)
      knownGeneV39.gnfAtlas2Distance.query (via kgTxInfo.name)
      knownGeneV39.gnfAtlas2Distance.target (via kgTxInfo.name)
      knownGeneV39.kgAlias.kgID (via kgTxInfo.name)
      knownGeneV39.kgColor.kgID (via kgTxInfo.name)
      knownGeneV39.kgProtAlias.kgID (via kgTxInfo.name)
      knownGeneV39.kgSpAlias.kgID (via kgTxInfo.name)
      knownGeneV39.kgTargetAli.qName (via kgTxInfo.name)
      knownGeneV39.kgXref.kgID (via kgTxInfo.name)
      knownGeneV39.knownAttrs.kgID (via kgTxInfo.name)
      knownGeneV39.knownBlastTab.query (via kgTxInfo.name)
      knownGeneV39.knownBlastTab.target (via kgTxInfo.name)
      knownGeneV39.knownCanonical.protein (via kgTxInfo.name)
      knownGeneV39.knownCanonical.transcript (via kgTxInfo.name)
      knownGeneV39.knownCds.name (via kgTxInfo.name)
      knownGeneV39.knownGene.name (via kgTxInfo.name)
      knownGeneV39.knownGeneMrna.name (via kgTxInfo.name)
      knownGeneV39.knownGenePep.name (via kgTxInfo.name)
      knownGeneV39.knownIsoforms.transcript (via kgTxInfo.name)
      knownGeneV39.knownToEnsembl.name (via kgTxInfo.name)
      knownGeneV39.knownToGnfAtlas2.name (via kgTxInfo.name)
      knownGeneV39.knownToHprd.name (via kgTxInfo.name)
      knownGeneV39.knownToLocusLink.name (via kgTxInfo.name)
      knownGeneV39.knownToMrna.name (via kgTxInfo.name)
      knownGeneV39.knownToMrnaSingle.name (via kgTxInfo.name)
      knownGeneV39.knownToMupit.name (via kgTxInfo.name)
      knownGeneV39.knownToPfam.name (via kgTxInfo.name)
      knownGeneV39.knownToRefSeq.name (via kgTxInfo.name)
      knownGeneV39.knownToSuper.gene (via kgTxInfo.name)
      knownGeneV39.knownToTag.name (via kgTxInfo.name)
      knownGeneV39.knownToU133.name (via kgTxInfo.name)
      knownGeneV39.knownToU95.name (via kgTxInfo.name)
      knownGeneV39.knownToVisiGene.name (via kgTxInfo.name)
      knownGeneV39.knownToWikipedia.name (via kgTxInfo.name)
      knownGeneV39.mmBlastTab.query (via kgTxInfo.name)
      knownGeneV39.rnBlastTab.query (via kgTxInfo.name)
      knownGeneV39.scBlastTab.query (via kgTxInfo.name)
      knownGeneV39.ucscScop.ucscId (via kgTxInfo.name)

Sample Rows
 
namecategorysourceAccisRefSeqsourceSizealiCoveragealiIdRatiogenoMapCountexonCountorfSizecdsScorestartCompleteendCompletenonsenseMediatedDecayretainedIntronbleedIntoIntronstrangeSpliceatacIntronscdsSingleInIntroncdsSingleInUtr3selenocysteinegenomicFrameShiftgenomicStop
uc001aaa.3nearCodingNR_046018.20165211130310.5000000000000
uc010nxr.1nearCodingAM992878.10154510.992233230256.5000000000000
uc010nxq.1codingAM992880.10148810.99798423402722.5110000000000
uc001aal.1codingNM_001005484.1191811119182033110000000000
uc001aaq.2noncodingDQ597235.10270.96296312710151000000000000
uc001aar.2noncodingDQ599768.10320.2513210127.5000000000000
uc001aau.3codingNR_028325.10437010.9990852311701166110116430000000
uc021oeh.1codingAK302889.1011760.999150.99574834801922110000000000
uc009vjk.2codingAK293878.1014460.9965420.9923664311701358110100000000
uc021oei.1codingDQ574721.10260.9615381261468658110000000000

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