Schema for kgTxInfo

Database: hg18 Primary Table: kgTxInfo Row Count: 66,803 Data last updated: 2009-03-03
Format description: Various bits of information about a transcript from the txGraph/txCds system (aka KG3)
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`name`	uc001aaa.2	`varchar(255)`	values	Name of transcript
`category`	noncoding	`varchar(255)`	values	coding/nearCoding/noncoding for now
`sourceAcc`	BC032353.1	`varchar(255)`	values	Accession of genbank transcript patterned on (may be refSeq)
`isRefSeq`	0	`tinyint(3) unsigned`	range	Is a refSeq
`sourceSize`	1673	`int(11)`	range	Number of bases in source, excluding poly-A tail.
`aliCoverage`	0.896593	`double`	range	Fraction of bases in source aligning.
`aliIdRatio`	0.995119	`double`	range	matching/total bases in alignment
`genoMapCount`	3	`int(11)`	range	Number of times source aligns in genome.
`exonCount`	3	`int(11)`	range	Number of exons (excludes gaps from frame shift/stops)
`orfSize`	0	`int(11)`	range	Size of ORF
`cdsScore`	19.5	`double`	range	Score of best CDS according to txCdsPredict
`startComplete`	0	`tinyint(3) unsigned`	range	Starts with ATG
`endComplete`	0	`tinyint(3) unsigned`	range	Ends with stop codon
`nonsenseMediatedDecay`	0	`tinyint(3) unsigned`	range	If true, is a nonsense mediated decay candidate.
`retainedIntron`	0	`tinyint(3) unsigned`	range	True if has a retained intron compared to overlapping transcripts
`bleedIntoIntron`	0	`int(11)`	range	If nonzero number of bases start or end of tx bleeds into intron
`strangeSplice`	0	`int(11)`	range	Count of splice sites not gt/ag, gc/ag, or at/ac
`atacIntrons`	0	`int(11)`	range	Count of number of at/ac introns
`cdsSingleInIntron`	0	`tinyint(3) unsigned`	range	True if CDS is single exon and in intron of other transcript.
`cdsSingleInUtr3`	0	`tinyint(3) unsigned`	range	True if CDS is single exon and in 3' UTR of other transcript.
`selenocysteine`	0	`tinyint(3) unsigned`	range	If true TGA codes for selenocysteine
`genomicFrameShift`	0	`tinyint(3) unsigned`	range	True if genomic version has frame shift we cut out
`genomicStop`	0	`tinyint(3) unsigned`	range	True if genomic version has stop codon we cut out

Connected Tables and Joining Fields


	hg18.bioCycPathway.kgID (via kgTxInfo.name) hg18.ccdsKgMap.geneId (via kgTxInfo.name) hg18.ceBlastTab.query (via kgTxInfo.name) hg18.dmBlastTab.query (via kgTxInfo.name) hg18.drBlastTab.query (via kgTxInfo.name) hg18.foldUtr3.name (via kgTxInfo.name) hg18.foldUtr5.name (via kgTxInfo.name) hg18.gnfAtlas2Distance.query (via kgTxInfo.name) hg18.gnfAtlas2Distance.target (via kgTxInfo.name) hg18.gnfU95Distance.query (via kgTxInfo.name) hg18.gnfU95Distance.target (via kgTxInfo.name) hg18.humanHprdP2P.query (via kgTxInfo.name) hg18.humanHprdP2P.target (via kgTxInfo.name) hg18.humanVidalP2P.query (via kgTxInfo.name) hg18.humanVidalP2P.target (via kgTxInfo.name) hg18.humanWankerP2P.query (via kgTxInfo.name) hg18.humanWankerP2P.target (via kgTxInfo.name) hg18.keggPathway.kgID (via kgTxInfo.name) hg18.kgAlias.kgID (via kgTxInfo.name) hg18.kgColor.kgID (via kgTxInfo.name) hg18.kgProtAlias.kgID (via kgTxInfo.name) hg18.kgProtMap2.qName (via kgTxInfo.name) hg18.kgSpAlias.kgID (via kgTxInfo.name) hg18.kgTargetAli.qName (via kgTxInfo.name) hg18.kgXref.kgID (via kgTxInfo.name) hg18.knownBlastTab.query (via kgTxInfo.name) hg18.knownBlastTab.target (via kgTxInfo.name) hg18.knownCanonical.protein (via kgTxInfo.name) hg18.knownCanonical.transcript (via kgTxInfo.name) hg18.knownGene.name (via kgTxInfo.name) hg18.knownGeneMrna.name (via kgTxInfo.name) hg18.knownGenePep.name (via kgTxInfo.name) hg18.knownIsoforms.transcript (via kgTxInfo.name) hg18.knownToAllenBrain.name (via kgTxInfo.name) hg18.knownToEnsembl.name (via kgTxInfo.name) hg18.knownToGnf1h.name (via kgTxInfo.name) hg18.knownToGnfAtlas2.name (via kgTxInfo.name) hg18.knownToHInv.name (via kgTxInfo.name) hg18.knownToHprd.name (via kgTxInfo.name) hg18.knownToKeggEntrez.name (via kgTxInfo.name) hg18.knownToLocusLink.name (via kgTxInfo.name) hg18.knownToMupit.name (via kgTxInfo.name) hg18.knownToPfam.name (via kgTxInfo.name) hg18.knownToRefSeq.name (via kgTxInfo.name) hg18.knownToSuper.gene (via kgTxInfo.name) hg18.knownToTreefam.name (via kgTxInfo.name) hg18.knownToU133.name (via kgTxInfo.name) hg18.knownToU133Plus2.name (via kgTxInfo.name) hg18.knownToU95.name (via kgTxInfo.name) hg18.knownToVisiGene.name (via kgTxInfo.name) hg18.mmBlastTab.query (via kgTxInfo.name) hg18.rnBlastTab.query (via kgTxInfo.name) hg18.scBlastTab.query (via kgTxInfo.name) hg18.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

name	category	sourceAcc	isRefSeq	sourceSize	aliCoverage	aliIdRatio	genoMapCount	exonCount	orfSize	cdsScore	startComplete	endComplete	retainedIntron	bleedIntoIntron
uc001aaa.2	noncoding	BC032353.1	0	1673	0.896593	0.995119	3	3	0	19.5	0	0	0	0
uc009vip.1	noncoding	AX748260.1	0	3101	0.891648	0.983502	2	2	0	-23.5	0	0	1	1688
uc009vjg.1	noncoding	BC048429.1	0	1917	0.369327	0.977401	5	3	0	234	0	0	0	0
uc001aal.1	coding	NM_001005484.1	1	918	1	1	1	1	918	1805.5	1	1	0	0
uc009vjh.1	coding	AY972817.1	0	888	1	0.994369	2	3	738	1331	1	0	0	0
uc001aaq.1	noncoding	DQ599874.1	0	32	0.96875	1	28	1	0	151	0	0	0	0
uc001aar.1	noncoding	DQ599768.1	0	32	0.75	1	36	1	0	142.5	0	0	0	0
uc001aas.1	noncoding	DQ574670.1	0	32	0.96875	1	27	1	0	0	0	0	0	0
uc001aat.1	noncoding	DQ596298.1	0	28	1	1	16	1	0	151	0	0	0	0
uc001aau.1	noncoding	DQ599768.1	0	32	1	1	36	1	0	177	0	0	0	0

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