Schema for kgTxInfo

Database: mm10 Primary Table: kgTxInfo Row Count: 63,814 Data last updated: 2018-04-13
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`	uc007afh.1	`varchar(255)`	values	Name of transcript
`category`	coding	`varchar(255)`	values	coding/nearCoding/noncoding for now
`sourceAcc`	NM_008866.2	`varchar(255)`	values	Accession of genbank transcript patterned on (may be refSeq)
`isRefSeq`	1	`tinyint(3) unsigned`	range	Is a refSeq
`sourceSize`	2447	`int(11)`	range	Number of bases in source, excluding poly-A tail.
`aliCoverage`	0.994279	`double`	range	Fraction of bases in source aligning.
`aliIdRatio`	1	`double`	range	matching/total bases in alignment
`genoMapCount`	1	`int(11)`	range	Number of times source aligns in genome.
`exonCount`	9	`int(11)`	range	Number of exons (excludes gaps from frame shift/stops)
`orfSize`	693	`int(11)`	range	Size of ORF
`cdsScore`	1494.5	`double`	range	Score of best CDS according to txCdsPredict
`startComplete`	1	`tinyint(3) unsigned`	range	Starts with ATG
`endComplete`	1	`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


	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) mm10.bioCycPathway.kgID (via kgTxInfo.name) mm10.ccdsKgMap.geneId (via kgTxInfo.name) mm10.ceBlastTab.query (via kgTxInfo.name) mm10.dmBlastTab.query (via kgTxInfo.name) mm10.drBlastTab.query (via kgTxInfo.name) mm10.foldUtr3.name (via kgTxInfo.name) mm10.foldUtr5.name (via kgTxInfo.name) mm10.hgBlastTab.query (via kgTxInfo.name) mm10.keggPathway.kgID (via kgTxInfo.name) mm10.kgAlias.kgID (via kgTxInfo.name) mm10.kgColor.kgID (via kgTxInfo.name) mm10.kgProtAlias.kgID (via kgTxInfo.name) mm10.kgProtMap2.qName (via kgTxInfo.name) mm10.kgSpAlias.kgID (via kgTxInfo.name) mm10.kgTargetAli.qName (via kgTxInfo.name) mm10.kgXref.kgID (via kgTxInfo.name) mm10.knownAttrs.kgID (via kgTxInfo.name) mm10.knownBlastTab.query (via kgTxInfo.name) mm10.knownBlastTab.target (via kgTxInfo.name) mm10.knownCanonical.transcript (via kgTxInfo.name) mm10.knownCds.name (via kgTxInfo.name) mm10.knownGene.name (via kgTxInfo.name) mm10.knownGeneMrna.name (via kgTxInfo.name) mm10.knownGenePep.name (via kgTxInfo.name) mm10.knownIsoforms.transcript (via kgTxInfo.name) mm10.knownToEnsembl.name (via kgTxInfo.name) mm10.knownToKeggEntrez.name (via kgTxInfo.name) mm10.knownToLocusLink.name (via kgTxInfo.name) mm10.knownToLynx.name (via kgTxInfo.name) mm10.knownToMrna.name (via kgTxInfo.name) mm10.knownToMrnaSingle.name (via kgTxInfo.name) mm10.knownToPfam.name (via kgTxInfo.name) mm10.knownToRefSeq.name (via kgTxInfo.name) mm10.knownToSuper.gene (via kgTxInfo.name) mm10.knownToTag.name (via kgTxInfo.name) mm10.knownToVisiGene.name (via kgTxInfo.name) mm10.knownToWikipedia.name (via kgTxInfo.name) mm10.rnBlastTab.query (via kgTxInfo.name) mm10.scBlastTab.query (via kgTxInfo.name) mm10.ucscScop.ucscId (via kgTxInfo.name)

Sample Rows

name	category	sourceAcc	isRefSeq	sourceSize	aliCoverage	aliIdRatio	genoMapCount	exonCount	orfSize	cdsScore	startComplete	endComplete	bleedIntoIntron	atacIntrons
uc007afh.1	coding	NM_008866.2	1	2447	0.994279	1	1	9	693	1494.5	1	1	0	0
uc007afg.1	coding	AK050549.1	0	765	0.997386	1	1	8	651	1438.5	1	1	1695	0
uc007afi.2	coding	NM_011541.4	1	2727	0.979465	1	1	10	906	2012	1	1	0	1
uc011wht.1	coding	NM_001159750.1	1	2724	0.979442	1	1	10	903	2006	1	1	0	1
uc011whu.1	coding	NM_001159751.1	1	2620	0.978626	1	1	10	939	1843.5	1	1	0	1
uc057aty.1	nearCoding	AK048564.1	0	4057	0.6702	0.999632	1	1	0	201.5	0	0	0	0
uc007afn.2	coding	NM_133826.5	1	2063	1	1	1	14	1452	3081.5	1	1	0	0
uc057atz.1	coding	NM_001310442.1	1	2009	1	1	1	13	1398	2973.5	1	1	0	0
uc007afm.2	coding	AK081492.1	0	2319	0.999569	0.999569	1	6	591	1329.5	1	1	1644	0
uc007afo.2	coding	NM_011011.2	1	4677	1	1	1	4	1143	2484	1	1	0	0

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