Schema for refGene

Database: hg17 Primary Table: refGene Row Count: 78,119 Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	661	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`name`	NM_001099431	`varchar(255)`	values	Name of gene (usually transcript_id from GTF)
`chrom`	chr12	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	10036928	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	10043166	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	10037008	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	10042966	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	5	`int(10) unsigned`	range	Number of exons
`exonStarts`	10036928,10039005,10040711,...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	10037153,10039112,10040866,...	`longblob`		Exon end positions (or start positions for minus strand item)
`score`	0	`int(11)`	range	score
`name2`	CLEC1B	`varchar(255)`	values	Alternate name (e.g. gene_id from GTF)
`cdsStartStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values	Status of CDS start annotation (none, unknown, incomplete, or complete)
`cdsEndStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values	Status of CDS end annotation (none, unknown, incomplete, or complete)
`exonFrames`	2,0,1,1,0,	`longblob`		Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields


	hg17.all_est.qName (via refGene.name) hg17.all_mrna.qName (via refGene.name) hg17.altGraphX.mrnaRefs (via refGene.name) hg17.ccdsInfo.mrnaAcc (via refGene.name) hg17.dupSpMrna.dupMrnaID (via refGene.name) hg17.dupSpMrna.mrnaID (via refGene.name) hg17.kgXref.refseq (via refGene.name) hg17.knownToRefSeq.value (via refGene.name) hg17.mrnaOrientInfo.name (via refGene.name) hg17.mrnaRefseq.mrna (via refGene.name) hg17.mrnaRefseq.refseq (via refGene.name) hg17.refFlat.name (via refGene.name) hg17.refSeqAli.qName (via refGene.name) hg17.spMrna.mrnaID (via refGene.name) hg17.xenoEst.qName (via refGene.name) hg17.xenoMrna.qName (via refGene.name) hg17.xenoRefGene.name (via refGene.name) hg17.xenoRefSeqAli.qName (via refGene.name) hgFixed.gbCdnaInfo.acc (via refGene.name) hgFixed.gbMiscDiff.acc (via refGene.name) hgFixed.gbSeq.acc (via refGene.name) hgFixed.gbWarn.acc (via refGene.name) hgFixed.imageClone.acc (via refGene.name) hgFixed.refLink.mrnaAcc (via refGene.name) hgFixed.refSeqStatus.mrnaAcc (via refGene.name) hgFixed.refSeqSummary.mrnaAcc (via refGene.name) knownGeneV39.kgXref.refseq (via refGene.name) knownGeneV39.knownToRefSeq.value (via refGene.name)

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
661	NM_001099431	chr12	-	10036928	10043166	10037008	10042966	5	10036928,10039005,10040711,10041025,10042902,	10037153,10039112,10040866,10041145,10043166,	CLEC1B	cmpl	cmpl	2,0,1,1,0,
17	NM_080805	chr10	+	71231667	71388906	71232185	71388463	34	71231667,71252130,71253882,71301945,71317217,71318065,71319175,71324313,71324436,71325311,71327236,71332509,71334694,71335548,71 ...	71232479,71252201,71253889,71301972,71317253,71318092,71319202,71324340,71324463,71325338,71327293,71332617,71334721,71335584,71 ...	COL13A1	cmpl	cmpl	0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
116	NM_001320686	chr10	-	45970128	46060725	45971707	46025865	9	45970128,45972474,45984919,45987910,46004437,46007349,46025768,46028428,46060604,	45971773,45972537,45985135,45988245,46004528,46007501,46025881,46028526,46060725,	PTPN20	cmpl	cmpl	0,0,0,1,0,1,0,-1,-1,
588	NM_001895	chr20	-	401141	472434	412604	437195	13	401141,415019,416070,417321,418423,420897,424362,426364,427898,428476,433761,437094,472315,	412720,415106,416219,417422,418525,421008,424446,426424,427949,428578,433873,437304,472434,	CSNK2A1	cmpl	cmpl	1,1,2,0,0,0,0,0,0,0,2,0,-1,
2437	NR_130702	chr2	+	242746535	242818229	242818229	242818229	7	242746535,242752789,242772541,242788558,242796687,242817247,242817859,	242746704,242752930,242772644,242788716,242796792,242817397,242818229,	LINC01881	unk	unk	-1,-1,-1,-1,-1,-1,-1,
73	NR_130701	chr1	-	80950	785413	785413	785413	6	80950,228280,695274,781041,783816,785309,	81492,228430,695443,781134,783866,785413,	LINC01881	unk	unk	-1,-1,-1,-1,-1,-1,
1843	NR_026844	chr1	-	164946476	164948326	164948326	164948326	1	164946476,	164948326,	ANKRD36BP1	unk	unk	-1,
772	NM_001003895	chrY	-	24529501	24532286	24529875	24531960	2	24529501,24530368,	24529948,24532286,	CDY1B	cmpl	cmpl	2,0,
784	NM_001003895	chrY	+	26106388	26109173	26106714	26108799	2	26106388,26108726,	26108306,26109173,	CDY1B	cmpl	cmpl	0,2,
1698	NM_001378029	chr8	-	145968412	145983506	145969454	145974660	5	145968412,145974226,145974627,145976416,145983467,	145970794,145974353,145974714,145976469,145983506,	ZNF34	cmpl	cmpl	1,0,0,-1,-1,

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