Schema for refFlat

Database: hg38 Primary Table: refFlat Row Count: 88,819 Data last updated: 2020-08-17
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	ZNF639	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001375803	`varchar(255)`	values	Name of gene
`chrom`	chr3	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	179323030	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	179338583	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	179328293	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	179334422	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	5	`int(10) unsigned`	range	Number of exons
`exonStarts`	179323030,179328282,1793296...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	179323291,179328351,1793297...	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	hg38.kgAlias.alias (via refFlat.geneName) hg38.kgSpAlias.alias (via refFlat.geneName) hg38.kgXref.geneSymbol (via refFlat.geneName) hgFixed.refLink.name (via refFlat.geneName) visiGene.gene.name (via refFlat.geneName) hg38.ccdsInfo.mrnaAcc (via refFlat.name) hg38.kgXref.refseq (via refFlat.name) hg38.knownToRefSeq.value (via refFlat.name) hg38.mrnaOrientInfo.name (via refFlat.name) hg38.refGene.name (via refFlat.name) hg38.refSeqAli.qName (via refFlat.name) hgFixed.gbCdnaInfo.acc (via refFlat.name) hgFixed.gbSeq.acc (via refFlat.name) hgFixed.imageClone.acc (via refFlat.name) hgFixed.refLink.mrnaAcc (via refFlat.name) hgFixed.refSeqStatus.mrnaAcc (via refFlat.name) hgFixed.refSeqSummary.mrnaAcc (via refFlat.name) knownGeneV39.kgXref.refseq (via refFlat.name) knownGeneV39.knownToRefSeq.value (via refFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
ZNF639	NM_001375803	chr3	+	179323030	179338583	179328293	179334422	5	179323030,179328282,179329617,179332988,179333268,	179323291,179328351,179329728,179333123,179338583,
WASH7P	NR_024540	chr1	-	14361	29370	29370	29370	11	14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,	14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370,
MIR6859-1	NR_106918	chr1	-	17368	17436	17436	17436	1	17368,	17436,
MIR6859-2	NR_107062	chr1	-	17368	17436	17436	17436	1	17368,	17436,
MIR6859-3	NR_107063	chr1	-	17368	17436	17436	17436	1	17368,	17436,
MIR6859-4	NR_128720	chr1	-	17368	17436	17436	17436	1	17368,	17436,
MIR1302-2	NR_036051	chr1	+	30365	30503	30503	30503	1	30365,	30503,
MIR1302-9	NR_036266	chr1	+	30365	30503	30503	30503	1	30365,	30503,
MIR1302-10	NR_036267	chr1	+	30365	30503	30503	30503	1	30365,	30503,
MIR1302-11	NR_036268	chr1	+	30365	30503	30503	30503	1	30365,	30503,

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