Schema for refFlat

Database: oryCun2 Primary Table: refFlat Row Count: 1,750 Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	LOC100008986	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001082197	`varchar(255)`	values	Name of gene
`chrom`	chrUn0185	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	366227	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	371227	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	366283	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	370976	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	5	`int(10) unsigned`	range	Number of exons
`exonStarts`	366227,367283,368603,370345...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	366475,367431,368874,370980...	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	hgFixed.refLink.name (via refFlat.geneName) 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) oryCun2.mrnaOrientInfo.name (via refFlat.name) oryCun2.refGene.name (via refFlat.name) oryCun2.refSeqAli.qName (via refFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
LOC100008986	NM_001082197	chrUn0185	-	366227	371227	366283	370976	5	366227,367283,368603,370345,371197,	366475,367431,368874,370980,371227,
MIR302D	NR_126585	chr15	+	36770108	36770176	36770176	36770176	1	36770108,	36770176,
MIR302B	NR_126582	chr15	+	36769626	36769706	36769706	36769706	1	36769626,	36769706,
MIR191	NR_126593	chr9	-	16649736	16649828	16649828	16649828	1	16649736,	16649828,
MIR302A	NR_126584	chr15	+	36769945	36770014	36770014	36770014	1	36769945,	36770014,
MIR302C	NR_126583	chr15	+	36769769	36769837	36769837	36769837	1	36769769,	36769837,
LOC102723302	NR_110379	chr17	+	68749402	68749700	68749700	68749700	1	68749402,	68749700,
LOC102723302	NR_110379	chr17	-	68976224	68976522	68976522	68976522	1	68976224,	68976522,
LOC102723302	NR_110379	chr17	-	68986344	68986642	68986642	68986642	1	68986344,	68986642,
RN7SL1	NR_037953	chr17	+	68749402	68749700	68749700	68749700	1	68749402,	68749700,

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