Schema for refFlat

Database: sarHar1 Primary Table: refFlat Row Count: 72 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`	MIR216B	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NR_105683	`varchar(255)`	values	Name of gene
`chrom`	chr1_GL834734_random	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	1003763	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	1003913	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	1003913	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	1003913	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	1	`int(10) unsigned`	range	Number of exons
`exonStarts`	1003763,	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	1003913,	`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) sarHar1.mrnaOrientInfo.name (via refFlat.name) sarHar1.refGene.name (via refFlat.name) sarHar1.refSeqAli.qName (via refFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
MIR216B	NR_105683	chr1_GL834734_random	+	1003763	1003913	1003913	1003913	1	1003763,	1003913,
MIR340	NR_105682	chr1_GL834730_random	+	741011	741161	741161	741161	1	741011,	741161,
MIR140	NR_105685	chr1_GL834769_random	+	1909499	1909649	1909649	1909649	1	1909499,	1909649,
MIR216A	NR_105684	chr1_GL834734_random	+	1019941	1020091	1020091	1020091	1	1019941,	1020091,
MIR202	NR_105687	chr1_GL835536_random	+	120398	120548	120548	120548	1	120398,	120548,
MIR126	NR_105686	chr1_GL834949_random	+	4221	4371	4371	4371	1	4221,	4371,
MIR133A	NR_105690	chr2_GL841304_random	+	692703	692853	692853	692853	1	692703,	692853,
MIR1540	NR_105688	chr1_GL836570_random	+	10619	10769	10769	10769	1	10619,	10769,
MIR9	NR_105689	chr2_GL841279_random	+	926516	926666	926666	926666	1	926516,	926666,
MIR7	NR_105700	chr2_GL841540_random	+	2528668	2528818	2528818	2528818	1	2528668,	2528818,

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