Schema for xenoRefFlat

Database: equCab1 Primary Table: xenoRefFlat Row Count: 320,808 Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	Dlk1	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001190703	`varchar(255)`	values	Name of gene
`chrom`	chr24	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	42100515	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	42108213	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	42100582	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	42108179	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	6	`int(10) unsigned`	range	Number of exons
`exonStarts`	42100515,42102378,42105379,...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	42100642,42102513,42105521,...	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	equCab1.xenoMrna.qName (via xenoRefFlat.name) equCab1.xenoRefGene.name (via xenoRefFlat.name) equCab1.xenoRefSeqAli.qName (via xenoRefFlat.name) hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name) hgFixed.gbSeq.acc (via xenoRefFlat.name) hgFixed.imageClone.acc (via xenoRefFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
Dlk1	NM_001190703	chr24	+	42100515	42108213	42100582	42108179	6	42100515,42102378,42105379,42107430,42107536,42107936,	42100642,42102513,42105521,42107533,42107650,42108213,
MTRNR2L8	NM_001190702	chr8	-	77493298	77493852	77493558	77493633	3	77493298,77493436,77493524,	77493374,77493457,77493852,
MTRNR2L8	NM_001190702	chrM	+	1183	2422	2422	2422	5	1183,1609,1863,2264,2346,	1507,1663,2013,2306,2422,
mthfs	NM_001200691	chr1	+	111901515	111901734	111901515	111901734	1	111901515,	111901734,
HMGCR	NM_001130996	chr14	-	88597388	88614771	88599304	88614742	22	88597388,88597720,88597957,88598126,88598521,88599304,88599883,88600125,88600580,88602509,88603293,88604127,88605389,88605682,88 ...	88597483,88597931,88598053,88598265,88598767,88599468,88600042,88600266,88600751,88602615,88603451,88604322,88605568,88605933,88 ...
CG34384	NM_001260041	chr6	+	20382457	20417706	20382457	20417706	11	20382457,20383427,20383924,20385024,20387844,20391173,20391265,20400804,20403096,20404230,20417589,	20382554,20383534,20384053,20385153,20387951,20391264,20391316,20400909,20403204,20404332,20417706,
porin	NM_001259032	chr1	+	62019899	62020642	62019899	62020642	2	62019899,62020471,	62020052,62020642,
lap	NM_001260029	chr10	-	32087043	32149188	32087043	32149188	7	32087043,32095021,32096764,32098829,32099906,32100633,32149134,	32087150,32095124,32096842,32098934,32099969,32100762,32149188,
lap	NM_001260029	chr7	+	47428753	47483718	47428753	47483718	5	47428753,47460872,47468076,47481991,47483603,	47428882,47461004,47468181,47482089,47483718,
lap	NM_001260030	chr10	-	32087043	32149188	32087043	32149188	7	32087043,32095021,32096764,32098829,32099906,32100633,32149134,	32087150,32095124,32096842,32098934,32099969,32100762,32149188,

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