Schema for xenoRefFlat

Database: caeJap1 Primary Table: xenoRefFlat Row Count: 203,513 Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	vap-2	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001313448	`varchar(255)`	values	Name of gene
`chrom`	chrUn	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	37733017	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	37735227	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	37733017	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	37735227	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	10	`int(10) unsigned`	range	Number of exons
`exonStarts`	37733017,37733156,37733363,...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	37733111,37733314,37733470,...	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	caeJap1.xenoMrna.qName (via xenoRefFlat.name) caeJap1.xenoRefGene.name (via xenoRefFlat.name) caeJap1.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
vap-2	NM_001313448	chrUn	+	37733017	37735227	37733017	37735227	10	37733017,37733156,37733363,37733524,37733713,37734155,37734419,37734556,37734773,37735019,	37733111,37733314,37733470,37733669,37733806,37734364,37734498,37734706,37734880,37735227,
vap-2	NM_001313449	chrUn	+	37733284	37735227	37733284	37735227	9	37733284,37733363,37733524,37733713,37734155,37734419,37734556,37734773,37735019,	37733314,37733470,37733669,37733806,37734364,37734498,37734706,37734880,37735227,
sma-9	NM_001375119	chrUn	-	37740357	37753930	37741552	37753930	37	37740357,37741552,37742423,37742476,37742614,37742649,37742739,37744546,37744587,37745597,37745795,37746336,37746614,37746896,37 ...	37740398,37741698,37742462,37742484,37742624,37742694,37742763,37744549,37744719,37745747,37745981,37746522,37746719,37746898,37 ...
slc1a3a	NM_212640	chrUn	+	19764463	19765658	19764463	19765658	2	19764463,19765505,	19764529,19765658,
RPS17	NM_001265804	chrUn	+	56005006	56005329	56005006	56005329	2	56005006,56005210,	56005163,56005329,
CG4341	NM_134714	chrUn	-	6350938	6351034	6350938	6351034	1	6350938,	6351034,
LOC100193342	NM_001358712	chrUn	-	119481881	119482328	119481881	119482328	2	119481881,119482223,	119481977,119482328,
LOC100193342	NM_001358712	chrUn	-	81582485	81583566	81582485	81583566	2	81582485,81583314,	81582710,81583566,
RGS7	NM_001350116	chrUn	+	51116826	51120171	51116826	51120171	4	51116826,51116995,51119010,51120041,	51116919,51117149,51119152,51120171,
	NR_151866	chrUn	-	156226908	156227022	156227022	156227022	1	156226908,	156227022,

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