Schema for xenoRefFlat

Database: gorGor6 Primary Table: xenoRefFlat Row Count: 329,551 Data last updated: 2020-05-06
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	CCNL2	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001350497	`varchar(255)`	values	Name of gene
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	1534	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	13381	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	2627	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	5940	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	10	`int(10) unsigned`	range	Number of exons
`exonStarts`	1534,3173,3350,5310,5539,58...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	2979,3266,3462,5452,5644,59...	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	gorGor6.xenoRefGene.name (via xenoRefFlat.name) gorGor6.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
CCNL2	NM_001350497	chr1	-	1534	13381	2627	5940	10	1534,3173,3350,5310,5539,5847,7746,8463,10442,13271,	2979,3266,3462,5452,5644,5947,7871,8528,10586,13381,
CCNL2	NM_001320153	chr1	-	1534	14367	2627	5940	13	1534,3173,3350,5310,5539,5847,7857,8463,10442,13271,13636,14058,14340,	2979,3266,3462,5452,5644,6658,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NM_001320155	chr1	-	1534	14367	2627	5940	13	1534,3173,3350,5310,5539,5847,7857,8463,10442,13271,13636,14058,14340,	2979,3266,3462,5452,5644,5947,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NM_001350498	chr1	-	1534	14367	2627	5940	13	1534,3173,3350,5310,5539,5847,7746,8463,10442,13271,13636,14058,14340,	2979,3266,3462,5452,5644,5947,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NM_001350499	chr1	-	1534	14367	2627	6645	14	1534,3173,3350,5310,5539,5847,6379,7746,8463,10442,13271,13636,14058,14340,	2979,3266,3462,5452,5644,5947,6658,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NM_001350500	chr1	-	1534	14367	2627	6645	14	1534,3173,3350,5310,5539,5847,6379,7857,8463,10442,13271,13636,14058,14340,	2979,3266,3462,5452,5644,5947,6658,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NM_030937	chr1	-	1534	14367	2627	14282	12	1534,3173,3350,5310,5539,5847,8463,10442,13271,13636,14058,14340,	2979,3266,3462,5452,5644,5947,8528,10563,13381,13711,14282,14367,
CCNL2	NR_135154	chr1	-	1534	14367	14367	14367	12	1534,3173,3350,5302,5539,5847,8463,10442,13271,13636,14058,14340,	2979,3266,3464,5452,5644,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NR_146722	chr1	-	1534	14367	14367	14367	14	1534,3173,3350,5309,5539,5847,6379,7746,8463,10442,13271,13636,14058,14340,	2979,3266,3464,5452,5644,5947,6658,7871,8528,10563,13381,13711,14282,14367,
CCNL2	NR_146723	chr1	-	1534	14367	14367	14367	13	1534,3173,3350,5309,5539,5847,7746,8463,10442,13271,13636,14058,14340,	2979,3266,3464,5452,5644,6658,7871,8528,10563,13381,13711,14282,14367,

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