Schema for xenoRefFlat

Database: ce11 Primary Table: xenoRefFlat Row Count: 33,497 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`	LOC103632090	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001346596	`varchar(255)`	values	Name of gene
`chrom`	chrV	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	1263337	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	1263838	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	1263337	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	1263542	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	3	`int(10) unsigned`	range	Number of exons
`exonStarts`	1263337,1263509,1263757,	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	1263394,1263602,1263838,	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	ce11.xenoMrna.qName (via xenoRefFlat.name) ce11.xenoRefGene.name (via xenoRefFlat.name) ce11.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
LOC103632090	NM_001346596	chrV	-	1263337	1263838	1263337	1263542	3	1263337,1263509,1263757,	1263394,1263602,1263838,
LOC106578080	NM_001315011	chrIV	-	7083740	7084658	7083740	7084658	3	7083740,7084142,7084403,	7083848,7084183,7084658,
LOC106608436	NM_001314480	chrIV	-	9996152	9996539	9996152	9996539	1	9996152,	9996539,
OGDHL	NM_001347826	chrIV	-	4698481	4701775	4698481	4701490	7	4698481,4699462,4700301,4700965,4701211,4701466,4701649,	4698592,4699774,4700436,4701031,4701436,4701520,4701775,
OGDHL	NM_001347825	chrIV	-	4698481	4701775	4698481	4701775	7	4698481,4699462,4700301,4700965,4701211,4701466,4701649,	4698592,4699774,4700436,4701031,4701436,4701622,4701775,
Crt	NM_001043610	chrV	-	6099372	6100389	6099372	6100389	5	6099372,6099511,6100009,6100185,6100353,	6099417,6100000,6100066,6100278,6100389,
H2BC5	NM_001046246	chrV	-	8853001	8853314	8853005	8853314	1	8853001,	8853314,
Gspt2	NM_001109319	chrV	-	11110453	11112235	11110453	11112235	4	11110453,11111112,11111580,11111905,	11110546,11111457,11111847,11112235,
gnpda2	NM_001102854	chrIII	+	13389499	13390704	13389499	13390704	4	13389499,13389834,13390073,13390410,	13389631,13390023,13390076,13390704,
isoc2.S	NM_001095229	chrIV	-	12208320	12208539	12208320	12208539	1	12208320,	12208539,

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