Schema for xenoRefFlat

Database: micMur1 Primary Table: xenoRefFlat Row Count: 681,359 Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	description
`geneName`	gly-9	`varchar(255)`	Name of gene as it appears in genome browser.
`name`	NM_001382997	`varchar(255)`	Name of gene
`chrom`	scaffold_139283	`varchar(255)`	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	+ or - for strand
`txStart`	426	`int(10) unsigned`	Transcription start position (or end position for minus strand item)
`txEnd`	546	`int(10) unsigned`	Transcription end position (or start position for minus strand item)
`cdsStart`	426	`int(10) unsigned`	Coding region start (or end position for minus strand item)
`cdsEnd`	546	`int(10) unsigned`	Coding region end (or start position for minus strand item)
`exonCount`	1	`int(10) unsigned`	Number of exons
`exonStarts`	426,	`longblob`	Exon start positions (or end positions for minus strand item)
`exonEnds`	546,	`longblob`	Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name) hgFixed.gbSeq.acc (via xenoRefFlat.name) hgFixed.imageClone.acc (via xenoRefFlat.name) micMur1.xenoRefGene.name (via xenoRefFlat.name) micMur1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
gly-9	NM_001382997	scaffold_139283	-	426	546	426	546	1	426,	546,
dhs-9	NM_065745	scaffold_1392	-	299010	299109	299010	299109	1	299010,	299109,
Rhno1	NM_001326586	scaffold_39002	+	2	331	2	331	6	2,66,144,221,247,316,	64,117,219,247,289,331,
hs3st3b1a	NM_001076646	scaffold_250	+	589248	633454	589248	633454	4	589248,632927,633008,633370,	589409,633006,633062,633454,
stambpl1.L	NM_001092813	scaffold_7592	+	359	27071	359	27071	4	359,17622,18607,26966,	572,17691,18736,27071,
KCNMA1	NM_001322832	scaffold_6186	-	17040	17575	17040	17414	4	17040,17300,17405,17549,	17241,17351,17509,17575,
NPEPPS	NM_006310	scaffold_1723	+	26512	26593	26512	26593	1	26512,	26593,
Ubtf	NM_001302954	scaffold_42872	+	4168	5146	4168	5146	3	4168,4822,4907,	4745,4885,5146,
trappc9	NM_001142140	scaffold_1120	-	23980	38326	23980	38326	4	23980,26413,37741,38197,	24052,26545,38179,38326,
vash1	NM_001142178	scaffold_885	+	265078	272823	265078	272823	5	265078,266330,267915,270685,272745,	265165,266387,267981,271072,272823,

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