Schema for xenoRefFlat

Database: pteVam1 Primary Table: xenoRefFlat Row Count: 528,338 Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	description
`geneName`	CNRIP1	`varchar(255)`	Name of gene as it appears in genome browser.
`name`	NM_001371608	`varchar(255)`	Name of gene
`chrom`	scaffold_6470	`varchar(255)`	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	+ or - for strand
`txStart`	66087	`int(10) unsigned`	Transcription start position (or end position for minus strand item)
`txEnd`	83312	`int(10) unsigned`	Transcription end position (or start position for minus strand item)
`cdsStart`	66915	`int(10) unsigned`	Coding region start (or end position for minus strand item)
`cdsEnd`	83081	`int(10) unsigned`	Coding region end (or start position for minus strand item)
`exonCount`	10	`int(10) unsigned`	Number of exons
`exonStarts`	66087,66278,66407,66541,666...	`longblob`	Exon start positions (or end positions for minus strand item)
`exonEnds`	66188,66332,66527,66631,666...	`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) pteVam1.xenoRefGene.name (via xenoRefFlat.name) pteVam1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
CNRIP1	NM_001371608	scaffold_6470	-	66087	83312	66915	83081	10	66087,66278,66407,66541,66651,66756,80690,82989,83177,83263,	66188,66332,66527,66631,66699,67076,80843,83143,83252,83312,
sugp2.L	NM_001096065	scaffold_14832	+	22974	23861	22974	23861	2	22974,23765,	23094,23861,
Adcy9	NM_001371690	scaffold_94	-	288520	303266	288520	303266	4	288520,301636,302853,303158,	288568,301750,302953,303266,
Fut7	NM_001289456	scaffold_4661	+	63266	63555	63266	63555	2	63266,63414,	63413,63555,
ANAPC11	NM_001002247	scaffold_6304	+	59127	64035	59657	63531	8	59127,59644,63385,63591,63646,63739,63773,63996,	59193,59766,63531,63636,63700,63755,63783,64035,
KLF8	NM_001324104	scaffold_13402	-	34445	35019	35019	35019	4	34445,34679,34809,34910,	34466,34736,34894,35019,
TOP1ALPHA	NM_001203614	scaffold_19	+	1668	9342	1668	9342	6	1668,1710,1794,3553,8261,9266,	1695,1743,1848,3631,8314,9342,
HTA12	NM_120334	scaffold_5438	-	62659	74471	74156	74471	2	62659,74156,	62905,74471,
Zfp455	NM_001048204	scaffold_19790	+	6130	6634	6130	6634	2	6130,6617,	6251,6634,
Olfr297	NM_146618	scaffold_35202	+	403	934	403	934	2	403,862,	460,934,

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