Schema for xenoRefFlat

Database: dp3 Primary Table: xenoRefFlat Row Count: 122,793 Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	ZKSCAN1	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001205510	`varchar(255)`	values	Name of gene
`chrom`	chrXR_group6	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	147914	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	148316	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	147914	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	148316	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	2	`int(10) unsigned`	range	Number of exons
`exonStarts`	147914,148256,	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	148157,148316,	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	dp3.xenoMrna.qName (via xenoRefFlat.name) dp3.xenoRefGene.name (via xenoRefFlat.name) dp3.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
ZKSCAN1	NM_001205510	chrXR_group6	-	147914	148316	147914	148316	2	147914,148256,	148157,148316,
ZKSCAN1	NM_001205510	chr4_group3	-	8659636	8660020	8659636	8660020	2	8659636,8659837,	8659801,8660020,
SMAD9	NM_001195510	chr4_group4	+	1462299	1464749	1462299	1464749	4	1462299,1462568,1463060,1464342,	1462506,1462805,1463265,1464749,
RHOQ	NM_001205498	chr2	+	3778885	3779256	3778885	3779256	2	3778885,3779106,	3778981,3779256,
RHOQ	NM_001205498	chrXL_group1e	+	941677	942291	941677	942291	2	941677,942078,	941950,942291,
PAD1	NM_001278992	chrXL_group1e	-	10335992	10336752	10335992	10336752	4	10335992,10336100,10336362,10336659,	10336064,10336208,10336596,10336752,
POR	NM_001129959	chr4_group5	-	1967082	1970551	1967082	1970551	9	1967082,1967169,1967397,1967643,1968214,1968337,1969819,1969972,1970537,	1967137,1967379,1967613,1968126,1968234,1968457,1969945,1970144,1970551,
RXRG	NM_001257610	chrXL_group1a	-	2541901	2543059	2541901	2543059	3	2541901,2542375,2542789,	2542003,2542489,2543059,
KARS1	NM_001257593	chrXL_group3a	+	453215	455005	453215	455005	8	453215,453365,453422,453518,453665,453964,454486,454972,	453263,453373,453488,453617,453890,454411,454903,455005,
MAGOH	NM_001257602	chr3	+	17591236	17591732	17591236	17591732	2	17591236,17591549,	17591485,17591732,

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