Schema for xenoRefFlat

Database: tupBel1 Primary Table: xenoRefFlat Row Count: 845,862 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`	His4:CG33889	`varchar(255)`	Name of gene as it appears in genome browser.
`name`	NM_001032161	`varchar(255)`	Name of gene
`chrom`	scaffold_12000.1-47362	`varchar(255)`	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	+ or - for strand
`txStart`	212	`int(10) unsigned`	Transcription start position (or end position for minus strand item)
`txEnd`	525	`int(10) unsigned`	Transcription end position (or start position for minus strand item)
`cdsStart`	212	`int(10) unsigned`	Coding region start (or end position for minus strand item)
`cdsEnd`	525	`int(10) unsigned`	Coding region end (or start position for minus strand item)
`exonCount`	2	`int(10) unsigned`	Number of exons
`exonStarts`	212,489,	`longblob`	Exon start positions (or end positions for minus strand item)
`exonEnds`	488,525,	`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) tupBel1.xenoRefGene.name (via xenoRefFlat.name) tupBel1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
His4:CG33889	NM_001032161	scaffold_12000.1-47362	-	212	525	212	525	2	212,489,	488,525,
His4:CG33889	NM_001032161	scaffold_138793.1-125881	+	85122	85434	85122	85434	1	85122,	85434,
His2A:CG33832	NM_001032160	scaffold_11995.1-143015	+	118096	118443	118096	118443	1	118096,	118443,
KLF12	NM_007249	scaffold_129225.1-346810	-	15651	290161	15651	290161	4	15651,132684,172937,290069,	15818,132821,173484,290161,
anos1	NM_001113688	scaffold_57713.1-858	+	223	448	223	448	1	223,	448,
anos1	NM_001113688	scaffold_147517.1-17476	-	8761	8947	8761	8947	1	8761,	8947,
SELENOK	NM_001114878	scaffold_127482.1-580427	-	535606	536203	535917	536202	3	535606,535669,535873,	535643,535794,536203,
rtgdnf	NM_001281402	scaffold_141168.1-398392	+	103105	103417	103105	103417	1	103105,	103417,
POLR2J4	NR_003655	scaffold_15828.1-546815	+	286338	480528	480528	480528	2	286338,480468,	286374,480528,
ENTR1	NM_006643	scaffold_147100.1-5188	+	332	1767	332	1761	4	332,664,1038,1662,	444,727,1149,1767,

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