Schema for xenoRefFlat

Database: droSim1 Primary Table: xenoRefFlat Row Count: 385,171 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`	PUM1	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001134123	`varchar(255)`	values	Name of gene
`chrom`	chr3R	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	16416739	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	16417904	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	16416739	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	16417904	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	4	`int(10) unsigned`	range	Number of exons
`exonStarts`	16416739,16417485,16417567,...	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	16417409,16417567,16417651,...	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	droSim1.xenoMrna.qName (via xenoRefFlat.name) droSim1.xenoRefGene.name (via xenoRefFlat.name) droSim1.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
PUM1	NM_001134123	chr3R	+	16416739	16417904	16416739	16417904	4	16416739,16417485,16417567,16417714,	16417409,16417567,16417651,16417904,
Drat	NM_001273850	chr2R	-	2137122	2141824	2137683	2138896	4	2137122,2137677,2138168,2141552,	2137644,2138101,2139003,2141824,
Vps13	NM_001273852	chrU	-	12719204	12720095	12719204	12720095	5	12719204,12719325,12719529,12719807,12720050,	12719264,12719460,12719751,12720049,12720095,
Rpe	NM_001273851	chr2R	-	2178092	2179185	2178230	2179087	4	2178092,2178215,2178660,2178901,	2178204,2178527,2178843,2179185,
hnrnpa3	NM_001328148	chr2R	-	9950813	9952892	9950813	9952892	2	9950813,9952837,	9950866,9952892,
SEPTIN8	NM_001169035	chr3R	+	5054974	5056753	5054974	5056753	2	5054974,5055805,	5055046,5056753,
5-HT2A	NM_001170035	chr3R	+	497701	512319	501406	511972	11	497701,498073,501334,501508,501639,506432,506718,507391,509744,510892,511782,	498045,498079,501449,501624,502454,506657,506917,507832,510095,511189,512319,
PLCXD1	NM_018390	chr3R	+	21782546	22083075	22083075	22083075	4	21782546,21782672,21782771,22083039,	21782588,21782708,21782798,22083075,
PLCXD1	NM_018390	chr3R	-	21782536	21782807	21782807	21782807	3	21782536,21782730,21782770,	21782654,21782745,21782807,
SLC35C1	NM_018389	chr3R	+	17129879	17130149	17129879	17130149	1	17129879,	17130149,

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