Schema for xenoRefFlat

Database: proCap1 Primary Table: xenoRefFlat Row Count: 669,761 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`	col3a1.S	`varchar(255)`	Name of gene as it appears in genome browser.
`name`	NM_001090075	`varchar(255)`	Name of gene
`chrom`	scaffold_2274	`varchar(255)`	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	+ or - for strand
`txStart`	15777	`int(10) unsigned`	Transcription start position (or end position for minus strand item)
`txEnd`	16955	`int(10) unsigned`	Transcription end position (or start position for minus strand item)
`cdsStart`	15777	`int(10) unsigned`	Coding region start (or end position for minus strand item)
`cdsEnd`	16955	`int(10) unsigned`	Coding region end (or start position for minus strand item)
`exonCount`	6	`int(10) unsigned`	Number of exons
`exonStarts`	15777,15907,16082,16221,169...	`longblob`	Exon start positions (or end positions for minus strand item)
`exonEnds`	15865,16019,16197,16264,169...	`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) proCap1.xenoRefGene.name (via xenoRefFlat.name) proCap1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
col3a1.S	NM_001090075	scaffold_2274	-	15777	16955	15777	16955	6	15777,15907,16082,16221,16924,16934,	15865,16019,16197,16264,16933,16955,
Dhx37	NM_001105926	scaffold_13198	+	78	10996	78	10993	14	78,1509,3919,4216,5796,6291,7422,8440,8717,8908,9082,9270,10597,10907,	337,1621,4026,4405,5921,6408,7595,8555,8855,8910,9175,9344,10695,10996,
STK4	NM_001015602	scaffold_72718	-	7287	7404	7287	7404	1	7287,	7404,
PAMR1	NM_001015591	scaffold_13316	+	33070	33250	33070	33250	1	33070,	33250,
RBFOX2	NM_001349989	scaffold_12326	+	20464	20692	20464	20692	1	20464,	20692,
RBFOX2	NM_001349990	scaffold_6603	+	12500	39934	12500	34454	27	12500,15372,18243,22612,32129,32677,34409,34591,34727,34947,35522,35753,35931,36145,36336,36443,37790,37808,37935,37981,38104,38 ...	12601,15433,18272,22653,32218,32750,34556,34689,34898,35250,35710,35767,36120,36208,36432,36589,37799,37917,37971,38020,38135,38 ...
RBFOX2	NM_001349990	scaffold_6182	-	16830	36747	16830	36747	12	16830,18806,19910,20944,21131,22280,22762,26853,28277,29112,31034,36642,	16875,18821,19979,20947,21161,22358,22813,26913,28373,29166,31103,36747,
dnai4	NM_001113033	scaffold_2530	+	3249	17528	3249	17528	3	3249,9943,17402,	3321,10042,17528,
CP	NR_046371	scaffold_8244	-	27885	60622	60622	60622	8	27885,31597,34381,45723,49610,53496,58386,60390,	28017,31710,34468,45864,49685,53616,58595,60622,
ANO1	NM_001378094	scaffold_189905	-	679	1721	679	1721	2	679,1607,	737,1721,

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