Schema for refFlat

Schema for refFlat

Database: bosTau4 Primary Table: refFlat Row Count: 10,349
Format description: A gene prediction with additional geneName field.

field	example	SQL type	info	description
`geneName`	RCAN1	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001034679	`varchar(255)`	values	Name of gene
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	327876	`int unsigned`	range	Transcription start position
`txEnd`	339078	`int unsigned`	range	Transcription end position
`cdsStart`	327956	`int unsigned`	range	Coding region start
`cdsEnd`	337478	`int unsigned`	range	Coding region end
`exonCount`	4	`int unsigned`	range	Number of exons
`exonStarts`	327876,331232,333962,337305,	`longblob`		Exon start positions
`exonEnds`	328043,331406,334122,339078,	`longblob`		Exon end positions

Connected Tables and Joining Fields


	bosTau4.gbCdnaInfo.acc (via refFlat.name) bosTau4.gbSeq.acc (via refFlat.name) bosTau4.gbStatus.acc (via refFlat.name) bosTau4.imageClone.acc (via refFlat.name) bosTau4.mrnaOrientInfo.name (via refFlat.name) bosTau4.refGene.name (via refFlat.name) bosTau4.refLink.mrnaAcc (via refFlat.name) bosTau4.refSeqAli.qName (via refFlat.name) bosTau4.refSeqStatus.mrnaAcc (via refFlat.name) bosTau4.refSeqSummary.mrnaAcc (via refFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
RCAN1	NM_001034679	chr1	+	327876	339078	327956	337478	4	327876,331232,333962,337305,	328043,331406,334122,339078,
KCNE1	NM_001077977	chr1	+	377375	383871	383292	383682	3	377375,378426,383242,	377447,378521,383871,
MGC134427	NM_001077124	chr1	-	436007	437027	436209	436965	1	436007,	437027,
KCNE2	NM_001077084	chr1	-	460824	468632	461113	461485	2	460824,468526,	461497,468632,
CRYZL1	NM_001035037	chr1	+	988441	1022153	997170	1021860	13	988441,997164,998806,999699,1001812,1003535,1012150,1013410,1015778,1017532,1018682,1021174,1021760,	988497,997236,998884,999772,1001857,1003604,1012284,1013522,1015877,1017654,1018788,1021220,1022153,
DONSON	NM_001083445	chr1	+	1032584	1042625	1032584	1041991	10	1032584,1033632,1034646,1035752,1037144,1037946,1038136,1039087,1040465,1041853,	1032881,1033713,1034850,1035931,1037323,1038028,1038241,1039286,1040678,1042625,
SON	NM_001083694	chr1	-	1042884	1073741	1043635	1073692	13	1042884,1044313,1044530,1046385,1050565,1051692,1058902,1059284,1061333,1062792,1066892,1070450,1073615,	1043794,1044429,1044602,1046533,1050682,1051803,1059091,1059431,1061495,1065935,1068695,1070617,1073741,
GAPDHS	NM_001040552	chr18	+	45619717	45628601	45619774	45628448	11	45619717,45621974,45623126,45623407,45625670,45625841,45626325,45626696,45627009,45628187,45628375,	45619841,45622113,45623223,45623514,45625761,45625960,45626407,45626848,45627172,45628285,45628601,
PSMB8	NM_001040480	chr23	-	7379662	7383039	7379893	7383016	6	7379662,7380220,7380778,7381692,7381963,7382869,	7379982,7380425,7380908,7381804,7382111,7383039,
TMEM50B	NM_001034786	chr1	+	1135358	1172197	1153831	1170764	7	1135358,1153790,1155902,1157299,1164351,1167219,1170718,	1135459,1153930,1156015,1157367,1164444,1167277,1172197,

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