Schema for refFlat
  Database: criGriChoV2    Primary Table: refFlat    Row Count: 589   Data last updated: 2019-05-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName Ccnd1varchar(255) values Name of gene as it appears in genome browser.
name NM_001244048varchar(255) values Name of gene
chrom LT883673v1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 38421055int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 38427536int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 38421055int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 38427536int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 38421055,38421851,38425127,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 38421220,38422000,38425287,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      criGriChoV2.mrnaOrientInfo.name (via refFlat.name)
      criGriChoV2.refGene.name (via refFlat.name)
      criGriChoV2.refSeqAli.qName (via refFlat.name)
      hgFixed.gbCdnaInfo.acc (via refFlat.name)
      hgFixed.gbSeq.acc (via refFlat.name)
      hgFixed.imageClone.acc (via refFlat.name)
      hgFixed.refLink.mrnaAcc (via refFlat.name)
      hgFixed.refSeqStatus.mrnaAcc (via refFlat.name)
      hgFixed.refSeqSummary.mrnaAcc (via refFlat.name)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Ccnd1NM_001244048LT883673v1-38421055384275363842105538427536538421055,38421851,38425127,38425722,38427338,38421220,38422000,38425287,38425938,38427536,
LOC100689011NM_001243997LT883719v1-3027343051703027343051707302734,302883,303086,303329,304127,304630,305091,302772,302913,303203,303605,304384,304900,305170,
LOC100689010NM_001243995LT883719v1+228028522838112280285228379172280285,2280563,2281064,2282725,2283127,2283414,2283786,2280358,2280833,2281340,2283001,2283241,2283447,2283811,
Scarb1NM_001244848LT883686v1+4120036419010941201914187216134120036,4162781,4164471,4165780,4167502,4169257,4173969,4179141,4181695,4183505,4184293,4187087,4190008,4120317,4162939,4164613,4165984,4167598,4169373,4174136,4179260,4181769,4183557,4184440,4187216,4190109,
AdslNM_001244045LT883664v1+14139481614141973214139483414141936913141394816,141400040,141402408,141403025,141407285,141408239,141409840,141410931,141411140,141412925,141414276,141418180,14141928 ...141394987,141400244,141402453,141403105,141407457,141408286,141409931,141411001,141411288,141413016,141414366,141418357,14141973 ...
Xbp1NM_001244047LT883677v1-30502345103084034510530502,31362,32406,33516,34304,31057,31508,32541,33613,34510,
Casp3NM_001244046LT883664v1-755068775589477550687755894767550687,7552356,7552733,7553934,7556510,7558894,7550917,7552477,7552909,7554063,7556635,7558947,
Mir532NR_105252LT883834v1+76020760977609776097176020,76097,
S100bNM_001246806LT883697v1-233547823389822335478233561722335478,2338931,2335625,2338982,
Casp8NM_001246796LT883664v1+1763056881763225351763057181763223998176305688,176310695,176313207,176313426,176314995,176316898,176320346,176322263,176306023,176310804,176313346,176313477,176315060,176317040,176320845,176322535,

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