Schema for refFlat
  Database: ci2    Primary Table: refFlat    Row Count: 1,263   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName pax1/9varchar(255) values Name of gene as it appears in genome browser.
name NM_001032422varchar(255) values Name of gene
chrom scaffold_7274varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 0int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1305int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 0int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1305int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 0,1213,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 121,1305,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      ci2.mrnaOrientInfo.name (via refFlat.name)
      ci2.refGene.name (via refFlat.name)
      ci2.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
pax1/9NM_001032422scaffold_7274+013050130520,1213,121,1305,
opsin3NM_001032468chr12p+100965810136691009701101334471009658,1010286,1011116,1011539,1012055,1012622,1013200,1009750,1010471,1011216,1011693,1012167,1012742,1013669,
LOC100176946NM_001032489chr03p-116795911719071168120117185061167959,1168600,1169012,1169417,1169941,1171675,1168305,1168790,1169136,1169722,1170096,1171907,
dead1aNM_001032421scaffold_248-600808638760531861841860080,61340,61950,62615,63132,63572,63939,66291,66898,67148,69111,69876,71775,73686,80656,86040,86133,86282,60578,61410,62076,62777,63241,63824,64106,66453,67021,67262,69302,69918,71874,73788,80701,86065,86209,86387,
cinutNM_001032464chr14p-228856122938602288648229382072288561,2289659,2290275,2291242,2292173,2292877,2293762,2288765,2289779,2290387,2291387,2292270,2293068,2293860,
pax258NM_001032480scaffold_199+64132642186414864218164132,64218,
pax258NM_001032480scaffold_71+31918399283191839736831918,32664,34618,36410,37906,39037,39411,39659,32087,32862,34695,36550,37970,39193,39480,39928,
LOC445731NM_001032533chr02q+61293062098861344762070613612930,613430,614299,615079,615833,616425,616939,617577,617982,619539,619822,620169,620628,612974,613601,614379,615207,615964,616541,617094,617718,618067,619692,619965,620242,620988,
fut13NM_001032530chr01p-355964035613053559992356129713559640,3561305,
ona2NM_001032525chr09q-427713042797254277753427959754277130,4278463,4278659,4279164,4279461,4278330,4278558,4278888,4279351,4279725,

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