Schema for refFlat
  Database: ci3    Primary Table: refFlat    Row Count: 1,304   Data last updated: 2017-04-10
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ci-hmg20varchar(255) values Name of gene as it appears in genome browser.
name NM_001128115varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 343978int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 345617int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 344709int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 345588int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 343978,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 345617,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      ci3.mrnaOrientInfo.name (via refFlat.name)
      ci3.refGene.name (via refFlat.name)
      ci3.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
ci-hmg20NM_001128115chr1-3439783456173447093455881343978,345617,
rcl2NM_001349031chr9-229873823010452298856230070152298738,2299505,2300083,2300695,2301029,2299022,2299721,2300274,2300796,2301045,
zf(mynd)-12NM_001129871chr13-164999216520961650168165208751649992,1650607,1651103,1651583,1652030,1650315,1650788,1651247,1651750,1652096,
zf(mynd)-8NM_001129870chr4-359524135968393595769359678133595241,3596004,3596704,3595931,3596362,3596839,
zf(traf/ring)-4NM_001129869chr7-125577712601391256029126006091255777,1256075,1256643,1257132,1257822,1258326,1259589,1259916,1260094,1256074,1256204,1256733,1257288,1257961,1258505,1259700,1260083,1260139,
zf(bed)-3NM_001128901chr1-8910418932078911858931024891041,892266,892292,892342,892265,892291,892341,893207,
zf(c2h2)-116NM_001128903chr1-91640092276091644992270818916400,916672,917057,917165,917335,917689,918084,918499,918877,919389,919915,920405,920802,921253,921381,921591,921990,922579,916462,916838,917106,917236,917445,917835,918285,918610,918989,919565,920060,920485,920920,921326,921418,921683,922057,922760,
mir4159NR_034555chr3-481715648172214817221481722114817156,4817221,
LOC100178922NM_001302638chr12+506961550719255069615507192565069615,5070662,5071199,5071200,5071540,5071810,5070594,5070801,5071200,5071349,5071731,5071925,
LOC100183808NM_001285411chr7-155470815561551554856155614721554708,1555813,1555515,1556155,

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