Schema for refFlat
  Database: galGal2    Primary Table: refFlat    Row Count: 7,494   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 LSG1varchar(255) values Name of gene as it appears in genome browser.
name NM_001006549varchar(255) values Name of gene
chrom chr9varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 12227997int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 12239925int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 12228006int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 12239554int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned range Number of exons
exonStarts 12227997,12228160,12228445,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 12228087,12228278,12228566,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      galGal2.mrnaOrientInfo.name (via refFlat.name)
      galGal2.refGene.name (via refFlat.name)
      galGal2.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
LSG1NM_001006549chr9+122279971223992512228006122395541412227997,12228160,12228445,12229728,12230708,12232267,12233062,12234236,12234941,12235824,12236288,12237196,12237882,12239374,12228087,12228278,12228566,12229815,12230795,12232328,12233239,12234662,12235043,12235968,12236412,12237276,12238056,12239925,
ATP5A1ZNM_204286chr14-1088536109648210886661096370121088536,1089386,1089749,1090845,1091061,1091419,1092507,1092829,1093094,1094101,1095341,1096310,1088748,1089537,1089894,1090953,1091286,1091571,1092656,1092996,1093268,1094271,1095420,1096482,
NESNM_205033chrUn+12175512612177089012175514012177047412121755126,121756786,121757506,121758090,121758760,121759016,121759445,121759594,121759843,121770004,121770376,121770431,121755953,121756911,121757580,121758753,121758802,121759445,121759594,121759843,121761640,121770375,121770429,121770890,
PPP3R1NM_204376chr3+591064759439305910762594181965910647,5932765,5938271,5939570,5940548,5941771,5910765,5932805,5938448,5939630,5940733,5943930,
SH3GL2NM_204530chrZ-14170562141882571417060414188257814170562,14173036,14176101,14178272,14179690,14182157,14186091,14188185,14170804,14173170,14176205,14178431,14179824,14182301,14186164,14188257,
CTAGE1NM_204732chr3+547412054791175474125547903745474120,5474720,5475462,5479013,5474249,5474860,5475573,5479117,
MYL12ANM_205341chr2+1008849821008921601008901251008918304100884982,100890111,100890482,100891657,100885063,100890309,100890644,100892160,
RARBNM_205326chr2+366274293695000636758461369498141036627429,36636297,36758139,36882819,36905609,36932591,36939247,36944875,36946418,36949617,36627456,36636392,36758639,36882968,36905751,36932752,36939424,36945080,36946577,36950006,
CD40NM_204665chr20+10138825101425371013887210142495810138825,10140035,10140304,10140518,10141637,10141784,10142058,10142351,10138920,10140117,10140430,10140662,10141701,10141883,10142084,10142537,
TLR2BNM_001161650chr4+20637859206403122063785920640312220637859,20639657,20639403,20640312,

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