Schema for refFlat
  Database: hg19    Primary Table: refFlat    Row Count: 81,407   Data last updated: 2020-08-17
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName VDAC1varchar(255) values Name of gene as it appears in genome browser.
name NR_036625varchar(255) values Name of gene
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 133307561int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 133340459int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 133340459int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 133340459int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 133307561,133309481,1333115...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 133308553,133309539,1333117...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hg19.kgAlias.alias (via refFlat.geneName)
      hg19.kgSpAlias.alias (via refFlat.geneName)
      hg19.kgXref.geneSymbol (via refFlat.geneName)
      hgFixed.refLink.name (via refFlat.geneName)
      visiGene.gene.name (via refFlat.geneName)
      hg19.ccdsInfo.mrnaAcc (via refFlat.name)
      hg19.kgXref.refseq (via refFlat.name)
      hg19.knownToRefSeq.value (via refFlat.name)
      hg19.mrnaOrientInfo.name (via refFlat.name)
      hg19.refGene.name (via refFlat.name)
      hg19.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
VDAC1NR_036625chr5-1333075611333404591333404591333404599133307561,133309481,133311561,133316419,133326545,133326692,133327996,133328636,133340337,133308553,133309539,133311712,133316647,133326598,133326845,133328046,133328709,133340459,
MIR6859-1NR_106918chr1-17368174361743617436117368,17436,
MIR6859-2NR_107062chr1-17368174361743617436117368,17436,
MIR6859-3NR_107063chr1-17368174361743617436117368,17436,
MIR6859-4NR_128720chr1-17368174361743617436117368,17436,
MIR1302-2NR_036051chr1+30365305033050330503130365,30503,
MIR1302-9NR_036266chr1+30365305033050330503130365,30503,
MIR1302-10NR_036267chr1+30365305033050330503130365,30503,
MIR1302-11NR_036268chr1+30365305033050330503130365,30503,
FAM138ANR_026818chr1-34610360813608136081334610,35276,35720,35174,35481,36081,

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