Schema for refFlat
  Database: hg38    Primary Table: refFlat    Row Count: 88,819   Data last updated: 2020-08-17
Format description: A gene prediction with additional geneName field.
fieldexampleSQL type info description
geneName ZNF639varchar(255) values Name of gene as it appears in genome browser.
name NM_001375803varchar(255) values Name of gene
chrom chr3varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 179323030int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 179338583int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 179328293int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 179334422int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 179323030,179328282,1793296...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 179323291,179328351,1793297...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hg38.kgAlias.alias (via refFlat.geneName)
      hg38.kgSpAlias.alias (via refFlat.geneName)
      hg38.kgXref.geneSymbol (via refFlat.geneName)
      hgFixed.refLink.name (via refFlat.geneName)
      visiGene.gene.name (via refFlat.geneName)
      hg38.ccdsInfo.mrnaAcc (via refFlat.name)
      hg38.kgXref.refseq (via refFlat.name)
      hg38.knownToRefSeq.value (via refFlat.name)
      hg38.mrnaOrientInfo.name (via refFlat.name)
      hg38.refGene.name (via refFlat.name)
      hg38.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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
ZNF639NM_001375803chr3+1793230301793385831793282931793344225179323030,179328282,179329617,179332988,179333268,179323291,179328351,179329728,179333123,179338583,
WASH7PNR_024540chr1-143612937029370293701114361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370,
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,

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