Schema for refFlat
  Database: mm39    Primary Table: refFlat    Row Count: 47,741   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 Xkr4varchar(255) values Name of gene as it appears in genome browser.
name NM_001011874varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 3284704int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3741721int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3286244int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3741571int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 3284704,3491924,3740774,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3287191,3492124,3741721,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      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)
      mm39.kgXref.refseq (via refFlat.name)
      mm39.knownToRefSeq.value (via refFlat.name)
      mm39.mrnaOrientInfo.name (via refFlat.name)
      mm39.refGene.name (via refFlat.name)
      mm39.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Xkr4NM_001011874chr1-328470437417213286244374157133284704,3491924,3740774,3287191,3492124,3741721,
Rp1NM_001370921chr1-4190088443052641902264423048234190088,4212834,4218034,4218834,4234077,4240427,4267756,4276882,4296833,4298665,4301275,4313355,4313639,4313765,4315253,4331749, ...4190296,4212989,4218186,4218967,4234164,4240627,4267864,4277060,4297046,4298842,4301367,4313485,4313671,4313842,4315329,4331828, ...
Rp1NM_001195662chr1-436106844794644363203447941044361068,4422132,4422424,4479392,4363235,4422304,4423060,4479464,
Rp1NM_011283chr1-441372944305374414822442304844413729,4422132,4422424,4430422,4420314,4422304,4423060,4430537,
Sox17NM_001289464chr1-456115045675774561938456362944561150,4563322,4563994,4566513,4562891,4563713,4564086,4567577,
Sox17NM_001289465chr1-456115045675774561938456537844561150,4563994,4565358,4566513,4562891,4564086,4566165,4567577,
Sox17NM_001289466chr1-456115045675774561938456537844561150,4563994,4565358,4566513,4562891,4564086,4565421,4567577,
Sox17NM_001289467chr1-456115045675774561938456281434561150,4563994,4566513,4562891,4564086,4567577,
Sox17NM_011441chr1-456115045675774561938456362954561150,4563322,4563994,4565358,4566513,4562891,4563689,4564086,4566165,4567577,
Mrpl15NM_001177658chr1-484342048559494846686485590054843420,4847747,4852790,4854173,4855795,4847024,4847871,4852956,4854328,4855949,

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