Schema for refFlat
  Database: rn6    Primary Table: refFlat    Row Count: 19,160   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName Vom2r3varchar(255) values Name of gene as it appears in genome browser.
name NM_001099460varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 396699int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 409676int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 396699int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 409676int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 396699,399544,400255,401911...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 396905,399827,401059,402136...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)
      rn6.mrnaOrientInfo.name (via refFlat.name)
      rn6.refGene.name (via refFlat.name)
      rn6.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Vom2r3NM_001099460chr1+3966994096763966994096766396699,399544,400255,401911,407503,408792,396905,399827,401059,402136,407627,409676,
Robo3NM_001108135chr8-398927913990747839894499399071272639892791,39894003,39894974,39895213,39895742,39896088,39896378,39896912,39897260,39897381,39898207,39898731,39899132,39899406,39 ...39893708,39894807,39895085,39895365,39895955,39896227,39896573,39897052,39897303,39897405,39898393,39898903,39899254,39899632,39 ...
Sbno2NM_001108068chr7+124718231251569912493675125152833312471823,12487359,12489271,12490966,12493572,12501641,12504563,12504869,12505139,12505374,12505586,12505779,12506719,12507190,12 ...12471916,12487532,12489345,12491078,12493741,12501803,12504647,12504966,12505294,12505508,12505677,12505923,12506837,12507296,12 ...
RrltNM_001161691chr1-110196411169261101964111692681101964,1102695,1103428,1103490,1104126,1104637,1104700,1116610,1102031,1102837,1103490,1103579,1104375,1104692,1104898,1116926,
Usp8NM_001106502chr3+11917381711922248411918500711922181919119173817,119184992,119187038,119192182,119195251,119197970,119199733,119201716,119203320,119203743,119207837,119211502,11921200 ...119173956,119185111,119187183,119192268,119195414,119198013,119199878,119201879,119203465,119203967,119208398,119211583,11921226 ...
Efhd2NM_001031648chr5-1604077761604238111604091371604237844160407776,160410158,160411452,160423479,160409269,160410293,160411600,160423811,
Dnali1NM_001031647chr5-1430533641430622031430548101430622016143053364,143057033,143057503,143060146,143061499,143062120,143054846,143057198,143057682,143060316,143061645,143062203,
Stoml2NM_001031646chr5-584725605847615858472687584761571058472560,58473681,58474018,58474249,58474522,58474800,58474990,58475186,58475740,58476112,58472816,58473810,58474098,58474394,58474657,58474902,58475049,58475286,58475878,58476158,
Ercc3NM_001031644chr18+250376672506838025037705250681511525037667,25037937,25040467,25042314,25042915,25043224,25043992,25045743,25051498,25055043,25059181,25061186,25062237,25063733,25 ...25037733,25038143,25040704,25042364,25043051,25043389,25044197,25046058,25051683,25055246,25059278,25061304,25062356,25063886,25 ...
Smurf1NM_001109598chr12+114338141152646511433836115235731811433814,11500476,11501740,11503718,11504005,11505204,11506904,11508975,11510276,11511761,11513643,11516816,11518285,11519299,11 ...11433891,11500515,11501849,11503852,11504071,11505280,11507146,11509060,11510423,11511960,11513747,11516931,11518464,11519437,11 ...

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