Schema for refFlat
  Database: panTro1    Primary Table: refFlat    Row Count: 2,922   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName SLFNL1varchar(255) values Name of gene as it appears in genome browser.
name NM_001246488varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 42111973int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 42118054int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 42112426int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 42116984int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 42111973,42113556,42113957,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 42112549,42113700,42114479,...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)
      panTro1.refGene.name (via refFlat.name)
      panTro1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
SLFNL1NM_001246488chr1-42111973421180544211242642116984642111973,42113556,42113957,42116549,42117187,42117858,42112549,42113700,42114479,42117102,42117259,42118054,
ATG4ANM_001246528chrX+11073541811079991011073560611079943314110735418,110771290,110773998,110776473,110779558,110779840,110782592,110783306,110783615,110783676,110795617,110797442,11079869 ...110735616,110771401,110774070,110776572,110779660,110779913,110782672,110783494,110783675,110783695,110795731,110797500,11079880 ...
RBMXL2NM_001246649chr9+717907671810127179231718041017179076,7181012,
PLRG1NM_001246648chr3-17317904517319296617317921917319285215173179045,173179821,173180504,173181640,173182490,173183133,173183324,173184723,173186993,173188383,173188670,173189556,17319025 ...173179279,173180015,173180644,173181749,173182593,173183235,173183474,173184816,173187095,173188471,173188761,173189610,17319040 ...
PDIA6NM_001246647chr12-11632990116414951163299011641408211632990,11641389,11633134,11641495,
PDIA6NM_001246647chr12_random-5927279594132759276765941327115927279,5928343,5930776,5932196,5932396,5933238,5934205,5935279,5936635,5940651,5941268,5927745,5928440,5930935,5932269,5932481,5933379,5934320,5935410,5936742,5940778,5941327,
PPP6R2NM_001280495chr23+49633795496396974963379549639697849633795,49634889,49636364,49637767,49638388,49638902,49639239,49639570,49634006,49634954,49636480,49637853,49638469,49639000,49639297,49639697,
PPP6R2NM_001280495chr23_random+164677561659085116467831165907011316467756,16469295,16472085,16472568,16475472,16476682,16584952,16584979,16586055,16586318,16587179,16590319,16590652,16467897,16469361,16472198,16472682,16475599,16476836,16584969,16585121,16586215,16586407,16587384,16590571,16590851,
CD4NM_001009043chr10+7305678733540373162757335384107305678,7316207,7316445,7330208,7330825,7332122,7333195,7334475,7334901,7335353,7305768,7316324,7316610,7330367,7331059,7332470,7333396,7334597,7334931,7335403,
FMO3NM_001009092chr1+1500743081501007891500743081501007898150074308,150085803,150089689,150090092,150092814,150097347,150099550,150100446,150074440,150085992,150089852,150090235,150093014,150097703,150099623,150100789,

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