Schema for refFlat
  Database: musFur1    Primary Table: refFlat    Row Count: 65   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName AK6varchar(255) values Name of gene as it appears in genome browser.
name NM_001286170varchar(255) values Name of gene
chrom GL897005varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1739806int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1757148int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1739850int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1756921int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 1739806,1740806,1749591,174...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1739878,1740899,1749650,175...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)
      musFur1.mrnaOrientInfo.name (via refFlat.name)
      musFur1.refGene.name (via refFlat.name)
      musFur1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
AK6NM_001286170GL897005+173980617571481739850175692151739806,1740806,1749591,1749977,1756728,1739878,1740899,1749650,1750123,1757148,
TAF9NM_001286171GL897005+173980617425491741647174244531739806,1740806,1741630,1739878,1740899,1742549,
AZIN2NM_001293742GL896903-147995481483927914802204148381471114799548,14804864,14823257,14824564,14826400,14827313,14828422,14836346,14838042,14838917,14839143,14802343,14805079,14823370,14824727,14826566,14827448,14828595,14836520,14838225,14839038,14839279,
AZIN1NM_001301777GL897038+1784438181513518020051812912131784438,1789111,1796519,1801908,1804162,1804752,1806613,1807921,1808448,1809404,1811958,1812369,1812800,1784752,1789250,1796665,1802107,1804336,1804925,1806748,1808003,1808523,1809567,1812074,1812584,1815135,
OAZ3NM_001301425GL897134-5480015511775481025511115548001,549005,549602,550520,550944,548245,549091,549778,550657,551177,
OAZ3NM_001290471GL897134-5480015547685481025546115548001,549005,549602,550520,554576,548245,549091,549778,550657,554768,
APOBEC1NM_001310163GL896932+14038942140492651403897914049121514038942,14045693,14047386,14048175,14048971,14038995,14045721,14047784,14048294,14049265,
AZIN1NM_001291555GL897038+1784438181513518020051812912121784438,1789111,1801908,1804162,1804752,1806613,1807921,1808448,1809404,1811958,1812369,1812800,1784752,1789250,1802107,1804336,1804925,1806748,1808003,1808523,1809567,1812074,1812584,1815135,
PEG10NM_001291199GL897028-566259156759675667859567575125662591,5675746,5669093,5675967,
PEG10NM_001291198GL897028-566259156759675666714567575125662591,5675746,5669093,5675967,

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