Schema for refFlat
  Database: danRer7    Primary Table: refFlat    Row Count: 17,283   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName thrap3bvarchar(255) values Name of gene as it appears in genome browser.
name NM_214815varchar(255) values Name of gene
chrom chr19varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 4660591int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 4674161int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 4661653int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 4671944int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 4660591,4660829,4662038,466...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 4660818,4661881,4662185,466...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer7.mrnaOrientInfo.name (via refFlat.name)
      danRer7.refGene.name (via refFlat.name)
      danRer7.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)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
thrap3bNM_214815chr19-4660591467416146616534671944124660591,4660829,4662038,4663851,4666382,4667526,4667698,4667991,4668263,4669319,4671816,4673951,4660818,4661881,4662185,4664125,4666543,4667602,4667810,4668167,4668854,4670069,4671954,4674161,
tp53bp2aNM_214814chr13+51842553619851869753478420518425,520585,521352,523112,523412,523973,524318,525823,526487,527566,528366,528847,530131,531899,532147,533876,534271,534742,53 ...518706,520736,521466,523174,523514,524148,524500,525988,526671,527689,528491,529238,530850,532037,532281,534043,534471,534810,53 ...
gemin4NM_001018144chr15-23937229239421972393732123942033223937229,23942023,23940485,23942197,
stk35lNM_001008627chr6+38776560387898593877671738781321338776560,38780593,38788884,38777183,38781357,38789859,
nr6a1bNM_001033720chr21+771673977595557716739775950697716739,7739453,7743288,7745771,7748647,7752022,7755106,7755308,7759390,7716775,7739681,7743344,7745923,7748833,7752277,7755228,7755461,7759555,
znf971NM_001013346Zv9_scaffold3519+1662021721541685941718983166202,168566,170804,166362,168721,172154,
s100sNM_001003989chr19+822047182318228227348823111948220471,8226981,8227311,8230927,8220737,8227037,8227465,8231822,
wnt3aNM_001007185chr2-359927736526983599277365269853599277,3600387,3619993,3621903,3652624,3599757,3600653,3620029,3622145,3652698,
gpkowNM_001007207chr8-377039223773023137704408377302151137703922,37706444,37706622,37710313,37710526,37712920,37714594,37719014,37725963,37729734,37730033,37704537,37706530,37706692,37710437,37710695,37713053,37714802,37719121,37726103,37729907,37730231,
spata6NM_001017814chr8-158043971582247915804818158205781315804397,15806282,15809256,15813909,15814124,15816062,15817059,15819402,15819701,15820232,15820378,15820500,15822378,15804984,15806380,15809353,15814019,15814165,15816180,15817314,15819483,15819826,15820274,15820427,15820638,15822479,

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