Schema for refFlat
  Database: hg18    Primary Table: refFlat    Row Count: 79,204   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 SAE1varchar(255) values Name of gene as it appears in genome browser.
name NM_001145714varchar(255) values Name of gene
chrom chr19varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 52325931int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 52405733int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 52326027int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 52398835int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 52325931,52338590,52345298,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 52326125,52338702,52345472,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hg18.kgAlias.alias (via refFlat.geneName)
      hg18.kgSpAlias.alias (via refFlat.geneName)
      hg18.kgXref.geneSymbol (via refFlat.geneName)
      hgFixed.refLink.name (via refFlat.geneName)
      visiGene.gene.name (via refFlat.geneName)
      hg18.ccdsInfo.mrnaAcc (via refFlat.name)
      hg18.kgXref.refseq (via refFlat.name)
      hg18.knownToRefSeq.value (via refFlat.name)
      hg18.mrnaOrientInfo.name (via refFlat.name)
      hg18.mrnaRefseq.refseq (via refFlat.name)
      hg18.refGene.name (via refFlat.name)
      hg18.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
SAE1NM_001145714chr19+52325931524057335232602752398835852325931,52338590,52345298,52347994,52350210,52364914,52398767,52404255,52326125,52338702,52345472,52348137,52350310,52365020,52398837,52405733,
TNPO2NM_001382241chr19-126710141269574612673159126927912612671014,12673139,12673411,12673565,12673885,12674636,12675241,12675527,12677053,12677305,12677495,12678009,12678383,12682434,12 ...12673057,12673267,12673486,12673665,12673991,12674732,12675340,12675615,12677212,12677413,12677582,12678181,12678609,12682587,12 ...
PPP1R2NM_001316325chr3-1967225121967514371967249821967379087196722512,196727103,196731778,196732905,196735847,196737883,196751015,196725029,196727271,196731873,196732983,196735992,196737991,196751437,
POLR2ENM_001316324chr19-103757710463911040484104285981037577,1040470,1040882,1041085,1041906,1042790,1044754,1046257,1039719,1040550,1040961,1041144,1041987,1042906,1044902,1046391,
ARFIP2NM_001376563chr11-645432464591376454918645785976454324,6455523,6455846,6456543,6456945,6457777,6459036,6455074,6455698,6456004,6456765,6457064,6457985,6459137,
ARFIP2NM_001376564chr11-645432464591376454918645785976454324,6455523,6455846,6456543,6456945,6457777,6459036,6455074,6455698,6456001,6456765,6457064,6457874,6459137,
HMGN3NM_001201362chr6-79967680800011187996868480000996579967680,79970015,79974982,79981407,80000981,79968825,79970066,79975012,79981458,80001118,
PDE4DIPNM_001350520chr1-14356278014364338914356381414364306540143562780,143565521,143565874,143567096,143568172,143568968,143571115,143574674,143575491,143577166,143577948,143579277,14358305 ...143563856,143565568,143566013,143567240,143568399,143569085,143571355,143574799,143575681,143577286,143578080,143579529,14358323 ...
ABI2NM_001375725chr2+2039013612040051372039014822040003209203901361,203939844,203953175,203964013,203968623,203975543,203984252,203989881,204000144,203901599,203940012,203953352,203964111,203968748,203975702,203984339,203990049,204005137,
KRT16P1NR_073414chr17+18283946182869331828693318286933718283946,18284992,18285212,18285483,18285733,18286161,18286476,18284556,18285075,18285369,18285644,18285859,18286382,18286933,

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