Schema for refFlat
  Database: hg16    Primary Table: refFlat    Row Count: 78,196   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 ARFIP2varchar(255) values Name of gene as it appears in genome browser.
name NM_001370411varchar(255) values Name of gene
chrom chr11varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 6462057int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 6466870int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 6462651int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 6465960int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 6462057,6463256,6463594,646...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 6462807,6463431,6463737,646...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hg16.atlasOncoGene.locusSymbol (via refFlat.geneName)
      hg16.jaxOrtholog.humanSymbol (via refFlat.geneName)
      hg16.kgAlias.alias (via refFlat.geneName)
      hg16.kgXref.geneSymbol (via refFlat.geneName)
      hgFixed.refLink.name (via refFlat.geneName)
      visiGene.gene.name (via refFlat.geneName)
      hg16.altGraphX.mrnaRefs (via refFlat.name)
      hg16.kgXref.refseq (via refFlat.name)
      hg16.knownToRefSeq.value (via refFlat.name)
      hg16.mrnaOrientInfo.name (via refFlat.name)
      hg16.mrnaRefseq.refseq (via refFlat.name)
      hg16.refGene.name (via refFlat.name)
      hg16.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
ARFIP2NM_001370411chr11-646205764668706462651646596086462057,6463256,6463594,6464276,6464678,6465510,6465861,6466769,6462807,6463431,6463737,6464498,6464797,6465607,6465962,6466870,
CLK2P1NR_002711chr7-23366606233684182336841823368418123366606,23368418,
DEFB119NR_073151chr20-30709965307234523072345230723452430709965,30711154,30721125,30723225,30710242,30711194,30721162,30723452,
ACTG1P17NR_036446chr15-81120467811343508113435081134350381120467,81133083,81134333,81122001,81133184,81134350,
MCTS1NM_001137554chrX+1184926551185091161184928101185002216118492655,118493363,118494035,118496181,118498967,118500139,118492824,118493516,118494133,118496315,118499035,118509116,
CALR4PNR_161259chr1-51397455514193215141932151419321951397455,51399214,51401895,51402763,51403341,51405137,51409543,51418413,51419039,51397623,51399328,51402131,51402922,51403433,51405340,51409645,51418510,51419321,
MIR6818NR_106876chr22+28727591287276562872765628727656128727591,28727656,
MPNDNM_001159846chr19+4294523431108342945904310999114294523,4294704,4296741,4303893,4305041,4305320,4308249,4308511,4309079,4310159,4310912,4294597,4294991,4296978,4304026,4305126,4305417,4308418,4308582,4309169,4310252,4311083,
TRAPPC2LNM_001318525chr16+88667680886732328866770488671513588667680,88669172,88670216,88670446,88671467,88667737,88669345,88670304,88670526,88673232,
CUX2NM_015267chr12+10988392111020031110988393411019808222109883921,110063956,110067646,110113517,110141174,110143202,110145089,110146229,110148297,110153966,110156677,110156955,11015804 ...109883997,110064067,110067694,110113596,110141309,110143326,110145166,110146296,110148346,110154071,110156869,110157014,11015809 ...

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