Schema for refFlat
  Database: panTro4    Primary Table: refFlat    Row Count: 2,855   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 NDUFAF1varchar(255) values Name of gene as it appears in genome browser.
name NM_001079923varchar(255) values Name of gene
chrom chr15varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 38290742int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 38300895int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 38290742int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 38300895int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 38290742,38291746,38298375,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 38290892,38291821,38298561,...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)
      panTro4.mrnaOrientInfo.name (via refFlat.name)
      panTro4.refGene.name (via refFlat.name)
      panTro4.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
NDUFAF1NM_001079923chr15-38290742383008953829074238300895438290742,38291746,38298375,38300322,38290892,38291821,38298561,38300895,
ZDHHC23NM_001243057chr3+1172799191172903371172799311172903374117279919,117285438,117288049,117290069,117280092,117286149,117288217,117290337,
SCHIP1NM_001243055chr3+1636143881636719801636146081636713957163614388,163641178,163660825,163662325,163663436,163666711,163671343,163614638,163641297,163660943,163662523,163663560,163666805,163671980,
TMEM87ANM_001243054chr15-391487773921160339150032392115432039148777,39156136,39156659,39157914,39158395,39165273,39166167,39167168,39169653,39171696,39174803,39175915,39178118,39182486,39 ...39150074,39156167,39156715,39157976,39158469,39165377,39166226,39167275,39169724,39171790,39174903,39176099,39178180,39182604,39 ...
ST3GAL2NM_001037307chr16-69723143697403056972314369740305669723143,69724142,69724527,69729800,69736758,69739966,69723200,69724262,69724573,69729980,69736952,69740305,
PSME3NM_001251895chr17-145381431454965314540324145494621114538143,14543440,14543654,14543808,14544021,14544618,14545123,14548223,14548524,14548713,14549420,14540405,14543527,14543709,14543876,14544090,14544731,14545172,14548328,14548587,14548746,14549653,
DHRS4L1NM_001251894chr14+228806072289583422880607228954321022880607,22881849,22886782,22887904,22891292,22892263,22892433,22893135,22893739,22895317,22880735,22882027,22886836,22887954,22891299,22892334,22892485,22893270,22893795,22895834,
GOLT1BNM_001252004chr12-66997367670117506699786267011620666997367,66997838,67000728,67004544,67006147,67011595,66997440,66997871,67000810,67004723,67006239,67011750,
TCEAL8NM_001252003chrX-1038041291038062511038047491038051033103804129,103805728,103806201,103805141,103805801,103806251,
TCEAL8NM_001252003chrX-34773390347745303477401534774369134773390,34774530,

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