Schema for refFlat
  Database: equCab1    Primary Table: refFlat    Row Count: 1,960   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 C23H9orf72varchar(255) values Name of gene as it appears in genome browser.
name NM_001301184varchar(255) values Name of gene
chrom chr23varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 35672097int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 35691567int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 35673695int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 35691523int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 35672097,35674025,35675254,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 35673882,35674135,35675312,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      equCab1.mrnaOrientInfo.name (via refFlat.name)
      equCab1.refGene.name (via refFlat.name)
      equCab1.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
C23H9orf72NM_001301184chr23-356720973569156735673695356915231035672097,35674025,35675254,35678519,35681079,35683296,35685559,35686347,35689913,35691079,35673882,35674135,35675312,35678755,35681196,35683369,35685624,35686443,35689973,35691567,
GOSR1NM_001301246chr11+428767174292874842876737429248611042876717,42879573,42883358,42883799,42887351,42890333,42914258,42921482,42924736,42928405,42876768,42879694,42883446,42883907,42887443,42890408,42914288,42921565,42928377,42928748,
RAP1ANM_001301245chr5+27046474271139312709279327108717927046474,27090184,27092766,27097465,27099630,27102308,27104102,27108630,27111551,27046550,27090266,27092850,27097534,27099687,27102449,27104246,27108746,27113931,
RLIMNM_001301238chrUn-2229592382229836702229646082229687175222959238,222967522,222968548,222982574,222983480,222966206,222967606,222968741,222982638,222983670,
HTR3ANM_001301236chr7+19008024190203891900805519020389919008024,19010401,19011667,19013653,19015240,19017523,19018038,19018353,19020090,19008122,19010568,19011712,19013763,19015410,19017684,19018249,19018575,19020389,
ZMPSTE24NM_001301234chr2-162013511624797916202852162479791016201351,16206241,16209042,16224455,16229689,16231150,16231890,16239077,16245875,16247856,16203077,16206385,16209147,16224640,16229831,16231303,16232007,16239164,16246022,16247979,
ITGB1NM_001301217chr29+3948450398091239484503974840173948450,3953469,3955699,3958713,3960794,3961485,3964418,3966011,3966417,3967961,3968253,3970000,3970458,3971759,3973669,3974765, ...3948471,3953536,3955785,3958936,3960965,3961724,3964574,3966107,3966507,3968102,3968453,3970239,3970681,3971992,3973836,3974846, ...
IFRD1NM_001301221chr4+698044546982697169804693698262871269804454,69808934,69809183,69810071,69812279,69815342,69815479,69815737,69821483,69823723,69824259,69826197,69804784,69809039,69809268,69810196,69812437,69815393,69815655,69815846,69821618,69823852,69824355,69826971,
RBPJNM_001301219chr3-920962309216214092097328921619781192096230,92097797,92098266,92099898,92105219,92105488,92109162,92113851,92121828,92138175,92161961,92097644,92097901,92098422,92100039,92105332,92105626,92109337,92114017,92121924,92138214,92162140,
CDC5LNM_001301220chr20+366799523672984236680093367277111636679952,36682478,36684001,36684752,36686261,36691317,36692979,36694548,36706150,36707940,36709735,36711437,36711815,36714816,36 ...36680138,36682582,36684163,36684880,36686361,36691536,36693124,36694737,36706299,36708103,36709900,36711518,36712058,36715014,36 ...

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