Schema for refFlat
  Database: ce6    Primary Table: refFlat    Row Count: 53,463   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 gcy-11varchar(255) values Name of gene as it appears in genome browser.
name NM_001373625varchar(255) values Name of gene
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 17046157int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 17055497int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 17046205int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 17055470int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 23int(10) unsigned range Number of exons
exonStarts 17046157,17046486,17046702,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 17046432,17046646,17046816,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      ce6.mrnaOrientInfo.name (via refFlat.name)
      ce6.refGene.name (via refFlat.name)
      ce6.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
gcy-11NM_001373625chrX-170461571705549717046205170554702317046157,17046486,17046702,17046863,17047282,17047508,17048533,17048901,17049073,17049387,17049822,17049998,17050154,17050643,17 ...17046432,17046646,17046816,17047197,17047463,17047670,17048756,17049006,17049322,17049520,17049910,17050104,17050315,17050800,17 ...
F35B3.7NM_078352chrX-170351101704299517035238170428481617035110,17035601,17036598,17036823,17036949,17037143,17037284,17037990,17038380,17039146,17039288,17040084,17041104,17041265,17 ...17035334,17035694,17036781,17036901,17037048,17037229,17037358,17038132,17038463,17039224,17039400,17040271,17041216,17041469,17 ...
C30G4.4NM_001307882chrX-170570781706663017057078170666301117057078,17057203,17058098,17059113,17059233,17059564,17065039,17065927,17066037,17066391,17066603,17057154,17057295,17058162,17059140,17059309,17059625,17065197,17065989,17066057,17066469,17066630,
C30G4.4NM_001307881chrX-170570781706663017057078170666301017057078,17057203,17058098,17059113,17059233,17059564,17065039,17065927,17066037,17066603,17057154,17057295,17058162,17059140,17059309,17059625,17065158,17065989,17066057,17066630,
acs-9NM_078327chrX-168779931688044316878064168803881116877993,16878218,16878623,16878885,16879042,16879187,16879387,16879606,16879843,16880111,16880307,16878171,16878372,16878833,16878992,16879131,16879270,16879562,16879800,16880046,16880202,16880443,
Y13C8A.1NM_001381179chrX+16883642168843901688364216884390216883642,16884319,16883781,16884390,
F39F10.4NM_001383698chrX-16902307169036211690234216902659316902307,16902591,16903509,16902550,16903067,16903621,
fbxb-114NM_078337chrX+16921749169230621692176916922778216921749,16921910,16921861,16923062,
F52G3.1NM_078343chrX+169637871697275516964060169723851516963787,16964055,16965109,16965929,16966405,16967868,16968159,16968419,16969033,16969337,16969832,16970244,16970730,16971935,16 ...16963871,16964166,16965244,16966157,16966618,16968035,16968232,16968811,16969274,16969498,16970190,16970510,16971569,16972206,16 ...
F52G3.5NM_078344chrX-16973142169760601697323516976047916973142,16973421,16974016,16974674,16974865,16975061,16975150,16975374,16975956,16973373,16973612,16974204,16974820,16975014,16975100,16975315,16975428,16976060,

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