Schema for refFlat
  Database: calJac1    Primary Table: refFlat    Row Count: 263   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName NME1varchar(255) values Name of gene as it appears in genome browser.
name NM_001204876varchar(255) values Name of gene
chrom Contig723varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 414554int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 424514int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 417013int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 424285int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 414554,417009,422314,423596...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 414658,417139,422416,423709...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      calJac1.mrnaOrientInfo.name (via refFlat.name)
      calJac1.refGene.name (via refFlat.name)
      calJac1.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
NME1NM_001204876Contig723+4145544245144170134242855414554,417009,422314,423596,424167,414658,417139,422416,423709,424514,
GTF2A1LNM_001204841Contig1944+48361435648361419034836,6750,14082,5099,6840,14356,
GTF2A1LNM_001204841Contig4689-22428549592242854882622428,24020,26670,51227,51551,54861,23019,24105,26726,51351,51653,54959,
STON1NM_001204840Contig4689-74018932607720893213374018,81331,91283,77283,81534,93260,
TNNI3KNM_001204802Contig1479-3194353773853198823773854319435,323223,374717,377325,319959,323303,374887,377385,
TNNI3KNM_001204802Contig6693+317526247931752624791231752,36004,41683,41916,45877,46566,59464,60110,61124,61307,61491,62374,31853,36143,41828,42021,45972,46716,59551,60167,61217,61365,61686,62479,
MEF2BNM_001205200Contig2797-3115193374913117423156379311519,312248,312528,312715,312995,313649,314463,315583,337406,311968,312360,312622,312849,313143,313784,314667,315666,337491,
TNFSF12NM_001205139Contig2760+1279091366681279881365767127909,128347,128965,129940,130083,136005,136324,128186,128395,129041,129994,130119,136130,136668,
SELENOKNM_001199915Contig3141-2274032341322277372339605227403,228002,228719,230306,233941,227741,228089,228803,230397,234132,
SELENOWNM_001199908Contig9078+79653877967978982333679653,81711,81855,82051,82252,87424,79818,81736,81909,82126,82351,87796,

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