Schema for refFlat
  Database: mm8    Primary Table: refFlat    Row Count: 47,024   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 Ndst1varchar(255) values Name of gene as it appears in genome browser.
name NM_001348101varchar(255) values Name of gene
chrom chr18varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 60809862int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 60872115int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 60814613int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 60838604int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 15int(10) unsigned range Number of exons
exonStarts 60809862,60815332,60816546,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 60814733,60815435,60816656,...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)
      mm8.ccdsInfo.mrnaAcc (via refFlat.name)
      mm8.dupSpMrna.dupMrnaID (via refFlat.name)
      mm8.dupSpMrna.mrnaID (via refFlat.name)
      mm8.kgXref.refseq (via refFlat.name)
      mm8.knownToRefSeq.value (via refFlat.name)
      mm8.mrnaOrientInfo.name (via refFlat.name)
      mm8.mrnaRefseq.mrna (via refFlat.name)
      mm8.mrnaRefseq.refseq (via refFlat.name)
      mm8.refGene.name (via refFlat.name)
      mm8.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Ndst1NM_001348101chr18-608098626087211560814613608386041560809862,60815332,60816546,60817297,60820704,60822435,60823807,60824876,60825740,60828141,60829105,60830444,60832969,60838091,60 ...60814733,60815435,60816656,60817468,60820879,60822559,60823904,60825059,60825869,60828327,60829260,60830532,60833464,60839001,60 ...
Tsg101NM_001348089chr7-467569704678799146757636467770011046756970,46758943,46760379,46769048,46771543,46775072,46776926,46778766,46781399,46787842,46757726,46759183,46760582,46769140,46771610,46775199,46777013,46778832,46781484,46787991,
Ndst1NM_001348100chr18-608098626087378960814613608386041560809862,60815332,60816546,60817297,60820704,60822435,60823807,60824876,60825740,60828141,60829105,60830444,60832969,60838091,60 ...60814733,60815435,60816656,60817468,60820879,60822559,60823904,60825059,60825869,60828327,60829260,60830532,60833464,60839001,60 ...
Daw1NM_001372244chr1+830387788308959683038822830892131383038778,83058316,83059368,83061273,83062279,83066929,83070367,83071640,83076244,83077109,83084912,83088229,83089178,83038862,83058389,83059513,83061332,83062402,83067029,83070475,83071747,83076347,83077224,83084989,83088392,83089596,
CalrNM_007591chr8-87732192877370368773275187736903987732192,87733048,87734169,87734482,87734678,87734975,87735966,87736354,87736812,87732949,87733141,87734313,87734596,87734888,87735070,87736170,87736456,87737036,
Capn3NM_007601chr2+12015503312019636012015531312019594024120155033,120172123,120173550,120175931,120176621,120177773,120179514,120181108,120182394,120183234,120186212,120186676,12018730 ...120155622,120172193,120173669,120176065,120176790,120177917,120179598,120181194,120182472,120183395,120186382,120186688,12018751 ...
Nos1NM_008712chr5+11812786811821987011812824611821484328118127868,118140313,118154855,118156810,118157702,118158740,118161500,118164850,118166340,118169019,118171087,118171796,11817375 ...118128956,118140440,118154984,118156956,118157865,118158832,118161642,118164990,118166515,118169121,118171282,118171882,11817389 ...
Ablim1NM_001290816chr19-570859825725088157090473572505642157085982,57092656,57093736,57095159,57096246,57097045,57098130,57100174,57102711,57114502,57117015,57121340,57122109,57133062,57 ...57090587,57092737,57093814,57095225,57096311,57097148,57098222,57100321,57102759,57114632,57117051,57121496,57122187,57133121,57 ...
Cdh26NM_001291189chr2+17835992217841677417836019517841635614178359922,178370800,178379213,178386835,178389463,178390082,178391993,178395966,178397540,178399416,178400991,178401729,17841102 ...178360246,178370905,178379375,178386983,178389630,178390211,178392179,178396235,178397683,178399662,178401207,178401860,17841110 ...
Adipor1NM_001306069chr1+1362320741362497611362394251362480698136232074,136239331,136240368,136241161,136242319,136244492,136247467,136247940,136232400,136239566,136240485,136241333,136242506,136244680,136247661,136249761,

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