Schema for refFlat
  Database: canFam3    Primary Table: refFlat    Row Count: 2,325   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 F7varchar(255) values Name of gene as it appears in genome browser.
name NM_001048033varchar(255) values Name of gene
chrom chr22varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 60572510int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 60582727int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 60572510int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 60582692int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 60572510,60574934,60576542,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 60572580,60575095,60576567,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      canFam3.mrnaOrientInfo.name (via refFlat.name)
      canFam3.refGene.name (via refFlat.name)
      canFam3.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
F7NM_001048033chr22+60572510605827276057251060582692860572510,60574934,60576542,60576643,60578855,60579661,60581512,60582096,60572580,60575095,60576567,60576754,60578999,60579771,60581636,60582727,
KDM5CNM_001048032chrX+449218154495181844921823449515672644921815,44925994,44928338,44928766,44929464,44930360,44930594,44931798,44933749,44934000,44934773,44935047,44941538,44941771,44 ...44921973,44926072,44928461,44928937,44929599,44930484,44930776,44931957,44933869,44934159,44934955,44935210,44941658,44941966,44 ...
KCNA1NM_001313824chr27-39933824399353123993382439935312139933824,39935312,
ARSANM_001048083chr10+16691926166943461669192616694346816691926,16692223,16692544,16692834,16693269,16693488,16693825,16694026,16692144,16692464,16692763,16693004,16693394,16693616,16693928,16694346,
RPS18NM_001048082chr12+271295727186572713002271861462712957,2713445,2717968,2718133,2718338,2718538,2713005,2713544,2718055,2718235,2718430,2718657,
AGERNM_001048081chr12-1574250157712915744221577111111574250,1574650,1574884,1575182,1575521,1575740,1576021,1576228,1576452,1576776,1577053,1574525,1574777,1574911,1575321,1575646,1575923,1576109,1576293,1576645,1576883,1577129,
HSD17B14NM_001047981chr1+10751805710753687310751853910753670210107518057,107518427,107519140,107519339,107519891,107524138,107535812,107536166,107536330,107536528,107518089,107518627,107519179,107519422,107519958,107524230,107535917,107536234,107536427,107536873,
RHCENM_001048036chr2+744669277450345074466987745032411074466927,74475907,74480069,74484218,74485113,74486801,74489155,74494476,74498092,74503214,74467135,74476094,74480220,74484369,74485280,74486939,74489289,74494556,74498166,74503450,
KLRD1NM_001048035chr27-35701185357066973570120235706661635701185,35702172,35703110,35705002,35705210,35706654,35701323,35702276,35703262,35705065,35705303,35706697,
CYP4A11NM_001048034chr15+136634471367409813663487136732141213663447,13664483,13665409,13665925,13667346,13667841,13668440,13668642,13668939,13670395,13670600,13673045,13663682,13664625,13665454,13666053,13667471,13667996,13668547,13668833,13669073,13670460,13670677,13674098,

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