Schema for refFlat
  Database: galGal3    Primary Table: refFlat    Row Count: 7,422   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 PSMD3varchar(255) values Name of gene as it appears in genome browser.
name NM_001031362varchar(255) values Name of gene
chrom chrUn_randomvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 29461885int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 29465500int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 29462174int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 29465475int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 29461885,29462329,29462553,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 29462252,29462380,29462711,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      galGal3.mrnaOrientInfo.name (via refFlat.name)
      galGal3.refGene.name (via refFlat.name)
      galGal3.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
PSMD3NM_001031362chrUn_random-294618852946550029462174294654751129461885,29462329,29462553,29462969,29463187,29463473,29463742,29464057,29464406,29465299,29465330,29462252,29462380,29462711,29463084,29463291,29463664,29463879,29464195,29464597,29465329,29465500,
PEMTNM_001006164chr14-481224448505754813735485049384812244,4813729,4814323,4818074,4821533,4827692,4847881,4850373,4813638,4813790,4814398,4818186,4821679,4827808,4847989,4850575,
SRRDNM_001201445chr15+738001773817937380036738164077380017,7380212,7380336,7380560,7380743,7381125,7381415,7380146,7380253,7380467,7380659,7380898,7381171,7381793,
DEFB4ANM_001201399chr3+1102561251102586301102573891102584414110256125,110257304,110257630,110258425,110256191,110257447,110257751,110258630,
GHRHRNM_001201396chr2+1041919106006210419921059652121041919,1044729,1046704,1049403,1051147,1052208,1053264,1054030,1055487,1056168,1057715,1059529,1042037,1044832,1046805,1049501,1051280,1052362,1053325,1054100,1055579,1056298,1057757,1060062,
CD38NM_001201388chr4-79543246795649587954327379564898879543246,79545248,79547248,79549809,79551016,79551811,79552510,79564659,79543355,79545335,79547341,79549886,79551099,79551947,79552640,79564958,
AHRRNM_001201387chr2-912917729135765891291772913576581091291772,91295322,91296235,91297231,91298372,91299987,91301286,91318216,91350765,91357596,91292889,91295464,91296354,91297428,91298506,91300114,91301376,91318317,91350947,91357658,
LOC422426NM_001197243chr4+26033718260415682603378926040934926033718,26035400,26035690,26036744,26037603,26038555,26038730,26039736,26040899,26033888,26035487,26035924,26036767,26037749,26038641,26038832,26039845,26041568,
CEP41NM_001199393chr1-84017184847284071084841411840171,841241,841636,842590,842950,843287,843897,844334,846968,847879,848381,840841,841457,841751,842658,843102,843432,843967,844396,847016,847943,848472,
DTD1NM_001199402chr3-16266214162795581626835916279523616266214,16268338,16272622,16274784,16277203,16279480,16266831,16268515,16272720,16275020,16277294,16279558,

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