Schema for refFlat
  Database: xenLae2    Primary Table: refFlat    Row Count: 11,099   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 vamp2.Lvarchar(255) values Name of gene as it appears in genome browser.
name NM_001087475varchar(255) values Name of gene
chrom chr3Lvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 136297680int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 136321299int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 136297722int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 136320008int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 136297680,136313117,1363151...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 136297724,136313232,1363152...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)
      xenLae2.mrnaOrientInfo.name (via refFlat.name)
      xenLae2.refGene.name (via refFlat.name)
      xenLae2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
vamp2.LNM_001087475chr3L+1362976801363212991362977221363200085136297680,136313117,136315100,136319704,136319991,136297724,136313232,136315259,136319756,136321299,
vamp2.SNM_001087474chrUn_NW_016698620v1+762124476212442762,1081,877,1244,
syp.SNM_001087473chr8S+35477640354891803547771235487963735477640,35479552,35483842,35484136,35484567,35487684,35488310,35477730,35479618,35483967,35484332,35484768,35487967,35489180,
arhgap21.LNM_001090055chr6L+226199962274016422620213227392592522619996,22620043,22654485,22663717,22678924,22684578,22686959,22708555,22724521,22727209,22727420,22728262,22729233,22729768,22 ...22620029,22620270,22654665,22663742,22679026,22684657,22687014,22710395,22724680,22727306,22727457,22728388,22729530,22729833,22 ...
actb.LNM_001088953chr9_10L-84596292846009348459673684599928684596292,84596974,84597235,84598049,84599805,84600883,84596880,84597156,84597674,84598289,84599934,84600934,
gltp.LNM_001091149chr1L-1463743841463955391463752641463954505146374384,146377658,146378008,146379411,146395347,146375447,146377809,146378142,146379470,146395539,
acot2.SNM_001091148chr8S+540684254114915407133541075935406842,5409157,5410180,5407638,5409360,5411491,
crkl.LNM_001094126chr1L+1525610931525742461525612721525725063152561093,152565313,152572371,152561583,152565776,152574246,
olfm1.LNM_001094125chr8L-481853348502394818890484995944818533,4822943,4824338,4849893,4818896,4823099,4824488,4850239,
nans.LNM_001094124chr1L-1074923161075082991074931401075082426107492316,107494166,107499416,107500118,107503592,107508110,107493350,107494433,107499571,107500218,107503808,107508299,

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