Schema for refFlat
  Database: bosTau3    Primary Table: refFlat    Row Count: 14,971   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 TMEM268varchar(255) values Name of gene as it appears in genome browser.
name NM_001024561varchar(255) values Name of gene
chrom chr8varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 85721710int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 85746750int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 85725090int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 85745597int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 85721710,85725012,85730696,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 85721805,85725199,85730806,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      bosTau3.refGene.name (via refFlat.name)
      bosTau3.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
TMEM268NM_001024561chr8+85721710857467508572509085745597985721710,85725012,85730696,85733454,85734285,85737913,85739946,85740905,85745417,85721805,85725199,85730806,85733562,85734435,85738024,85740027,85741091,85746750,
PRR5LNM_001015519chr15-63600778636741666360164463651219963600778,63611071,63613988,63613992,63618654,63633304,63648921,63651055,63674024,63602039,63611201,63613992,63614085,63618712,63633353,63649002,63651342,63674166,
DCUN1D3NM_001015518chr25+19714958197694101976676019769252319714958,19766655,19768768,19715092,19767191,19769410,
EIF2B2NM_001015593chr10+80680107806871268068013680686731880680107,80680403,80680684,80681740,80683028,80684048,80685233,80686573,80680299,80680524,80680833,80681904,80683124,80684186,80685300,80687126,
LSM1NM_001017952chr27-32623828326340413262415932633874432623828,32627387,32628886,32633828,32624330,32627503,32628955,32634041,
FIS1NM_001034784chr25+34278250342819083427831034281699534278250,34279231,34280640,34281167,34281601,34278355,34279364,34280717,34281273,34281908,
FBXO15NM_001035021chr17+280558212809370828062595280935991028055821,28062579,28064493,28069547,28070211,28073918,28075097,28076117,28092053,28093329,28055957,28062690,28064598,28069790,28070421,28074045,28075180,28076260,28092178,28093708,
EXOSC2NM_001046561chr11+96519460965282979651948196527997996519460,96521206,96522966,96523298,96524447,96525483,96526702,96527280,96527916,96519603,96521308,96523012,96523388,96524513,96525552,96526879,96527409,96528297,
GSTM3NM_001046560chr3+31018244310212923101827431021193731018244,31019171,31019921,31020090,31020520,31020704,31021094,31018322,31019238,31020003,31020191,31020616,31020815,31021292,
SMG9NM_001046559chr18-491542874917459849154715491711981449154287,49156031,49156455,49156783,49157621,49160268,49160739,49162841,49166063,49167909,49168103,49168462,49171048,49174461,49154794,49156176,49156584,49156891,49157728,49160354,49160835,49162953,49166176,49168007,49168368,49168537,49171204,49174598,

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