Schema for refFlat
  Database: bosTau8    Primary Table: refFlat    Row Count: 14,943   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 HS3ST5varchar(255) values Name of gene as it appears in genome browser.
name NM_001076215varchar(255) values Name of gene
chrom chr9varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 36551273int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 36844171int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 36838721int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 36843359int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 36551273,36665997,36727928,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 36551382,36666189,36728041,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      bosTau8.mrnaOrientInfo.name (via refFlat.name)
      bosTau8.refGene.name (via refFlat.name)
      bosTau8.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
HS3ST5NM_001076215chr9+36551273368441713683872136843359536551273,36665997,36727928,36838689,36842428,36551382,36666189,36728041,36838828,36844171,
CLDN2NM_205781chrX-60134284601369566013617260136865160134284,60136956,
TMEM176ANM_205779chr4+1142070631142123131142087001142120797114207063,114208684,114209361,114210581,114210813,114211572,114212037,114207081,114208895,114209472,114210638,114211023,114211683,114212313,
TLR3NM_001008664chr27+15232458152433991523506115243203515232458,15235053,15237007,15240082,15242974,15232564,15235505,15237199,15241932,15243399,
NFIL3NM_001075240chr8+87891325878931858789149587892884187891325,87893185,
ZSCAN12NM_001077138chr23+30079856300914143008078330090123430079856,30080716,30086980,30088840,30079976,30081203,30087119,30091414,
USHBP1NM_001077137chr7+5768516577753557689505777464125768516,5769098,5769469,5772893,5773194,5773504,5773916,5774701,5775580,5776559,5776896,5777274,5769004,5769247,5769893,5773019,5773331,5773645,5774090,5774951,5775802,5776666,5777019,5777535,
TNFSF18NM_001077136chr16-41541494415527084154426641552554341541494,41546978,41552395,41544613,41547009,41552708,
TMCC2NM_001077135chr16+283696528752402837110287420252836965,2848680,2871232,2873517,2873890,2837317,2849193,2872176,2873653,2875240,
CIBAR2NM_001077134chr18-11196383112082231119657011208095911196383,11197172,11199010,11202047,11202160,11203374,11203589,11206007,11208075,11196684,11197274,11199124,11202155,11202163,11203476,11203658,11206242,11208223,

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