Schema for refFlat
  Database: oreNil2    Primary Table: refFlat    Row Count: 198   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 dmc1varchar(255) values Name of gene as it appears in genome browser.
name NM_001279453varchar(255) values Name of gene
chrom chrLG8-24varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 8384476int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 8389109int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 8384742int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 8388867int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 8384476,8385078,8385216,838...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 8384799,8385123,8385363,838...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)
      oreNil2.mrnaOrientInfo.name (via refFlat.name)
      oreNil2.refGene.name (via refFlat.name)
      oreNil2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
dmc1NM_001279453chrLG8-24+8384476838910983847428388867138384476,8385078,8385216,8385481,8386794,8386948,8387066,8387251,8387416,8387628,8388347,8388507,8388797,8384799,8385123,8385363,8385564,8386847,8386990,8387139,8387343,8387490,8387743,8388408,8388624,8389109,
rad51bNM_001279450chrLG15-9427307943564894276569435071109427307,9427854,9429969,9431167,9431437,9431704,9432078,9432977,9434993,9435530,9427780,9427976,9430099,9431281,9431532,9431796,9432196,9433115,9435135,9435648,
socs3aNM_001319870GL831217-1+185306818536861853068185368611853068,1853686,
prkaa2NM_001319869chrLG23+134857281349654313485802134957281013485728,13487109,13489117,13490928,13492687,13492966,13493574,13493908,13494397,13495477,13485902,13487251,13489211,13491073,13492775,13493191,13493737,13494247,13494524,13496543,
plin2NM_001311340chrLG3-768704076906707687281769037797687040,7687208,7687852,7688409,7689117,7689573,7689927,7690347,7690628,7687158,7687719,7687969,7688588,7689403,7689656,7690123,7690393,7690670,
rpl18NM_001279463chrLG11-15548798155544141554884315554391715548798,15550059,15552086,15552366,15553491,15553711,15554388,15548919,15550129,15552210,15552465,15553599,15553798,15554414,
kiss2NM_001279468chrLG15-867850386803448678694868031228678503,8680200,8678957,8680344,
zgc:114181NM_001279465GL831461-1-35475237707135503937673512354752,355771,357495,357730,358261,361614,361792,362540,374910,375661,376624,377021,355118,355919,357637,357895,358422,361699,361990,362629,375073,375805,376735,377071,
nr0b1bNM_001279472GL831144-1-598249759838785982673598371535982497,5983199,5983207,5982913,5983207,5983878,
ghrNM_001279455chrLG7-31300410313270353130051331318028931300410,31301733,31301970,31302260,31303419,31304978,31306461,31317949,31327017,31301359,31301803,31302061,31302405,31303598,31305157,31306597,31318037,31327035,

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