Schema for refFlat
  Database: ci1    Primary Table: refFlat    Row Count: 1,035   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName LOC100183592varchar(255) values Name of gene as it appears in genome browser.
name NM_001130096varchar(255) values Name of gene
chrom Scaffold_140varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 118692int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 120118int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 118882int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 120112int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 118692,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 120118,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      ci1.mrnaOrientInfo.name (via refFlat.name)
      ci1.refGene.name (via refFlat.name)
      ci1.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
LOC100183592NM_001130096Scaffold_140-1186921201181188821201121118692,120118,
LOC100183594NM_001130095Scaffold_140-1201501228221204001227851120150,122822,
ci-arm37NM_001163698Scaffold_73+23818272412417126941723818,24133,24759,25186,25620,26195,26699,23849,24383,24892,25262,25781,26400,27241,
ci-morn40NM_001161804Scaffold_371-11184153131137515170911184,11923,12536,13014,13456,13823,14538,14879,15116,11443,12079,12642,13086,13557,13949,14644,14993,15313,
gpx_eNM_001190358Scaffold_115-2287922299822291892298011228792,229982,
gpx_dNM_001190355Scaffold_725-24074256942509025684124074,25694,
gpx7NM_001190351Scaffold_361-23265256042406825546323265,24646,25402,24229,24914,25604,
gpx_cNM_001190345Scaffold_223-93060947429335094720593060,93567,93839,94385,94624,93423,93692,94043,94535,94742,
gpx_bNM_001190339Scaffold_184-28486304992865230483528486,29123,29307,29825,30405,28722,29248,29511,29975,30499,
txnrd3NM_001190331Scaffold_1-85495786105585546986087817854957,855873,856405,856666,857060,857521,857933,858311,858555,858897,859147,859485,859902,860318,860511,860635,860860,855538,855995,856514,856774,857217,857595,858042,858381,858695,859013,859290,859657,860040,860428,860572,860791,861055,

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