Schema for refFlat
  Database: susScr3    Primary Table: refFlat    Row Count: 5,345   Data last updated: 2020-09-02
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName MFSD6varchar(255) values Name of gene as it appears in genome browser.
name NM_001097457varchar(255) values Name of gene
chrom chr15varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 106423161int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 106480159int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 106423184int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 106480134int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 106423161,106453428,1064747...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 106424743,106453526,1064748...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)
      susScr3.mrnaOrientInfo.name (via refFlat.name)
      susScr3.refGene.name (via refFlat.name)
      susScr3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MFSD6NM_001097457chr15+1064231611064801591064231841064801346106423161,106453428,106474732,106475797,106477761,106479936,106424743,106453526,106474894,106475896,106478042,106480159,
LGALS9NM_001348969chr12+460022044602136046002285460208221046002204,46006405,46009316,46010704,46013822,46014445,46015154,46015697,46015883,46020675,46002324,46006497,46009518,46010815,46013858,46014496,46015196,46015786,46016046,46021360,
PRXL2ANM_001359939chr14+88863046888785958886925488877951788863046,88864554,88869252,88871212,88873950,88874674,88877837,88863098,88864684,88869432,88871304,88874091,88874839,88878595,
PRXL2ANM_001359938chr14+88863046888785958886925488877951688863046,88869252,88871212,88873950,88874674,88877837,88863098,88869432,88871304,88874091,88874839,88878595,
PRXL2ANM_001359937chr14+88863046888785958886307788877951688863046,88869269,88871212,88873950,88874674,88877837,88863098,88869432,88871304,88874091,88874839,88878595,
BCHENM_001357509chr13-1134113101134717271134126611134672494113411310,113419471,113465732,113471591,113412786,113419638,113467257,113471727,
SERTM2NM_001354500chrX+1059525881059635641059595731059598463105952588,105952949,105958786,105952793,105953046,105963564,
SLC22A1NM_001348975chr1-9139435916436391398079164258119139435,9141534,9143407,9146306,9150118,9153881,9154228,9155226,9156353,9158007,9163847,9139874,9141634,9143520,9146415,9150333,9153991,9154343,9155395,9156508,9158111,9164363,
HADHBNM_001348972chr3-11965038511969042111965120511968220116119650385,119653802,119654672,119655206,119656394,119656514,119657720,119659647,119660153,119662811,119667008,119670756,11967610 ...119651241,119653967,119654747,119655294,119656442,119656594,119657842,119659828,119660341,119662899,119667108,119670801,11967620 ...
LGALS9NM_001348971chr12+46002204460156004600228546015244746002204,46006405,46009316,46010704,46013822,46014445,46015154,46002324,46006497,46009518,46010815,46013858,46014496,46015600,

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