Schema for refFlat
  Database: oviAri1    Primary Table: refFlat    Row Count: 955   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 AQP5varchar(255) values Name of gene as it appears in genome browser.
name NM_001009273varchar(255) values Name of gene
chrom chr3varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 145549429int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 145568648int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 145549430int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 145568648int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 145549429,145550592,1455509...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 145549616,145550676,1455511...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)
      oviAri1.mrnaOrientInfo.name (via refFlat.name)
      oviAri1.refGene.name (via refFlat.name)
      oviAri1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
AQP5NM_001009273chr3-1455494291455686481455494301455686486145549429,145550592,145550965,145552223,145568633,145568637,145549616,145550676,145551130,145552568,145568637,145568648,
GPR50NM_001009726chrX-99392710993972789939271099397278399392710,99393365,99397090,99393251,99394129,99397278,
CR2NM_001009724chr12+5085545511348150855935109778145085545,5085851,5096166,5096328,5097199,5097640,5099033,5100457,5102009,5103161,5105105,5109687,5112757,5112981,5085801,5086067,5096236,5096576,5097287,5097723,5099354,5100595,5102084,5103185,5105181,5109793,5112870,5113481,
LPONM_001009722chr11+8316131833943383161318338835118316131,8320887,8322603,8323165,8324001,8325644,8327586,8336165,8338292,8338717,8339328,8316220,8320925,8322725,8323265,8324208,8325685,8327737,8336423,8338339,8338835,8339433,
GHRLNM_001009721chr19-57408065574125285740818057412041557408065,57408687,57411617,57411933,57412509,57408200,57408796,57411731,57412068,57412528,
ITGB2NM_001009485chr1-28427782428430672528427788428429421016284277824,284278133,284280106,284280490,284280884,284281356,284282879,284283725,284285576,284286602,284287581,284288046,28428914 ...284277947,284278300,284280198,284280651,284281014,284281398,284283019,284283815,284285671,284286758,284287809,284288153,28428924 ...
CFL1NM_001009484chr21-47866288478687194786628847868708347866288,47866572,47868705,47866306,47866880,47868719,
PRNPNM_001009481chr13+49523545495417424953938649540191749523545,49526046,49539376,49539485,49539493,49539889,49541336,49523598,49526143,49539485,49539493,49539668,49541011,49541742,
NPPCNM_001009479chr2-2457430532457438232457430532457438232245743053,245743767,245743344,245743823,
CAV1NM_001009477chr4-54877515549115895487758654911589454877515,54877781,54909959,54911560,54877723,54877928,54910124,54911589,

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