Schema for refFlat
  Database: ce11    Primary Table: refFlat    Row Count: 54,631   Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName F43B10.1varchar(255) values Name of gene as it appears in genome browser.
name NM_001270347varchar(255) values Name of gene
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 16638225int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 16643558int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 16638721int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 16643502int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 16638225,16639142,16639252,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 16638782,16639202,16639591,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      ce11.mrnaOrientInfo.name (via refFlat.name)
      ce11.refGene.name (via refFlat.name)
      ce11.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
F43B10.1NM_001270347chrX-166382251664355816638721166435021116638225,16639142,16639252,16639641,16639834,16640404,16640740,16640957,16641415,16642242,16643298,16638782,16639202,16639591,16639783,16639935,16640692,16640910,16641054,16641718,16642295,16643558,
F43B10.1NM_001270348chrX-166382181664306816638721166428151116638218,16639142,16639252,16639641,16639834,16640404,16640740,16640957,16641415,16642242,16642755,16638782,16639202,16639591,16639783,16639935,16640692,16640910,16641054,16641718,16642295,16643068,
osm-1NM_078280chrX+165406731655121116541418165511462516540673,16541812,16542009,16542177,16542888,16543014,16543133,16543571,16543742,16544603,16544982,16545267,16546121,16546423,16 ...16541457,16541956,16542122,16542283,16542968,16543090,16543345,16543695,16544241,16544938,16545219,16545558,16546376,16546529,16 ...
cah-3NM_001383694chrX+16478451164893961648753316489111616478451,16486856,16487480,16488057,16488250,16488912,16478516,16487071,16487573,16488204,16488605,16489396,
T25D1.3NM_001375202chrX+16505647165135211650597616506901416505647,16506570,16513218,16513426,16506275,16507157,16513381,16513521,
T25D1.7NR_167317chrX+16519481165215901652159016521590116519481,16521590,
pat-9NM_078279chrX+16536836165402091653688916539546616536836,16537689,16538001,16538326,16538903,16539171,16536983,16537940,16538124,16538721,16539078,16540209,
eat-17NM_001307855chrX-163984821641684016399209164168401216398482,16399325,16399543,16400465,16401238,16401876,16406386,16407735,16408003,16408856,16413199,16416727,16399269,16399481,16400302,16400631,16401354,16401969,16407073,16407951,16408100,16408953,16413306,16416840,
eat-17NM_001307919chrX-16399209164012881639920916401288516399209,16399325,16399543,16400465,16401238,16399269,16399481,16400302,16400631,16401288,
eat-17NM_001307854chrX-163992091640887316399209164088731016399209,16399325,16399543,16400465,16401238,16401876,16406386,16407735,16408003,16408856,16399269,16399481,16400302,16400631,16401354,16401969,16407073,16407942,16408100,16408873,

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