Schema for refFlat
  Database: bosTau6    Primary Table: refFlat    Row Count: 14,950   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 HECTD3varchar(255) values Name of gene as it appears in genome browser.
name NM_001098961varchar(255) values Name of gene
chrom chr3varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 101623082int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 101631050int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 101623153int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 101630522int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 21int(10) unsigned range Number of exons
exonStarts 101623082,101623673,1016240...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 101623522,101623834,1016241...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      bosTau6.mrnaOrientInfo.name (via refFlat.name)
      bosTau6.refGene.name (via refFlat.name)
      bosTau6.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
HECTD3NM_001098961chr3+10162308210163105010162315310163052221101623082,101623673,101624065,101624237,101624618,101624819,101625076,101625602,101625970,101626693,101627028,101627260,10162748 ...101623522,101623834,101624158,101624373,101624734,101624933,101625159,101625768,101626052,101626876,101627081,101627325,10162758 ...
HDAC6NM_001098960chrX+919942919201321491995475920128963091994291,91995445,91995650,91995894,91998408,91998599,91999320,91999573,92000879,92001110,92004631,92004855,92005013,92005153,92 ...91994361,91995568,91995779,91995983,91998493,91998640,91999417,91999671,92000984,92001179,92004758,92004921,92005073,92005243,92 ...
RBISNM_001110068chr14+79754127797592317975647479759169479754127,79756471,79758715,79759097,79754187,79756588,79758832,79759231,
AQP11NM_001110069chr29-18477127184887131847716118488671318477127,18480187,18488052,18477213,18480304,18488713,
CHST11NM_001192668chr5+68385644686457746838577368645445368385644,68508579,68644590,68385891,68508665,68645774,
KIF18ANM_001192909chr15-594998155957570659500338595757061659499815,59503117,59508697,59509540,59540588,59546602,59549885,59559742,59564368,59564673,59566225,59568403,59569645,59570183,59 ...59500421,59503227,59508805,59509979,59540824,59546724,59550050,59559905,59564475,59564748,59566402,59568601,59569756,59570288,59 ...
PHYKPLNM_001192899chr7-406440464066934640644746406693461340644046,40644715,40645358,40647166,40647656,40661197,40661675,40663250,40663444,40664136,40666907,40668349,40669287,40644283,40644796,40645489,40647256,40647811,40661423,40661758,40663367,40663532,40664211,40667067,40668468,40669346,
PRDM13NM_001193010chr9-50873668508814085087366850881408450873668,50879221,50879601,50881264,50875395,50879342,50879733,50881408,
GRIN2BNM_001192921chr5+964088039676151696408803967615161296408803,96531036,96621004,96697850,96698767,96699975,96705191,96707935,96750951,96752903,96755891,96759620,96409214,96531635,96621119,96698053,96698939,96700129,96705317,96708165,96751112,96753091,96756130,96761516,
SGK3NM_001193021chr14+330049823306571133020389330640291733004982,33020250,33026084,33028547,33034414,33040007,33043407,33045924,33051165,33051358,33052490,33052696,33053570,33055842,33 ...33005063,33020467,33026168,33028620,33034490,33040095,33043457,33045982,33051249,33051490,33052603,33052733,33053657,33055938,33 ...

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