Schema for refFlat
  Database: xenTro9    Primary Table: refFlat    Row Count: 8,806   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName cfap61varchar(255) values Name of gene as it appears in genome browser.
name NM_001079044varchar(255) values Name of gene
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 24503861int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 24644944int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 24507573int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 24644767int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 24int(10) unsigned range Number of exons
exonStarts 24503861,24507550,24508167,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 24503988,24507716,24508321,...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)
      xenTro9.mrnaOrientInfo.name (via refFlat.name)
      xenTro9.refGene.name (via refFlat.name)
      xenTro9.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
cfap61NM_001079044chr5+245038612464494424507573246447672424503861,24507550,24508167,24508401,24508702,24509467,24511350,24516356,24525373,24527076,24527641,24529060,24531141,24538396,24 ...24503988,24507716,24508321,24508478,24508770,24509594,24511483,24516510,24525462,24527157,24527820,24529100,24531281,24538523,24 ...
bpiNM_001015694chr10-308279513084958230828965308495261530827951,30829630,30829981,30830483,30830730,30831206,30832863,30833344,30834119,30835081,30836008,30836359,30837562,30844915,30 ...30829004,30829707,30830045,30830526,30830798,30831374,30832923,30833521,30834211,30835145,30836072,30836515,30837688,30845027,30 ...
tet3NM_001097187chr3-11297476011302382511297502611302138611112974760,112977288,112980088,112980385,112980841,112981897,112984476,112984980,112991304,113021152,113023780,112976741,112977625,112980226,112980475,112980992,112982106,112984570,112985071,112993848,113021782,113023825,
ubp1NM_001011473chr10-3337812335232233385323352275153337812,3339790,3341827,3342266,3342505,3343930,3345367,3345598,3345831,3346327,3346701,3346917,3347297,3349242,3352192,3338570,3339842,3341970,3342346,3342596,3344024,3345422,3345678,3345942,3346480,3346808,3347023,3347374,3349385,3352322,
mir216NR_049613chr5-26049024260491152604911526049115126049024,26049115,
traipNM_001017318chr4-11575027311576242711575214011576239815115750273,115752745,115753001,115753219,115753751,115755056,115755542,115755867,115756920,115757212,115757433,115758085,11575861 ...115752260,115752796,115753127,115753274,115753907,115755145,115755632,115755955,115757034,115757307,115757561,115758125,11575869 ...
hs6st1NM_001017317chr5-1293545651294170631293563361294168242129354565,129416333,129357045,129417063,
grk5NM_001017316chr3-12180440312182818212180479612182794916121804403,121805839,121806269,121807521,121808833,121809566,121810302,121810730,121811088,121811794,121812012,121813192,12181466 ...121804907,121805971,121806407,121807659,121809042,121809656,121810340,121810921,121811229,121811858,121812105,121813293,12181474 ...
mir23a-1NR_049638chr3+1299986691299987471299987471299987471129998669,129998747,
trdmt1NM_001004959chr6+203444052036306320344641203629601120344405,20348975,20351632,20351952,20353093,20354813,20358551,20359904,20360882,20362410,20362853,20344708,20349085,20351709,20352024,20353159,20354883,20358635,20360251,20360940,20362540,20363063,

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