Schema for refFlat
  Database: danRer6    Primary Table: refFlat    Row Count: 18,296   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 magvarchar(255) values Name of gene as it appears in genome browser.
name NM_001007062varchar(255) values Name of gene
chrom chr15varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 33247569int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 33260593int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 33247599int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 33260405int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 33247569,33249831,33252393,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 33247648,33250200,33252690,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer6.mrnaOrientInfo.name (via refFlat.name)
      danRer6.refGene.name (via refFlat.name)
      danRer6.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
magNM_001007062chr15+332475693326059333247599332604051033247569,33249831,33252393,33252783,33255489,33256021,33256406,33258978,33259900,33260243,33247648,33250200,33252690,33253041,33255750,33256330,33256506,33259081,33259954,33260593,
cdca8NM_001007456chr19-46408338464127484640833846412451846408338,46408533,46410170,46410324,46410502,46411850,46412357,46412710,46408434,46408616,46410235,46410397,46410540,46411979,46412458,46412748,
mybpc2bNM_001013511chr24+373537453740705537353745374065452637353745,37356228,37359071,37359279,37362597,37363677,37367101,37367654,37368113,37368684,37370655,37371087,37371276,37373029,37 ...37353809,37356377,37359189,37359328,37362657,37363844,37367234,37367779,37368219,37368854,37370821,37371194,37371306,37373172,37 ...
tnfbNM_001024447chr15-35421491354245453542194035424503435421491,35423329,35424169,35424323,35422353,35423398,35424236,35424545,
pimr213NM_001030117Zv8_scaffold3089+69879993447008774181869879,71395,73019,73445,74148,74440,75068,99229,70223,72730,73162,73646,74325,74529,75178,99344,
afg1lbNM_001025482chr20-321129923218089932113277321808871332112992,32114692,32115246,32124006,32124826,32127245,32157959,32168725,32173573,32174802,32175028,32178840,32180778,32113406,32114806,32115387,32124107,32124897,32127328,32158018,32168825,32173701,32174904,32175080,32179163,32180899,
cx27.5NM_001362429chr5+21651677216575722165642121657144221651677,21656407,21651849,21657572,
git2bNM_001362634chr10+384996513853312738499741385295581938499651,38502982,38506096,38506295,38506548,38508747,38511514,38511695,38511929,38512102,38512265,38512448,38514259,38516218,38 ...38499793,38503116,38506209,38506401,38506635,38508878,38511609,38511741,38511981,38512175,38512363,38512560,38514402,38516371,38 ...
cog8NM_001013506chr18+647642664828726476426648257746476426,6479320,6480221,6482197,6476639,6480139,6480390,6482872,
cog8NM_001013506chr18-651648465168236516484651681316516484,6516823,

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