Schema for refFlat
  Database: danRer3    Primary Table: refFlat    Row Count: 19,345   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 psip1avarchar(255) values Name of gene as it appears in genome browser.
name NM_001020726varchar(255) values Name of gene
chrom chr23varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 18317519int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 18367665int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 18317541int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 18367407int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned range Number of exons
exonStarts 18317519,18333271,18333492,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 18317613,18333348,18333631,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer3.mrnaOrientInfo.name (via refFlat.name)
      danRer3.refGene.name (via refFlat.name)
      danRer3.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
psip1aNM_001020726chr23+183175191836766518317541183674071418317519,18333271,18333492,18335705,18335924,18349366,18349525,18349703,18363744,18363921,18364125,18364355,18367196,18367376,18317613,18333348,18333631,18335789,18336020,18349429,18349604,18349797,18363794,18363980,18364227,18364554,18367293,18367665,
pak1ip1NM_200945chr6+103558401037242610355982103724081010355840,10358923,10359206,10362879,10363073,10364934,10365880,10369292,10370786,10372280,10356081,10359086,10359327,10362954,10363126,10365080,10365978,10369389,10370913,10372426,
ube2d4NM_001089453chr19+61642710616565786164288561655521761642710,61648346,61649099,61651294,61651475,61653208,61655475,61642909,61648410,61649131,61651372,61651581,61653302,61656578,
brca2NM_001110394chr15-1142467115900111428081158578271142467,1144767,1144983,1145930,1146177,1146435,1146791,1146993,1147224,1147464,1147894,1148209,1148500,1148800,1149253,1149415, ...1143165,1144893,1145237,1146069,1146344,1146637,1146901,1147141,1147380,1147819,1148065,1148397,1148691,1149165,1149323,1149517, ...
ndufa9aNM_001013459chrUn+17799398317800331517799403917800321510177993983,177997140,177997349,177998877,177999535,178001986,178002161,178002330,178002518,178003044,177994095,177997241,177997441,177999019,177999638,178002057,178002238,178002426,178002585,178003315,
rtbdnNM_001020730chrNA+1102299131102595611102346251102588167110229913,110234608,110234910,110236541,110240720,110258462,110259205,110229954,110234788,110235007,110236670,110240817,110259163,110259561,
calhm6NM_001079661chrUn+95653824956608289565402395660536295653824,95660107,95654569,95660828,
uvragNM_201069chrUn+31411404314675123141140431467512531411404,31420376,31420791,31428199,31467436,31411491,31420464,31420852,31428365,31467512,
ahcyl2bNM_201340chrUn-12836003612843414212836038612843413117128360036,128360486,128362564,128362882,128369263,128369452,128375480,128376042,128376508,128376676,128379604,128379786,12837997 ...128360393,128360607,128362643,128362951,128369362,128369547,128375551,128376131,128376572,128376793,128379711,128379881,12838007 ...
lcmt2NM_001128557chr9-267103042672213726710304267221371426710304,26711025,26711990,26713020,26713193,26713584,26713900,26714088,26716077,26716714,26718924,26719204,26719377,26722095,26710472,26711161,26712178,26713118,26713406,26713821,26713988,26714196,26716267,26716871,26719114,26719286,26719502,26722137,

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