Schema for refFlat
  Database: mm10    Primary Table: refFlat    Row Count: 47,382   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 Wdsub1varchar(255) values Name of gene as it appears in genome browser.
name NM_001159636varchar(255) values Name of gene
chrom chr2varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 59855193int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 59882606int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 59855270int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 59878527int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 59855193,59858609,59861560,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 59855275,59858750,59861737,...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)
      mm10.ccdsInfo.mrnaAcc (via refFlat.name)
      mm10.kgXref.refseq (via refFlat.name)
      mm10.knownToRefSeq.value (via refFlat.name)
      mm10.mrnaOrientInfo.name (via refFlat.name)
      mm10.refGene.name (via refFlat.name)
      mm10.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Wdsub1NM_001159636chr2-598551935988260659855270598785271159855193,59858609,59861560,59862619,59862816,59864301,59873215,59874238,59876666,59878129,59882400,59855275,59858750,59861737,59862726,59862857,59864335,59873309,59874328,59876851,59878550,59882606,
Rbm18NM_001159635chr2-36116078361367043611781436134247636116078,36120812,36122851,36127214,36134134,36136481,36117974,36120898,36122938,36127251,36134263,36136704,
Prrc2bNM_001159634chr2+321511473223453732182511322307423232151147,32182457,32183122,32185344,32187480,32191508,32193762,32194379,32194856,32199000,32200825,32204008,32206335,32208639,32 ...32151291,32182626,32183300,32185447,32187553,32191652,32194004,32194501,32194996,32199091,32201018,32204324,32206580,32208835,32 ...
Ildr2NM_001164528chr1+16625413816631683216625437516631079510166254138,166269304,166270498,166291415,166294590,166295751,166303501,166307719,166308846,166310759,166254466,166269637,166270618,166291472,166294737,166295928,166303615,166307933,166309543,166316832,
Perm1NM_172417chr4+1562159261562213071562170001562202224156215926,156216716,156219740,156220109,156215975,156219185,156219866,156221307,
Ostm1NM_172416chr10+42678915427024624267898342700538642678915,42683159,42692910,42696249,42698107,42700482,42679397,42683274,42693008,42696417,42698273,42702462,
Arhgef10lNM_172415chr4-14051448414064875614051498914061694928140514484,140516745,140521164,140536768,140542633,140544238,140546999,140552527,140562713,140564186,140565131,140568338,14057025 ...140515531,140516868,140521339,140536917,140542788,140544462,140547086,140552649,140562814,140564314,140565247,140568520,14057040 ...
Zc2hc1cNM_172414chr12+85288590852993588528957085296674385288590,85289551,85296401,85288785,85290881,85299358,
Rap2cNM_172413chrX-51003913510180185101500451017898351003913,51014970,51017625,51006750,51015283,51018018,
Gpc2NM_172412chr5-13827365913827993713827430913827981410138273659,138275454,138275706,138275928,138276207,138276583,138277406,138278214,138278838,138279648,138274569,138275624,138275846,138276075,138276338,138276746,138277487,138278537,138278997,138279937,

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