Schema for refFlat
  Database: danRer11    Primary Table: refFlat    Row Count: 18,968   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 stab2varchar(255) values Name of gene as it appears in genome browser.
name NM_001290178varchar(255) values Name of gene
chrom chr4_KZ115088v1_altvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 52914int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 98686int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 53013int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 98360int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 69int(10) unsigned range Number of exons
exonStarts 52914,53711,54407,61874,620...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 53094,53839,54514,61960,621...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer11.mrnaOrientInfo.name (via refFlat.name)
      danRer11.refGene.name (via refFlat.name)
      danRer11.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
stab2NM_001290178chr4_KZ115088v1_alt+529149868653013983606952914,53711,54407,61874,62058,62206,62388,64371,64644,64865,66700,67253,67581,67814,69130,69343,69478,69980,71405,71635,71840,72 ...53094,53839,54514,61960,62125,62302,62511,64568,64775,64999,66783,67397,67725,67877,69247,69397,69559,70133,71465,71731,71927,72 ...
syngap1bNM_001326467chr16+454560654568908345456383456866962145456065,45506663,45523843,45590019,45603496,45614012,45617181,45625035,45627048,45628775,45628993,45630197,45633443,45635848,45 ...45456405,45506800,45523949,45590396,45603618,45614166,45617280,45625275,45627384,45628920,45629138,45630434,45633645,45636087,45 ...
epycNM_001348483chr4-16320162163339411632083416330368716320162,16321184,16322184,16322831,16325754,16330188,16333739,16321005,16321280,16322387,16322990,16325911,16330375,16333941,
aph1bNM_200115chr7_KZ115231v1_alt+61807715136203770589661807,63592,66848,66998,67197,70421,62150,63763,66922,67121,67325,71513,
gipc2NM_200930chr2+956071095908499560929959025279560710,9580542,9583065,9587500,9588244,9590100,9590538,9561196,9580728,9583246,9587619,9588326,9590520,9590849,
cul4aNM_201027chr1+15779216864715803316740121157792,160185,160728,161005,161168,161342,161868,162055,162301,162506,162727,163098,164115,164437,165168,165394,166917,167306,16 ...158136,160301,160832,161075,161242,161505,161958,162138,162369,162625,162920,163203,164226,164523,165276,165508,167023,167479,16 ...
arl4dNM_199644chr12+27243058272457602724452327245126227243058,27244399,27243301,27245760,
arl4dNM_199644chr12_KZ115384v1_alt+1469241496271483881489912146924,148264,147167,149627,
rnf13NM_201044chr22+351319053517517035139405351744811035131905,35139382,35139609,35150189,35160280,35162543,35162787,35165099,35171872,35174128,35132029,35139519,35139690,35150315,35160368,35162634,35162893,35165193,35171953,35175170,
nonoNM_201579chr5-225936232260278022594160226008811022593623,22594337,22595414,22595946,22596930,22598444,22598635,22600452,22600733,22602693,22594253,22594417,22595445,22596131,22597127,22598540,22598937,22600646,22600881,22602780,

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