Schema for refFlat
  Database: danRer5    Primary Table: refFlat    Row Count: 17,742   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 kdrvarchar(255) values Name of gene as it appears in genome browser.
name NM_001024653varchar(255) values Name of gene
chrom chr20varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 20724778int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 20781327int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 20725849int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 20781099int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 32int(10) unsigned range Number of exons
exonStarts 20724778,20725463,20725701,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 20725451,20725687,20726066,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer5.mrnaOrientInfo.name (via refFlat.name)
      danRer5.refGene.name (via refFlat.name)
      danRer5.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
kdrNM_001024653chr20-207247782078132720725849207810993220724778,20725463,20725701,20726152,20728594,20728812,20730017,20730242,20731056,20731260,20731789,20733158,20733602,20735201,20 ...20725451,20725687,20726066,20726238,20728679,20728955,20730123,20730342,20731168,20731383,20731881,20733324,20733691,20735315,20 ...
cnn3bNM_001024073chr2+10685145107120201068538710711315710685145,10705994,10706960,10707158,10707407,10707894,10710967,10685444,10706116,10707027,10707296,10707524,10708041,10712020,
capn2bNM_001018227chr22+240607512408212124060823240818302124060751,24061562,24063553,24065863,24067973,24068354,24068507,24071483,24071667,24072935,24073224,24075489,24075792,24076984,24 ...24061060,24061632,24063672,24065997,24068142,24068438,24068593,24071552,24071828,24073099,24073236,24075701,24075829,24077050,24 ...
sfxn5aNM_001243309chr13+183484481840964318348513184092611418348448,18354996,18355141,18358595,18358871,18359516,18359638,18361490,18363199,18369186,18383241,18383432,18394444,18409183,18348570,18355065,18355219,18358622,18358926,18359542,18359692,18361547,18363265,18369277,18383357,18383518,18394562,18409643,
rcor1NM_001080041chr17+326022053262114232602327326197831232602205,32602581,32603291,32604625,32608354,32615827,32616128,32616468,32617434,32618524,32618704,32619741,32602484,32602641,32603372,32604678,32608516,32615946,32616204,32616519,32617638,32618584,32618940,32621142,
slc6a11aNM_001098387chr6+274816342749951127481713274984331527481634,27482524,27484547,27486861,27487110,27487377,27487623,27487935,27491268,27492437,27493902,27494099,27496133,27498316,27 ...27481882,27482659,27484688,27486949,27487243,27487512,27487727,27488060,27491381,27492575,27494005,27494200,27496304,27498939,27 ...
si:dkey-33c12.3NM_001201557chr13-10951829109569441095345210956804310951829,10953669,10955823,10953513,10953794,10956944,
ate1NM_001089468Zv7_NA1016+15261882821526188282515261,28822,54798,76509,88181,15475,28951,54831,76691,88282,
thumpd3NM_001089394chr6+468210144685003846821271468405571146821014,46821253,46822946,46823452,46827166,46828841,46829342,46832094,46834806,46840362,46849951,46821041,46821433,46823024,46823905,46827297,46828911,46829458,46832199,46834930,46840610,46850038,
stxbp5aNM_001099981chr20+354925243567821835492524356782182735492524,35499694,35565397,35571112,35590342,35606101,35611132,35620733,35623671,35627911,35629777,35629950,35632418,35632922,35 ...35492662,35499792,35565479,35571213,35590477,35606165,35611216,35620857,35623750,35628066,35629850,35630098,35632486,35632963,35 ...

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