Schema for refFlat
  Database: danRer10    Primary Table: refFlat    Row Count: 16,812   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 si:dkey-172m14.1varchar(255) values Name of gene as it appears in genome browser.
name NM_001201438varchar(255) values Name of gene
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 48367664int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 48377467int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 48368511int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 48377302int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 48367664,48369875,48374698,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 48368844,48370132,48374795,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      danRer10.mrnaOrientInfo.name (via refFlat.name)
      danRer10.refGene.name (via refFlat.name)
      danRer10.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
si:dkey-172m14.1NM_001201438chr5-48367664483774674836851148377302848367664,48369875,48374698,48374966,48375105,48376265,48376846,48377040,48368844,48370132,48374795,48375104,48375115,48376326,48376888,48377467,
ap1g2NM_001289858chr2-383072503833017438307788383271892238307250,38309430,38310211,38310931,38311137,38312901,38313088,38316644,38316852,38317291,38319598,38319842,38321141,38321300,38 ...38307914,38309529,38310363,38311064,38311282,38313006,38313216,38316734,38316975,38317346,38319739,38319956,38321197,38321399,38 ...
cdc73NM_001291396chr2+121629441221956512162955122186551712162944,12173591,12176830,12176995,12177219,12177376,12181599,12185763,12186561,12188128,12200961,12206973,12207540,12209749,12 ...12163086,12173697,12176900,12177058,12177272,12177465,12181813,12185862,12186640,12188193,12201019,12207009,12207628,12209911,12 ...
fut8aNM_001361235chr17+337668723395397733862419339529281133766872,33815648,33862161,33912651,33918728,33922663,33934269,33943954,33947948,33949852,33952595,33766993,33815705,33862622,33912770,33918891,33922778,33934507,33944201,33948125,33950003,33953977,
anxa11aNM_183410chr13+161488971619560616157849161949371516148897,16157841,16163917,16169682,16171090,16175740,16177033,16180209,16180453,16182286,16182461,16190217,16192172,16194675,16 ...16148968,16158069,16163991,16169883,16171178,16175835,16177147,16180300,16180533,16182343,16182555,16190313,16192231,16194798,16 ...
ndufb2NM_200791chr4+22759172227619182275929222761454422759172,22761166,22761379,22761553,22759378,22761299,22761469,22761918,
sdr16c5bNM_214771chr7+58397304584160325839762958415620758397304,58397609,58399289,58401060,58401244,58410677,58415523,58397430,58397950,58399421,58401160,58401389,58410803,58416032,
lrataNM_001204131chr1+25005977250072072500599625006756225005977,25006603,25006521,25007207,
atp6v1hNM_001291708chr2+308032263086333930803876308630531430803226,30803853,30809243,30809589,30811157,30816282,30823759,30824829,30828057,30838287,30839901,30843741,30849328,30862986,30803292,30803980,30809343,30809679,30811271,30816387,30823813,30824927,30828250,30838466,30840027,30843843,30849442,30863339,
opn1mw3NM_182892chr6+41193921411958784119399641195605541193921,41194432,41194904,41195159,41195491,41194357,41194601,41195070,41195399,41195878,

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