Schema for refFlat
  Database: allMis1    Primary Table: refFlat    Row Count: 54   Data last updated: 2020-08-17
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName LDHAvarchar(255) values Name of gene as it appears in genome browser.
name NM_001287263varchar(255) values Name of gene
chrom JH733035varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 740011int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 750087int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 740665int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 746382int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 740011,741370,742234,743275...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 740830,741494,742352,743449...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      allMis1.mrnaOrientInfo.name (via refFlat.name)
      allMis1.refGene.name (via refFlat.name)
      allMis1.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
LDHANM_001287263JH733035-7400117500877406657463828740011,741370,742234,743275,744006,745238,746256,750032,740830,741494,742352,743449,744180,745356,746391,750087,
LOC102563425NM_001371821JH735358-4336994473584341184470499433699,434899,435918,436771,438522,439657,442067,443306,446965,434253,435049,436032,436881,438676,439891,442274,443546,447358,
PSMC5NM_001293067JH731936-86956388037386965388021112869563,871051,871513,871940,872365,873268,874644,875111,876092,876669,878480,880172,869707,871138,871624,872039,872556,873395,874875,875168,876190,876739,878552,880373,
ESR2NM_001287264JH732368+42616494884261649488242616,49311,43050,49488,
ESR2NM_001287264JH733894-1988842333391988842333397198884,201722,206479,209138,218876,228395,233160,199056,201897,206613,209277,219176,228512,233339,
OTCNM_001287307JH733961-54851349955485556535485,134887,134953,5565,134942,134995,
OTCNM_001287307JH736875-2849352853452849352851121284935,285345,
OTCNM_001287307JH738800+46996353640548739053603111469963,487390,488125,496275,506769,527899,530779,530914,532212,535971,536389,470012,487533,488207,496363,506923,528022,530833,531064,532350,536380,536405,
FSTNM_001287297JH733803-8345198403358350328402066834519,835828,836988,837573,838124,840124,835115,836059,837213,837792,838316,840335,
TRAP1NM_001287295JH738167+118896621611955655341811889,20446,22607,24071,42828,43695,46533,53368,53986,56822,57100,59145,59740,60654,63102,64220,64770,65432,12046,20614,22690,24212,42900,43856,46643,53442,54142,56943,57170,59293,59926,60793,63188,64366,64843,66216,

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