Schema for refFlat
  Database: dm3    Primary Table: refFlat    Row Count: 37,634   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 CG34404varchar(255) values Name of gene as it appears in genome browser.
name NM_169651varchar(255) values Name of gene
chrom chr3Rvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 11189507int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 11192544int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 11190165int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 11192520int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 11189507,11190356,11191128,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 11190298,11191067,11191430,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      dm3.flyBaseToRefSeq.value (via refFlat.name)
      dm3.mrnaOrientInfo.name (via refFlat.name)
      dm3.refGene.name (via refFlat.name)
      dm3.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
CG34404NM_169651chr3R-11189507111925441119016511192520711189507,11190356,11191128,11191492,11191681,11192068,11192385,11190298,11191067,11191430,11191626,11192011,11192318,11192544,
Nuak1NM_001382105chr3R+6110311612862061169686128021136110311,6116821,6117294,6117558,6117837,6118915,6122455,6123161,6123490,6123967,6124170,6125355,6127665,6110434,6117174,6117494,6117776,6118435,6120040,6122831,6123419,6123619,6124097,6124313,6125474,6128620,
Nuak1NM_001382100chr3R+6110311613418961169686133199146110311,6116821,6117294,6117558,6117837,6118915,6122455,6123161,6123490,6123967,6124170,6125355,6129031,6133144,6110434,6117174,6117494,6117776,6118435,6120040,6122831,6123419,6123619,6124097,6124313,6125474,6133088,6134189,
CG46459NM_001382164chr3R+652236865246986522453652359126522368,6523347,6522524,6524698,
CG12224NM_141882chr3R-780642578077847806515780774337806425,7806733,7807327,7806576,7807272,7807784,
svpNM_001382014chr3R+810687381285078107316812757258106873,8115930,8119729,8126200,8126606,8107971,8116080,8120281,8126358,8128507,
CG46427NM_001382142chr3R-826353882641248263834826409218263538,8264124,
CG46427NM_001382141chr3R-826353882648618263834826409218263538,8264861,
CG11670NM_001382016chr3R+886777188698088867813886972858867771,8868606,8868972,8869443,8869642,8868365,8868716,8869390,8869573,8869808,
Tm1NM_001382175chr3R+111039411113450111110370111338291011103941,11110334,11110950,11120834,11121148,11125831,11126468,11127345,11128874,11133752,11104282,11110484,11111076,11120968,11121266,11125902,11126544,11127408,11128944,11134501,

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