Schema for refFlat
  Database: dm2    Primary Table: refFlat    Row Count: 35,517   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 glob1varchar(255) values Name of gene as it appears in genome browser.
name NM_001300414varchar(255) values Name of gene
chrom chr3Rvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 11722647int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 11730365int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 11723004int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 11723655int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 11722647,11723269,11723496,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 11723145,11723431,11723737,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      dm2.flyBaseToRefSeq.value (via refFlat.name)
      dm2.mrnaOrientInfo.name (via refFlat.name)
      dm2.refGene.name (via refFlat.name)
      dm2.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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
glob1NM_001300414chr3R-11722647117303651172300411723655411722647,11723269,11723496,11730223,11723145,11723431,11723737,11730365,
glob1NM_169679chr3R-11722647117303651172300411723655411722647,11723269,11723496,11730223,11723145,11723431,11723737,11730365,
glob1NM_001170154chr3R-11722652117303651172345111723655311722652,11723269,11730223,11723145,11723737,11730365,
PdfrNM_130651chrX+241025824331672429156243260992410258,2429129,2429655,2430627,2431018,2431347,2431710,2432049,2432272,2410573,2429586,2429766,2430779,2431276,2431644,2431974,2432210,2433167,
tempNM_130636chrX-211636221186712116849211819232116362,2117621,2118106,2117571,2118010,2118671,
rushNM_130567chrX+133537213382411336059133701021335372,1337828,1337041,1338241,
CG13362NM_130498chrX-6060616081226066466079903606061,607593,607972,607535,607655,608122,
NleNM_057946chr2L-5663655681215664255680644566365,566497,566679,567088,566438,566624,567030,568121,
dbeNM_057892chr2L-8686728698578687388697761868672,869857,
PhmNM_057877chr2R-19492774194960551949312619495902819492774,19493362,19493759,19493861,19494936,19495066,19495217,19495713,19493295,19493701,19493808,19493994,19495009,19495154,19495275,19496055,

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