Schema for refFlat
  Database: calJac4    Primary Table: refFlat    Row Count: 237   Data last updated: 2020-09-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName CD274varchar(255) values Name of gene as it appears in genome browser.
name NM_001267747varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 110217345int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 110229640int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 110217356int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 110229604int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 110217345,110218319,1102245...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 110217408,110218661,1102247...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      calJac4.mrnaOrientInfo.name (via refFlat.name)
      calJac4.refGene.name (via refFlat.name)
      calJac4.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
CD274NM_001267747chr1+1102173451102296401102173561102296046110217345,110218319,110224511,110227154,110228424,110229581,110217408,110218661,110224799,110227262,110228484,110229640,
PALM2AKAP2NM_001205006chr1+1563010621566151571563011161566136548156301062,156462005,156539496,156552840,156594668,156596008,156602446,156612914,156301121,156462051,156539577,156552971,156594783,156596030,156602548,156615157,
PALM2AKAP2NM_001371508chr1+15630106215682866015630111615682467412156301062,156462005,156539496,156552840,156594668,156596008,156602446,156675505,156792788,156812068,156818036,156824575,156301121,156462051,156539577,156552971,156594783,156596030,156602548,156675591,156795204,156812247,156818075,156828660,
PALM2AKAP2NM_001204128chr1+1567043191568286601567044201568246745156704319,156792788,156812068,156818036,156824575,156704555,156795204,156812247,156818075,156828660,
PALM2AKAP2NM_001371507chr1+1567044181568286571567044201568246744156704418,156792788,156812068,156824575,156704555,156795204,156812247,156828657,
DNAJC25NM_001204974chr1+1582477751582666581582478301582655414158247775,158260914,158263198,158265418,158248166,158261067,158263669,158266658,
GNG10NM_001204975chr1+1582754471582832531582755081582800003158275447,158279874,158282277,158275589,158280006,158283253,
GGTA1NM_001267732chr1-1681355861681563471681365951681563386168135586,168141097,168148841,168149983,168152036,168156258,168137289,168141235,168148958,168150049,168152072,168156347,
CYP2D19NM_001204438chr1+1878949511878991471878949991878990749187894951,187895838,187896537,187896778,187897397,187897728,187898083,187898656,187898895,187895179,187896010,187896690,187896939,187897574,187897870,187898271,187898798,187899147,
SELENOMNM_001199931chr1-1998884491998911921998886411998911315199888449,199888879,199889312,199889562,199891005,199888800,199888958,199889347,199889598,199891192,

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