Schema for refFlat
  Database: papAnu2    Primary Table: refFlat    Row Count: 509   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName BTDCvarchar(255) values Name of gene as it appears in genome browser.
name NM_001141938varchar(255) values Name of gene
chrom JH685005varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 84822int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 87355int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 85001int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 85917int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 84822,85742,87294,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 85057,85929,87355,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      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)
      papAnu2.mrnaOrientInfo.name (via refFlat.name)
      papAnu2.refGene.name (via refFlat.name)
      papAnu2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
BTDCNM_001141938JH685005-84822873558500185917384822,85742,87294,85057,85929,87355,
LOC101007932NM_001279520JH684887+1468481498691468481498698146848,147050,147561,148702,149080,149642,149817,149865,146921,147320,147837,148978,149197,149675,149865,149869,
IL3NM_001168737chr6+1256482561256503061256482561256503065125648256,125648515,125649848,125650065,125650210,125648418,125648557,125649938,125650107,125650306,
POLR3KNM_001168812JH684983+85541929198554192919385541,88390,92791,85652,88478,92919,
ZNF669NM_001168811JH685102-31685358573168535857331685,31727,35294,31727,31981,35857,
RPL10NM_001168802chrX+1417476301417500261417476301417500266141747630,141748452,141748604,141748922,141749632,141749873,141747653,141748511,141748712,141749061,141749795,141750026,
FLNANM_001168801chrX+14170696014172947614170696014172947646141706960,141710140,141710492,141710686,141711463,141711674,141711842,141712088,141712825,141713052,141713348,141713586,14171397 ...141707333,141710389,141710590,141710834,141711582,141711752,141712005,141712289,141712963,141713176,141713485,141713780,14171408 ...
AMACRNM_001112633chr6-33758321337769793375833033776970533758321,33767886,33773697,33774860,33776723,33758740,33768073,33773858,33775004,33776979,
TRIM5NM_001112632chr14+59535439595523635953543959552363759535439,59536453,59537193,59549454,59551090,59551482,59551770,59535862,59536549,59537424,59549477,59551191,59551509,59552363,
IL2NM_001112654chr5-1131552651131599541131552651131599544113155265,113157217,113159657,113159807,113155376,113157364,113159717,113159954,

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