Schema for refFlat
  Database: bosTau7    Primary Table: refFlat    Row Count: 15,132   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName CCDC51varchar(255) values Name of gene as it appears in genome browser.
name NM_001015619varchar(255) values Name of gene
chrom chr22varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 52378628int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 52387973int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 52378859int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 52381768int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 52378628,52380147,52381471,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 52379612,52380312,52381776,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      bosTau7.mrnaOrientInfo.name (via refFlat.name)
      bosTau7.refGene.name (via refFlat.name)
      bosTau7.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
CCDC51NM_001015619chr22-52378628523879735237885952381768552378628,52380147,52381471,52387489,52387740,52379612,52380312,52381776,52387568,52387973,
TYW3NM_001015620chr3-74138165741606487413842474160610674138165,74150312,74153168,74153458,74156397,74160436,74138641,74150446,74153240,74153557,74156478,74160648,
GABRPNM_001015618chr20-44197846862744356846314610441978,450720,451343,451956,455194,456923,457878,462304,463093,468510,443871,450908,451496,452094,455277,457141,457946,462423,463190,468627,
LOC517016NM_001015617chr8+24706373247070102470644924707010124706373,24707010,
RPUSD4NM_001015616chr29-30954953309643233095540930964319730954953,30956352,30957683,30957905,30962181,30963591,30964130,30955649,30956450,30957828,30957999,30962383,30963757,30964323,
POLINM_001024692chr24+553511145537492055351114553749201055351114,55352932,55356386,55360621,55362540,55363674,55364655,55367095,55372311,55374110,55351262,55353055,55356551,55360774,55362777,55363853,55364747,55367226,55372517,55374920,
CSRP3NM_001024689chr29+26759118267797972676958926779537626759118,26769561,26773933,26775822,26777876,26779460,26759147,26769701,26774102,26775955,26777970,26779797,
KCNJ12NM_001024690chr19+361331363616753536165823361670991136133136,36159598,36165763,36165946,36165951,36165955,36165961,36165968,36165974,36165997,36166002,36133206,36159717,36165946,36165951,36165955,36165961,36165968,36165974,36165997,36166002,36167535,
NLRP9NM_001024664chr18-62003147620280536200335562028053962003147,62004858,62005807,62008467,62010986,62012409,62017966,62023344,62027773,62003488,62005029,62005978,62008638,62011157,62012577,62018128,62024908,62028053,
MAGOHNM_001034245chr3+98772826987820889877292198781948598772826,98775915,98778329,98780675,98781848,98773009,98775974,98778440,98780758,98782088,

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