Schema for refFlat
  Database: felCat9    Primary Table: refFlat    Row Count: 429   Data last updated: 2019-03-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName HGFvarchar(255) values Name of gene as it appears in genome browser.
name NM_001009830varchar(255) values Name of gene
chrom chrA2varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 87722764int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 87799554int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 87723934int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 87799478int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 18int(10) unsigned range Number of exons
exonStarts 87722764,87731712,87731978,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 87724111,87731858,87732085,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      felCat9.mrnaOrientInfo.name (via refFlat.name)
      felCat9.refGene.name (via refFlat.name)
      felCat9.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
HGFNM_001009830chrA2-877227648779955487723934877994781887722764,87731712,87731978,87732590,87733588,87736441,87737748,87743532,87746702,87755188,87757903,87774132,87775618,87781465,87 ...87724111,87731858,87732085,87732737,87733663,87736538,87737787,87743666,87746805,87755316,87758078,87774251,87775739,87781608,87 ...
LEPNM_001009850chrA2+1465713861465753971465714151465729962146571386,146572636,146571559,146575397,
LPAR6NM_001309049chrA1+22918805229203442291905722920092122918805,22920344,
LPLNM_001042567chrB1-380743383809846038074369380984301038074338,38076636,38078534,38079916,38082234,38083702,38084693,38086308,38090951,38098342,38074370,38076741,38078717,38080037,38082477,38083936,38084805,38086488,38091121,38098460,
EFNB2NM_001114344chrA1-77088366771301447708836677130144577088366,77090096,77090957,77107822,77130022,77088755,77090210,77091050,77108106,77130144,
LAMP1NM_001163655chrA1+82349957823670918234996482366275982349957,82355010,82356955,82357292,82363801,82364528,82365408,82365544,82366135,82350016,82355132,82357175,82357451,82363989,82364654,82365475,82365715,82367091,
FELCATV1R2NM_001167474chrA1+91725271917261749172527191726174191725271,91726174,
CSF2NM_001309037chrA1+1111903861111922901111903861111922904111190386,111190641,111191340,111192184,111190545,111190683,111191466,111192290,
CXCR4NM_001009826chrC1-1300887951300925961300893351300925272130088795,130092512,130090382,130092596,
GDF9NM_001165900chrA1-1119464941119495091119464941119495092111946494,111949115,111947457,111949509,

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