Schema for refFlat
  Database: ornAna2    Primary Table: refFlat    Row Count: 705   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ORNANAV1R3238varchar(255) values Name of gene as it appears in genome browser.
name NM_001253630varchar(255) values Name of gene
chrom chrUn_DS181027v1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 80782int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 81709int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 80782int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 81709int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 80782,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 81709,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)
      ornAna2.mrnaOrientInfo.name (via refFlat.name)
      ornAna2.refGene.name (via refFlat.name)
      ornAna2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
ORNANAV1R3238NM_001253630chrUn_DS181027v1+80782817098078281709180782,81709,
ORNANAV1R3237NM_001253629chrUn_DS181027v1+65280662106528066210165280,66210,
ORNANAV1R3235NM_001253627chrUn_DS181027v1-23124240542312424054123124,24054,
ORNANAV1R3234NM_001253626chrUn_DS181027v1+10157111141015711114110157,11114,
MIR142NR_034731chrUn_DS198477v1-136114711471147111361,1471,
MIR1421JNR_034730chrUn_DS197957v1-964697609760976019646,9760,
MIR1421HNR_034728chrUn_DS197957v1-687369636963696316873,6963,
MIR1421G-1NR_034727chrUn_DS197957v1-612862406240624016128,6240,
MIR1421FNR_034726chrUn_DS197957v1-501851075107510715018,5107,
MIR1421ENR_034725chrUn_DS197957v1-393540404040404013935,4040,

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