Schema for refGene
  Database: sarHar1    Primary Table: refGene    Row Count: 72   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 601smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_105676varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1_GL834484_randomvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 2121689int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 2121839int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 2121839int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 2121839int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 2121689,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 2121839,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MIR190varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via refGene.name)
      hgFixed.gbMiscDiff.acc (via refGene.name)
      hgFixed.gbSeq.acc (via refGene.name)
      hgFixed.gbWarn.acc (via refGene.name)
      hgFixed.imageClone.acc (via refGene.name)
      hgFixed.refLink.mrnaAcc (via refGene.name)
      hgFixed.refSeqStatus.mrnaAcc (via refGene.name)
      hgFixed.refSeqSummary.mrnaAcc (via refGene.name)
      knownGeneV39.kgXref.refseq (via refGene.name)
      knownGeneV39.knownToRefSeq.value (via refGene.name)
      sarHar1.all_mrna.qName (via refGene.name)
      sarHar1.mrnaOrientInfo.name (via refGene.name)
      sarHar1.refFlat.name (via refGene.name)
      sarHar1.refSeqAli.qName (via refGene.name)
      sarHar1.xenoMrna.qName (via refGene.name)
      sarHar1.xenoRefGene.name (via refGene.name)
      sarHar1.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
601NR_105676chr1_GL834484_random+212168921218392121839212183912121689,2121839,0MIR190unkunk-1,
592NR_105678chr1_GL834650_random+102444610245961024596102459611024446,1024596,0MIR138-1unkunk-1,
603NR_105677chr1_GL834637_random+248583424859442485944248594412485834,2485944,0MIR181A-2unkunk-1,
589NR_105680chr1_GL834685_random-6382106383606383606383601638210,638360,0MIR1329unkunk-1,
604NR_105679chr1_GL834659_random+257423925743892574389257438912574239,2574389,0MIR352unkunk-1,
590NR_105682chr1_GL834730_random+7410117411617411617411611741011,741161,0MIR340unkunk-1,
592NR_105683chr1_GL834734_random+100376310039131003913100391311003763,1003913,0MIR216Bunkunk-1,
599NR_105685chr1_GL834769_random+190949919096491909649190964911909499,1909649,0MIR140unkunk-1,
592NR_105684chr1_GL834734_random+101994110200911020091102009111019941,1020091,0MIR216Aunkunk-1,
585NR_105687chr1_GL835536_random+1203981205481205481205481120398,120548,0MIR202unkunk-1,

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