Schema for refGene
  Database: gorGor5    Primary Table: refGene    Row Count: 468   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 727smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_106297varchar(255) values Name of gene (usually transcript_id from GTF)
chrom CYUI01014942v1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 18653296int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 18653408int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 18653408int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 18653408int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 18653296,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 18653408,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MIR29Cvarchar(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
        gorGor5.all_mrna.qName (via refGene.name)
      gorGor5.mrnaOrientInfo.name (via refGene.name)
      gorGor5.refFlat.name (via refGene.name)
      gorGor5.refSeqAli.qName (via refGene.name)
      gorGor5.xenoRefGene.name (via refGene.name)
      gorGor5.xenoRefSeqAli.qName (via refGene.name)
      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)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
727NR_106297CYUI01014942v1+18653296186534081865340818653408118653296,18653408,0MIR29Cunkunk-1,
714NR_106307CYUI01014949v1+16923262169233731692337316923373116923262,16923373,0MIR127unkunk-1,
714NR_106330CYUI01014949v1+16924775169248851692488516924885116924775,16924885,0MIR432unkunk-1,
602NM_001279589CYUI01015387v1+225196422541032251964225410312251964,2254103,0TICAM1cmplcmpl0,
646NM_001279587CYUI01015028v1-803898180409788038981804097838038981,8040650,8040877,8039073,8040757,8040978,0NDUFA2cmplcmpl1,2,0,
599NM_001279682CYUI01000036v1+1863601187300618636051872986111863601,1864187,1866061,1866475,1869013,1869376,1871036,1871402,1871751,1872304,1872806,1864098,1864302,1866192,1866681,1869211,1869505,1871225,1871576,1871911,1872441,1873006,0TAP2cmplcmpl0,1,2,1,0,0,0,0,0,1,0,
589NM_001279679CYUI01015337v1-5802905828665802905828661580290,582866,0TLR5cmplcmpl0,
91NM_001279676CYUI01000001v1-192174281930814019217428193081403519217428,19218364,19219301,19221351,19225093,19226428,19228001,19228755,19231108,19237099,19245517,19247133,19256090,19257337,19 ...19217479,19218532,19219490,19221417,19225208,19226481,19228076,19228884,19231204,19237327,19245709,19247220,19256178,19257471,19 ...0AOX1cmplcmpl0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0,
715NR_106408CYUI01014949v1+17069448170695591706955917069559117069448,17069559,0MIR380unkunk-1,
674NR_106378CYUI01014918v1+11756682117567921175679211756792111756682,11756792,0MIR577unkunk-1,

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