Schema for xenoRefGene
  Database: bisBis1    Primary Table: xenoRefGene    Row Count: 468,599   Data last updated: 2017-03-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_203643varchar(255) values Name of gene (usually transcript_id from GTF)
chrom JPYT01225855v1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 97int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1503int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 97int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1503int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 97,441,605,930,1344,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 244,518,762,1008,1503,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 best2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,1,0,0,0,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
        bisBis1.refGene.name (via xenoRefGene.name)
      bisBis1.refSeqAli.qName (via xenoRefGene.name)
      bisBis1.xenoRefFlat.name (via xenoRefGene.name)
      bisBis1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NM_203643JPYT01225855v1-971503971503597,441,605,930,1344,244,518,762,1008,1503,0best2incmplincmpl0,1,0,0,0,
603NR_129597KN265079v1-239942623995112399511239951112399426,2399511,0MIR148Aunkunk-1,
585NM_211348JPYT01113763v1+0222022210,222,0AGOS_AFR446Wincmplincmpl0,
585NM_001177562JPYT01231142v1-1565005005002156,436,198,500,0PPP2R1Bunkunk-1,-1,
657NM_001177562KN265046v1+949581294969749496974949697479495812,9495997,9496031,9496322,9496485,9496617,9496920,9495973,9496021,9496244,9496340,9496591,9496678,9496974,0PPP2R1Bunkunk-1,-1,-1,-1,-1,-1,-1,
585NM_001253862JPYT01114467v1+635435435446,99,193,234,31,159,223,354,0Tcf12unkunk-1,-1,-1,-1,
585NM_001253863JPYT01114467v1+635435435446,99,193,234,31,159,223,354,0Tcf12unkunk-1,-1,-1,-1,
585NM_001253864JPYT01114467v1+635435435446,99,193,234,31,159,223,354,0Tcf12unkunk-1,-1,-1,-1,
585NM_001253865JPYT01114467v1+635435435446,99,193,234,31,159,223,354,0Tcf12unkunk-1,-1,-1,-1,
585NM_011544JPYT01114467v1+635435435446,99,193,234,31,159,223,354,0Tcf12unkunk-1,-1,-1,-1,

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