Schema for xenoRefGene
  Database: otoGar3    Primary Table: xenoRefGene    Row Count: 530,019   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 635smallint(5) unsigned Indexing field to speed chromosome range queries.
name NR_110723varchar(255) Name of gene (usually transcript_id from GTF)
chrom GL873619varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 6603140int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 6603360int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 6603360int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 6603360int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned Number of exons
exonStarts 6603140,6603240,longblob Exon start positions (or end positions for minus strand item)
exonEnds 6603224,6603360,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 ZNF793-AS1varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-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 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)
      otoGar3.all_mrna.qName (via xenoRefGene.name)
      otoGar3.xenoMrna.qName (via xenoRefGene.name)
      otoGar3.xenoRefFlat.name (via xenoRefGene.name)
      otoGar3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
635NR_110723GL873619-660314066033606603360660336026603140,6603240,6603224,6603360,0ZNF793-AS1unkunk-1,-1,
585NM_001304513GL873856+51948523995195252314251948,52308,52282,52399,0HSD17B7cmplcmpl0,0,
595NM_001105344GL873666+139865014119661398650141126551398650,1409090,1411226,1411883,1411930,1398766,1409173,1411265,1411905,1411966,0CD8Bincmplincmpl0,2,1,-1,-1,
622NM_001095344GL873543-488506749157164885073491571644885067,4898162,4914155,4915635,4885187,4898264,4914260,4915716,0pigf.Sincmplcmpl0,0,0,0,
618NM_001095344GL873562+434744543480454347445434803924347445,4347841,4347526,4348045,0pigf.Sincmplcmpl0,0,
597NM_000791GL873744+166650916667781666778166677821666509,1666733,1666560,1666778,0DHFRunkunk-1,-1,
713NM_000791GL873537+16787328167874211678742116787421116787328,16787421,0DHFRunkunk-1,
105NM_000791GL873529+34071346341028413407134634071373334071346,34094781,34102787,34071373,34094796,34102841,0DHFRincmplincmpl0,-1,-1,
124NM_001354630GL873521+537225915377854853722773537785091753722591,53724625,53728393,53733730,53736167,53737863,53739846,53742294,53744932,53747147,53753801,53756530,53769161,53770819,53 ...53722889,53724715,53728493,53733804,53736240,53737958,53739947,53742407,53745026,53747301,53754175,53756678,53769271,53770883,53 ...0MLH1cmplcmpl0,2,2,0,2,0,0,2,1,2,0,2,0,2,0,0,0,
626NM_001282308GL873652-5423028543022354251015429260195423028,5423740,5424302,5424460,5424664,5424714,5424940,5424998,5425026,5425073,5425494,5426526,5426988,5427363,5427668,5427940, ...5423223,5423797,5424323,5424616,5424685,5424755,5424972,5425009,5425063,5425141,5425631,5426598,5427102,5427510,5427854,5428098, ...0STK25cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,2,0,0,0,0,0,1,0,0,-1,

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