Schema for xenoRefGene
  Database: gorGor3    Primary Table: xenoRefGene    Row Count: 554,749   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 1769smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_146017varchar(255) Name of gene (usually transcript_id from GTF)
chrom chr5varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 155273365int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 155293398int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 155273369int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 155292792int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned Number of exons
exonStarts 155273365,155273881,1552790...longblob Exon start positions (or end positions for minus strand item)
exonEnds 155273416,155274004,1552790...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 Gabrpvarchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,2,1,1,0,-1,-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
        gorGor3.all_mrna.qName (via xenoRefGene.name)
      gorGor3.xenoMrna.qName (via xenoRefGene.name)
      gorGor3.xenoRefFlat.name (via xenoRefGene.name)
      gorGor3.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
1769NM_146017chr5+15527336515529339815527336915529279214155273365,155273881,155279006,155279974,155282227,155286234,155289117,155290088,155292489,155292943,155293047,155293220,15529326 ...155273416,155274004,155279072,155280187,155282315,155286371,155289270,155290276,155292805,155293003,155293101,155293258,15529329 ...0Gabrpcmplcmpl0,0,0,0,0,2,1,1,0,-1,-1,-1,-1,-1,
101NR_024616chr20-29388644296144172961441729614417229388644,29614378,29388786,29614417,0INE1unkunk-1,-1,
14NM_001320185chr1+46800393472113934721139347211393346800393,47182527,47211368,46800495,47182555,47211393,0ZNF326unkunk-1,-1,-1,
13NM_001320185chr5+34591589352901753529017535290175434591589,34843076,35005937,35290145,34591610,34843102,35005967,35290175,0ZNF326unkunk-1,-1,-1,-1,
201NM_001320185chr1-1344880921347558981347539391347558983134488092,134753939,134755883,134488137,134754005,134755898,0ZNF326incmplincmpl-1,1,0,
585NR_033534CABD02413273+165724402440244021657,1867,1837,2440,0Olfr1300-ps1unkunk-1,-1,
1327NM_146620chr3+97328678973292249732867897329224397328678,97329039,97329146,97328747,97329060,97329224,0Olfr292incmplincmpl0,1,0,
204NM_146618chr1-1374227501375481371374227501375481374137422750,137422912,137448243,137548086,137422828,137422951,137448279,137548137,0Olfr297incmplincmpl0,0,0,0,
291NM_146618chr1+2287902662290451422287902662290451423228790266,229017918,229045079,228790311,229017981,229045142,0Olfr297incmplincmpl1,0,0,
120NM_002816chr20-49706889498705134987051349870513349706889,49866306,49870491,49706918,49866359,49870513,0PSMD12unkunk-1,-1,-1,

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