Schema for xenoRefGene
  Database: rheMac3    Primary Table: xenoRefGene    Row Count: 338,858   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1327smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001370204varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 97266075int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 97324626int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 97274357int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 97312198int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 16int(10) unsigned range Number of exons
exonStarts 97266075,97266399,97267108,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 97266317,97266788,97267289,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 SLC9B2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,-1,-1,0,1,0,0,1,2,...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)
      rheMac3.all_est.qName (via xenoRefGene.name)
      rheMac3.all_mrna.qName (via xenoRefGene.name)
      rheMac3.refGene.name (via xenoRefGene.name)
      rheMac3.refSeqAli.qName (via xenoRefGene.name)
      rheMac3.xenoMrna.qName (via xenoRefGene.name)
      rheMac3.xenoRefFlat.name (via xenoRefGene.name)
      rheMac3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1327NM_001370204chr5-972660759732462697274357973121981697266075,97266399,97267108,97267313,97268186,97274353,97276588,97279639,97290008,97291599,97293699,97295227,97296560,97310963,97 ...97266317,97266788,97267289,97268031,97268295,97274579,97276725,97279748,97290158,97291706,97293875,97295355,97296703,97311144,97 ...0SLC9B2cmplcmpl-1,-1,-1,-1,-1,0,1,0,0,1,2,0,1,0,0,-1,
16NM_001044327chr19+63586042639898616358604263989861763586042,63586306,63779309,63816206,63934543,63989619,63989723,63586102,63586348,63779358,63816289,63934585,63989630,63989861,0zgc:101130incmplincmpl0,0,0,1,0,1,0,
716NM_001294259chr19+17260476172688681726047617265240717260476,17261706,17265129,17265388,17265482,17265817,17268770,17260528,17261768,17265240,17265452,17265494,17265894,17268868,0Dda1incmplcmpl0,1,0,-1,-1,-1,-1,
1408NM_001294259chr7-1079681501079689701079687431079689673107968150,107968569,107968743,107968240,107968631,107968970,0Dda1cmplincmpl-1,-1,0,
716NM_001294258chr19+17260161172688681726016117265240717260161,17260476,17265129,17265388,17265482,17265817,17268770,17260242,17260527,17265240,17265452,17265494,17265894,17268868,0Dda1incmplincmpl0,0,1,-1,-1,-1,-1,
1408NM_001294258chr7-1079681501079690471079687431079690475107968150,107968569,107968743,107968913,107968978,107968240,107968631,107968851,107968976,107969047,0Dda1cmplincmpl-1,-1,1,0,0,
125NM_001294255chr11+55300488554636315530056455300696455300488,55300561,55463052,55463607,55300530,55300696,55463073,55463631,0ZNF736cmplincmpl-1,0,-1,-1,
1214NM_200318chr9-82486483824870868248648382487086182486483,82487086,0arl4abcmplcmpl0,
1232NM_001275144chr9+84836603848704328483660384870432784836603,84836967,84837579,84866311,84868602,84870240,84870336,84836838,84836972,84837720,84866444,84868874,84870321,84870432,0Papssincmplincmpl0,1,0,0,1,0,0,
585NR_003292chrUn_JH290932-1220661244111244111244114122066,122386,122537,124257,122377,122504,123707,124411,0Zxdaunkunk-1,-1,-1,-1,

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