Schema for xenoRefGene
  Database: caePb2    Primary Table: xenoRefGene    Row Count: 276,832   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1463smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001131583varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrUnvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 115131813int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 115132328int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 115131813int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 115132328int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 115131813,115132028,115132205,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 115131864,115132160,115132328,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 RPS15varchar(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 cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        caePb2.all_est.qName (via xenoRefGene.name)
      caePb2.all_mrna.qName (via xenoRefGene.name)
      caePb2.xenoMrna.qName (via xenoRefGene.name)
      caePb2.xenoRefFlat.name (via xenoRefGene.name)
      caePb2.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
1463NM_001131583chrUn+1151318131151323281151318131151323283115131813,115132028,115132205,115131864,115132160,115132328,0RPS15incmplcmpl0,0,0,
1202NM_001131582chrUn-80943101809464598094310180946459380943101,80946201,80946426,80943221,80946297,80946459,0EXOC6Bincmplincmpl0,0,0,
2051NM_001131581chrUn+1922466731922468981922468981922468982192246673,192246815,192246775,192246898,0TIMM10Bunkunk-1,-1,
2051NM_001131581chrUn+1922489851922490791922490791922490791192248985,192249079,0TIMM10Bunkunk-1,
637NM_001131577chrUn-684309768435216843097684352126843097,6843437,6843214,6843521,0CYB5Bincmplincmpl0,0,
939NM_001131576chrUn+46416045464182644641604546418264646416045,46416250,46416802,46417303,46417594,46418114,46416195,46416583,46417264,46417474,46417612,46418264,0EHD3cmplincmpl0,0,0,0,0,0,
1468NM_012016chrUn+1158251701158268101158251701158268104115825170,115825263,115825407,115826645,115825233,115825296,115825536,115826810,0Ern2incmplincmpl0,0,0,0,
594NM_076003chrUn-1212199121452812121991214528101212199,1212486,1212642,1212937,1213113,1213360,1213609,1213772,1214048,1214436,1212421,1212592,1212893,1213066,1213305,1213555,1213724,1213963,1214363,1214528,0gap-1incmplincmpl2,2,0,0,0,0,2,0,0,1,
870NM_001374500chrUn-37376002373766663737600237376179437376002,37376324,37376465,37376591,37376188,37376393,37376558,37376666,0HSD17B4cmplincmpl0,-1,-1,-1,
1109NM_001374500chrUn+68752936687535956875293668753595368752936,68753254,68753463,68753077,68753416,68753595,0HSD17B4incmplincmpl0,0,0,

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