Schema for xenoRefGene
  Database: cb1    Primary Table: xenoRefGene    Row Count: 234,068   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1093smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001268182varchar(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 66618603int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 66618985int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 66618603int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 66618985int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 66618603,66618913,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 66618651,66618985,longblob   Exon end positions (or start positions for minus strand item)
id 5150592int(10) unsigned range  
name2 elo-8varchar(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 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
        cb1.all_est.qName (via xenoRefGene.name)
      cb1.all_mrna.qName (via xenoRefGene.name)
      cb1.xenoRefFlat.name (via xenoRefGene.name)
      cb1.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
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsidname2cdsStartStatcdsEndStatexonFrames
1093NM_001268182chrUn+66618603666189856661860366618985266618603,66618913,66618651,66618985,5150592elo-8cmplcmpl0,0,
1156NM_001010972chrUn-74843440748435757484344074843575174843440,74843575,5131058ZYXincmplincmpl0,
1140NM_001011071chrUn-72853897728544277285389772854427372853897,72854203,72854390,72854113,72854343,72854427,5131059wdr83incmplincmpl0,1,0,
909NM_001010969chrUn-42475380424763024247538042476302242475380,42476179,42475428,42476302,5131060CYP4A22incmplincmpl0,0,
765NM_001009967chrUn-23649115236502632364911523650263623649115,23649456,23649636,23649840,23649945,23650140,23649193,23649510,23649795,23649900,23650095,23650263,5131061Pip5k1cincmplincmpl0,0,0,0,0,0,
1131NM_001009964chrUn-71674448716745657167444871674565171674448,71674565,5131062Tbx5incmplincmpl0,
1139NM_001009964chrUn+72628635726319777262863572631977372628635,72630790,72631932,72628821,72630835,72631977,5131063Tbx5incmplincmpl0,0,0,
717NM_001039599chrUn+17364311173646601736431117364660317364311,17364426,17364634,17364363,17364439,17364660,5123335COLEC12incmplincmpl2,0,1,
813NM_001193549chrUn-29931907299320182993190729932018129931907,29932018,5121362MYL6incmplincmpl0,
1157NM_016997chrUn+74992177749924057499217774992405274992177,74992348,74992309,74992405,5121359Celincmplincmpl0,0,

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