Schema for Other RefSeq - Non-S. cerevisiae RefSeq Genes
  Database: sacCer3    Primary Table: xenoRefGene    Row Count: 31,843   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_052819varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrVIIvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 158898int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 158985int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 158985int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 158985int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 158898,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 158985,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 F54F12.3varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      sacCer3.all_est.qName (via xenoRefGene.name)
      sacCer3.all_mrna.qName (via xenoRefGene.name)
      sacCer3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
586NR_052819chrVII-1588981589851589851589851158898,158985,0F54F12.3unkunk-1,
73NM_001086217chrXIV-5063536195535063536195532506353,619361,506569,619553,0dnaja2.Lincmplincmpl0,0,
589NM_001086214chrXV+5451035463065451035463062545103,545334,545280,546306,0psmc3.Sincmplincmpl0,0,
587NM_001086211chrII-2908122916312908122916314290812,291028,291340,291523,290998,291202,291493,291631,0ola1.Lincmplincmpl0,0,0,0,
591NM_001155440chrXVI+9115669117919115669117911911566,911791,0LOC100282532incmplincmpl0,
587NM_001155439chrVII-2817112835952817112835954281711,282365,282968,283544,281930,282863,283511,283595,0LOC100282531incmplincmpl0,0,0,0,
585NM_001185145chrVI-53259543785325954378153259,54378,0Arp1incmplcmpl0,
585NM_001185146chrVI-53259543785325954378153259,54378,0Arp1incmplcmpl0,
590NM_001324843chrXIII+7022997030407022997030405702299,702422,702638,702761,702842,702344,702575,702725,702824,703040,0LOC107764380incmplincmpl0,0,0,0,0,
591NM_001183691chrXV+8328128341958328128341951832812,834195,0YTM1cmplcmpl0,

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

Other RefSeq (xenoRefGene) Track Description
 

Description

This track shows known protein-coding and non-protein-coding genes for organisms other than S. cerevisiae, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark).

The item labels and display colors of features within this track can be configured through the controls at the top of the track description page.

  • Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely.
  • Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.
  • Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box.

Methods

The RNAs were aligned against the S. cerevisiae genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept.

Credits

This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518

Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979