Schema for xenoRefGene
  Database: tupBel1    Primary Table: xenoRefGene    Row Count: 845,862   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001301275varchar(255) Name of gene (usually transcript_id from GTF)
chrom scaffold_106709.1-20747varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 8018int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 15626int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 8018int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 8820int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned Number of exons
exonStarts 8018,8804,15497,longblob Exon start positions (or end positions for minus strand item)
exonEnds 8636,8820,15626,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 ZNF169varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,2,-1,longblob Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via
      hgFixed.gbMiscDiff.acc (via
      hgFixed.gbSeq.acc (via
      hgFixed.gbWarn.acc (via
      hgFixed.imageClone.acc (via
      tupBel1.all_est.qName (via
      tupBel1.all_mrna.qName (via (via
      tupBel1.xenoRefSeqAli.qName (via

Sample Rows

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

Other RefSeq (xenoRefGene) Track Description


This track shows known protein-coding and non-protein-coding genes for organisms other than human, 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.


The RNAs were aligned against the human 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.


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


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