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  Schema for RefSeq Genes - RefSeq Genes
  Database: bosTau4    Primary Table: refGene    Row Count: 10,349
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 587smallint unsigned range Indexing field to speed chromosome range queries.
name NM_001034679varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 327876int unsigned range Transcription start position
txEnd 339078int unsigned range Transcription end position
cdsStart 327956int unsigned range Coding region start
cdsEnd 337478int unsigned range Coding region end
exonCount 4int unsigned range Number of exons
exonStarts 327876,331232,333962,337305,longblob   Exon start positions
exonEnds 328043,331406,334122,339078,longblob   Exon end positions
score 0int range  
name2 RCAN1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none','unk','incmpl','cmpl') values enum('none','unk','incmpl','cmpl')
cdsEndStat cmplenum('none','unk','incmpl','cmpl') values enum('none','unk','incmpl','cmpl')
exonFrames 0,0,0,1,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

  Connected Tables and Joining Fields
        bosTau4.all_est.qName (via refGene.name)
      bosTau4.all_mrna.qName (via refGene.name)
      bosTau4.gbCdnaInfo.acc (via refGene.name)
      bosTau4.gbMiscDiff.acc (via refGene.name)
      bosTau4.gbSeq.acc (via refGene.name)
      bosTau4.gbStatus.acc (via refGene.name)
      bosTau4.gbWarn.acc (via refGene.name)
      bosTau4.imageClone.acc (via refGene.name)
      bosTau4.mrnaOrientInfo.name (via refGene.name)
      bosTau4.refFlat.name (via refGene.name)
      bosTau4.refLink.mrnaAcc (via refGene.name)
      bosTau4.refSeqAli.qName (via refGene.name)
      bosTau4.refSeqStatus.mrnaAcc (via refGene.name)
      bosTau4.refSeqSummary.mrnaAcc (via refGene.name)
      bosTau4.xenoMrna.qName (via refGene.name)

  Sample Rows

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

  RefSeq Genes (refGene) Track Description


The RefSeq Genes track shows known cow protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated daily.

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. This page is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

  • 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. Click here for more information about this feature.
  • 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.


RefSeq RNAs were aligned against the cow 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 0.1% of the best and at least 96% 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.

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.