Description

The RefSeq Genes track shows known $organism 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. 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

RefSeq RNAs over twenty base pairs were aligned against the $organism genome using BLAT. Those alignments with less than sixteen bases aligning outside of annotated repeats were discarded. Next, the alignment with the highest base identity between the RNA and the genomic sequence was chosen. For each RNA, alignments not within 0.1% of the base identity of the best alignment were discarded. Additional filtering takes place based on the quality of the display which is documented on the Assembly Page. For finished assemblies, the minimum base identity of alignments must be 95%, and the alignment must cover 25% of the bases in the RNA. For well-ordered assemblies, the minimum base identity of alignments must be 95%, and the alignment must cover 15% of the bases in the RNA. For low-coverage assemblies, the minimum base identity of alignments must be 94%, and the minimum alignment size must be 80 base-pairs.

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.

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.