MGC Genes Track Settings
 
Mammalian Gene Collection Full ORF mRNAs   (All Genes and Gene Predictions tracks)

Display mode:   

Color track by codons or bases: Help on mRNA coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion
View table schema
Data last updated: 2012-03-18

Description

This track shows alignments of mouse mRNAs from the Mammalian Gene Collection (MGC) having full-length open reading frames (ORFs) to the genome. The goal of the Mammalian Gene Collection is to provide researchers with unrestricted access to sequence-validated full-length protein-coding cDNA clones for human, mouse, and rat genes.

Display Conventions and Configuration

The track follows the display conventions for gene prediction tracks.

An optional codon coloring feature is available for quick validation and comparison of 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.

Methods

GenBank mouse MGC mRNAs identified as having full-length ORFs were aligned against the genome using blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 1% of the best and at least 95% base identity with the genomic sequence were kept.

Credits

The mouse MGC full-length mRNA track was produced at UCSC from mRNA sequence data submitted to GenBank by the Mammalian Gene Collection project.

References

Mammalian Gene Collection project references.

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