Description
These tracks show alignments of mouse mRNAs from the
Mammalian Gene Collection
(MGC) and
ORFeome Collaboration 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. The ORFeome project extended MGC to
provide additional human, mouse, and zebrafish clones.
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.
Visit the ORFeome Collaboration
members page for a list of credits and references.
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
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