The mRNA track shows alignments between human mRNAs in GenBank and the genome.
NOTE: As of April, 2008, we are again including GenBank sequences that contain the following URL as part of the record:
http://fulllength.invitrogen.comSome transcripts from this library are suspect. Some of these entries are the result of alignment to pseudogenes, followed by a "correction" of the mRNA to match the genomic sequence. It is therefore not the sequence of the actual mRNA and makes it appear that the mRNA is transcribed. Invitrogen no longer sells the clones. This collection also contains a large amount of very good transcript evidence that can be quite useful. We have created a table, gbWarn, which lists problematic mRNAs and ESTs by accession. In a future release, we will be providing a better indication of the problematic transcripts in the genome browser display.
This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.
The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.
To use the filter:
This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here.
GenBank human mRNAs were aligned against the genome using the blat program. 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 0.5% of the best and at least 96% base identity with the genomic sequence were kept.
The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.
Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.