Description
This track displays translated blat alignments of vertebrate and
invertebrate mRNA in
GenBank from organisms other than zebrafish.
Display Conventions and Configuration
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 strand information (+/-) for this track is in two parts. The
first + indicates the orientation of the query sequence whose
translated protein produced the match (here always 5' to 3', hence +).
The second + or - indicates the orientation of the matching
translated genomic sequence. Because the two orientations of a DNA
sequence give different predicted protein sequences, there are four
combinations. ++ is not the same as --, nor is +- the same as -+.
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:
- Type a term in one or more of the text boxes to filter the mRNA
display. For example, to apply the filter to all mRNAs expressed in a specific
organ, type the name of the organ in the tissue box. To view the list of
valid terms for each text box, consult the table in the Table Browser that
corresponds to the factor on which you wish to filter. For example, the
"tissue" table contains all the types of tissues that can be
entered into the tissue text box. Multiple terms may be entered at once,
separated by a space. Wildcards may also be used in the filter.
- If filtering on more than one value, choose the desired combination
logic. If "and" is selected, only mRNAs that match all filter
criteria will be highlighted. If "or" is selected, mRNAs that
match any one of the filter criteria will be highlighted.
- Choose the color or display characteristic that should be used to
highlight or include/exclude the filtered items. If "exclude" is
chosen, the browser will not display mRNAs that match the filter criteria.
If "include" is selected, the browser will display only those
mRNAs that match the filter criteria.
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, go to the
Codon and Base Coloring for Alignment Tracks page.
Several types of alignment gap may also be colored;
for more information, go to the
Alignment Insertion/Deletion Display Options page.
Methods
The mRNAs were aligned against the zebrafish genome using translated blat.
When a single mRNA aligned in multiple places, the alignment having the
highest base identity was found. Only those alignments having a base
identity level within 1% of the best and at least 25% base identity with the
genomic sequence were kept.
Credits
The mRNA track was produced at UCSC from mRNA sequence data
submitted to the international public sequence databases by
scientists worldwide.
References
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.
GenBank.
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.
PMID: 23193287; PMC: PMC3531190
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.
GenBank: update.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.
PMID: 14681350; PMC: PMC308779
Kent WJ.
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518
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US Server