Description
The $Organism mRNA track shows alignments between $organism mRNAs
in Genbank and the genome. Aligning regions (usually exons)
are shown as black boxes connected by lines for gaps (spliced
out introns usually). In full display, arrows on the introns
indicate the direction of transcription.
Method
Genbank $organism mRNAs are aligned against the genome using the
BLAT program. When a single mRNA aligns in multiple places,
the alignment having the highest base identity is found.
Only alignments that have a base identity level within 1% of
the best are kept. Alignments must also have at least 95%
base identity to be kept.
Using the Filter
The track filter can be used to change the color or include/exclude a subset of individual
items within a track. This is helpful when many items are shown in the track
display, especially when only some are relevant to the current task. To use the
filter:
- Enter a value in one or more of the text boxes to filter the mRNA display. For
example, to apply the filter to all liver mRNAs, type "liver" in the
tissue box. For a list of permissible filter values, consult the non-positional table in
the Table Browser that corresponds to the factor on which you wish to filter. For
example, the non-positional table "tissue" contains all of the types of tissues
that can be entered into the tissue text box. Wildcards can 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 of the filter criteria will
be highlighted. If "or" is selected, mRNAs that match any 1 of the filter criteria
will be highlighted.
- Choose the color or display characteristic that will 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.
- When you have finished configuring the filter, click the Submit button.
Credits
The $Organism mRNA track is produced at UCSC from mRNA sequence data
submitted to the international public sequence databases by
scientists worldwide.