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The following image shows how this works. The top panel of the IGB Main View window shows the normal, non-spliced view of a region containing overlapping genes from a human, AGBL4 which contains several very large introns, one of which completely encompasses another gene, BEND5. The Sliced View panel on the bottom shows AGBL4, and then BEND5, but with the gaps between exons reduced to 100bp.
Black has hash marks in the Sliced View coordinate axis indicate points where sequence was deleted from between the exons. Note how the Sliced View makes understanding and visualizing the exons easier than in the Main View, where exons are dwarfed by the much larger intronic regions.
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Sliced view example (click to enlarge)
The Sliced View Panel
The Sliced View panel provides you with the opportunity to concentrate on specific elements of gene models. Slicing redraws long and variable length introns into consistent, defined (and short) lengths, allowing you to focus on the exons of a selected annotation or set of annotations. By showing the exons relative to each other without intronic variability, you can find pattern irregularities, exonic discrepencies and possible alternate splicing more obvious.
Open the Sliced View panel, and be sure that the Slice Buffer is set to a number you like. The Slice Buffer is the size that IGB will use to draw in the introns. The default is 100bp, which is typically a very good size for most genes (see red box in image below); you may also set the slice buffer to 0 to completely eliminate the introns. In the main view, select one or all annotations to include in the slice by clicking or outlining with the Select tool (Selecting Items). In the following example we have selected all 4 gene models for human gene PDE4B.
IGB may take a few moments to display the sliced region. For easy comparison, the sliced view displays sliced versions of all annotation tracks and graphs in the region being viewed. Use the zoom and scroll bars to navigate in the sliced view panel. Note that the numbers in the Coordinates track in the sliced view panel indicate scale; they don't correspond to genomic coordinates. Endpoint matching in the upper and lower windows are independent of each other.
Viewing deletions and insertions
The Sliced View can help you see where sequences present in one transcript are absent from the others due to alterantive splicing.
To examine alternate splicing using the Sliced View
- select one of the transcripts in the Main View
- observe insertion icons IGB draws on the other transcripts
The following images illustrates this.
In the first image, the arrows show how IGB draws regions where an annotation is 'inserted'; the introns in 'non-inserted' tracks are elongated over the region of insertion.
In the next image, the bottom-most transcript was selected in the main view. The other three transcripts each include one or more exons that were present in the top transcript. The locations of these "sliced-out: (deleted) exons relative to the other exons is indicated with X marks (red boxes). The exons that are 'shorter' than the matching exon in the selected track are drawn shorter (blue box).
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You can stop the Sliced View from updating when you click items in the Main View by deselecting the Slice by Selection checkbox. This will stop the Sliced View from jumping around as you click in the Main View. |
Showing ORFs and stop codons
The Sliced View panel can show open reading frames and stop codons.
To visualize open reading frames and stop codones
- select an annotation in the Main View
- click the Sliced View tab
- check the Analyze ORFs checkbox
- use the Min ORF slider to adjust the mininum length of ORFs to show (in base pairs)
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The Slice Buffer is set to '0' to remove introns (red box) when the Analyze ORFs box is checked. |
Three rows of ORFs appear for + translations (blue box), and for each - translation (purple box). Stop codons are red hash marks, and the reading frames are marked as green lines. The color of the stops, the ORFS and the background can be changed using Preferences > Other Options (see Other Options).
