Transcript details panel

First of all, the transcript view allows access to transcript specific data like the protein and DNA sequence and colors the exons of the transcript on the sequences. Other transcripts of the gene can be visualized with respect to the current transcript and deletions, replacements and insertions that occur due to the splicing event are colour coded on the transcript sequence. Users can choose a protein structure that matches the transcript and this structure is then visualized and the correspondence of the gene structure (i.e. its exons) and the protein structure can interactively be explored. An exon or a group of exons can additionally be structurally classified in terms of different features like secondary structure content, solvent accessibility, structural contacts as well as domain classifications as defined by SCOP or PDP. Despite analyzing each exon individually, known splicing events, i.e. other known transcripts of the gene, can also be coloured on the structure level relative to the current transcript immediately showing deletions, insertions and replacements on the structure level.

Show transcript: By default this view is opened. It shows the amino acid sequence and the nucleic acid sequence of the transcript. In both sequences the exons are shown in alternating colors. If this view is not opened and you wish to see it click on the "Show transcript" button. Amino acids whose nucleotide triplet is provided by two neighboring exons (border amino acids) are coloured in green.

Show known alternatives:By clicking on this button you will view the alternative transcripts of this gene.(Alternative transcripts view)

Show structure information: Clicking on this button will lead you to an overview of the structure information that is available (Structure information view), the first model will be loaded immediatly. If no structure information is available this button is disabled.

Show all transcripts: When comparing different transcripts on the structure level it might be helpful to have the binary exon view at hand. Therefore you can open it in an additional window by clicking on this button.

Alternative transcripts view

In this view known alternative transcripts are compared to the currently selected transcript (which is used as the reference transcript). Deletions in the current transcript are colored red, replacements of the transcript sequence by another sequence are shown in blue. If an exon or several exons are inserted between two exons of the current transcript, the borders of the respective two exons are colored yellow and orange, respectively.

Structure information view

To access structure information, please click the Show structure information button. This will open the view shown below. The first model of the entry will be opened immediatly. To get information about the specific templates move the mouse over one of the red rectangles and the template, its sequence identity and the coverage will be shown as a tooltip. If you want to open a structure, just click on the corresponding template rectangle.. In the case that several such templates are available, you can choose one template at a time.

Structure visualization

Having selected a structure template for the swissprot entry, you have the following options to explore the correspondence of gene and protein structure as well as splicing events annotated for the entry. Structures are visualized with Jmol, therefore all the functionality available in Jmol is also available for the structure visualization in ProSAS. Please see the Jmol tutorial on their website for details.

Color the structure with respect to another known isoform: To visualize parts that are missing, replaced or inserted in another known isoform of the gene, just click on the isoform buttons (visualization options). The changes which are modelled in the structure are colored in red (deletions), in blue (replacements) and yellow / orange for insertions (the same way they are colored in the alternative transcript view showing changes on the sequence level).
Select rainbow button: If you want to color all exons on the structure level by a different color, just click this button. Each exon will be assigned to a specific color starting with blue and ending with red.
Restrict chain: for structures that contain several chains one may want to restrict the display to the chain modelling the structure. Click the corresponding button to do so. Analyzing the changes having all chains at hand, nevertheless might sometimes provide interesting insights into the effects of splicing on protein-protein interaction interfaces and complexes.
Select none button: to deselect all exons just click this button.

Everytime you visualize the changes with respect to another isoform on the protein structure level, a region report will be displayed besides the protein structure. This report provides features which may help you to judge the possible effects of a splicing event onto the stability of the resulting isoform. Currently the following features are provided, more are to follow.

Location: The location of the event may be N-Terminal, Internal or C-Terminal. Terminal events often affect more variable regions and may therefore be explainable on the structure level.
Distance: describes the distance between the loose ends originating from the splicing event of internal exons. If this gap is large, the protein needs to bridge a large distance to close the gap.
Avg. Hydro.: Average Kyte-Doolittle hydrophobicity of the part affected by the splicing event.
Start and End: Description of the start/end of the splicing event in terms of secondary structure element and solvent accessibility
SSE: secondary structure content of the affected region (alpha, beta, alpha and beta or unstructured). Especially changes in unstructured regions are easily explainable on the structure level.
Core SSE: content of core secondary structure elements in the affected region. A core element is defined as a secondary structure element of length at least 3 (strands) and 4 (helices) that has contact to at least one other core secondary structure element.
Aff. strands: describes if internal or peripheral strands are affected by the event.
PDP domains: if more than 75% of a domain as defined by PDP is affected it is displayed here.
SCOP domains: if more than 75% of a domain as defined by SCOP is affected by the event, the domain is shown here.

Alignment and template information is visualized below the structure.

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