ProSAS does not only contain splicing events annotated in Ensembl but does also display isoforms annotated in the Swissprot database. Isoforms annotated there are usually validated experimentally, though not always on the protein level (usually on the mRNA / cDNA level). Similar to Ensembl Transcripts, Swissprot entries may be analyzed in their structural context.
The entry view for an entry displays general information on the entry as well as known isoforms of the entry annotated in Swissprot. For every isoform (with the entry as reference) deletions (red), replacements (blue) and insertions (yellow/orange) are displayed on the entry sequence. Also, the resulting isoform sequence is shown.
Structure information view
To access structure information, please click the Show structure information button. This will open the view shown below where you can see the exons of the transcript as well as the positions of the structures that model the transcript. The first model of the transcript 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 entry, you have the following options to explore the correspondence of gene and protein structure as well as splicing events annotated for the gene. 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 a specific exon or a group of exons: The exon display above of the structure show all exons which are structurally covered but unselected in dark grey . Exons that are not covered by the structure are inactive and set to light grey . To color an exon in the structure just click on it , the exon will be colored in red . In the image below, the first exon of the transcript is selected and colored red in the structure.Color the structure with respect to another known transcript / isoform: To visualize parts that are missing, replaced or inserted in another known isoform of the gene, just click on the transcript 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 select an exon or visualize the changes with respect to another transcript 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 accessibilitySSE : 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.
