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ProSAS: a database for analyzing alternative splicing in the context of protein structures.

Birzele F, Küffner R, Meier F, Oefinger F, Potthast C, Zimmer R - Nucleic Acids Res. (2007)

Bottom Line: Nevertheless, the effects of splicing on the structure of a protein are largely unknown.The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures.ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events.

View Article: PubMed Central - PubMed

Affiliation: Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstrasse 17, D-80333 Munich, Germany.

ABSTRACT
Alternative splicing is known to be one of the major sources for functional diversity in higher eukaryotes. Several splicing isoforms have been characterized in the literature that play important roles in cellular processes like apoptosis or signal transduction pathways. Splicing events can often be detected on the mRNA level by large-scale cDNA or EST experiments and such data is collected and annotated in several databases. Nevertheless, the effects of splicing on the structure of a protein are largely unknown. The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures. ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events. Alternative isoforms annotated in Ensembl or SwissProt can be analyzed on the protein structure and protein function level using an intuitive user interface that provides several features and tools for a structure-based analysis of alternative splicing events. The ProSAS database is freely accessible at http://www.bio.ifi.lmu.de/ProSAS.

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Transcript details view for transcript ENSMUST00000091706_13 from gene ENSMUSG00000006611_13. The structure of the transcript is visualized with Jmol (Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/) and the difference with respect to transcript ENSMUST00000091707_13, namely the deletion of a larger N-terminal part is visualized on the structure. The alternatively spliced region is characterized with respect to different features such as solvent accessibility or secondary structure content.
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Figure 3: Transcript details view for transcript ENSMUST00000091706_13 from gene ENSMUSG00000006611_13. The structure of the transcript is visualized with Jmol (Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/) and the difference with respect to transcript ENSMUST00000091707_13, namely the deletion of a larger N-terminal part is visualized on the structure. The alternatively spliced region is characterized with respect to different features such as solvent accessibility or secondary structure content.

Mentions: The transcript view (Figure 3), as well as the SwissProt entry report that is designed in a very similar way, 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 color-coded on the transcript sequence.Figure 3.


ProSAS: a database for analyzing alternative splicing in the context of protein structures.

Birzele F, Küffner R, Meier F, Oefinger F, Potthast C, Zimmer R - Nucleic Acids Res. (2007)

Transcript details view for transcript ENSMUST00000091706_13 from gene ENSMUSG00000006611_13. The structure of the transcript is visualized with Jmol (Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/) and the difference with respect to transcript ENSMUST00000091707_13, namely the deletion of a larger N-terminal part is visualized on the structure. The alternatively spliced region is characterized with respect to different features such as solvent accessibility or secondary structure content.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238869&req=5

Figure 3: Transcript details view for transcript ENSMUST00000091706_13 from gene ENSMUSG00000006611_13. The structure of the transcript is visualized with Jmol (Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/) and the difference with respect to transcript ENSMUST00000091707_13, namely the deletion of a larger N-terminal part is visualized on the structure. The alternatively spliced region is characterized with respect to different features such as solvent accessibility or secondary structure content.
Mentions: The transcript view (Figure 3), as well as the SwissProt entry report that is designed in a very similar way, 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 color-coded on the transcript sequence.Figure 3.

Bottom Line: Nevertheless, the effects of splicing on the structure of a protein are largely unknown.The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures.ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events.

View Article: PubMed Central - PubMed

Affiliation: Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstrasse 17, D-80333 Munich, Germany.

ABSTRACT
Alternative splicing is known to be one of the major sources for functional diversity in higher eukaryotes. Several splicing isoforms have been characterized in the literature that play important roles in cellular processes like apoptosis or signal transduction pathways. Splicing events can often be detected on the mRNA level by large-scale cDNA or EST experiments and such data is collected and annotated in several databases. Nevertheless, the effects of splicing on the structure of a protein are largely unknown. The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures. ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events. Alternative isoforms annotated in Ensembl or SwissProt can be analyzed on the protein structure and protein function level using an intuitive user interface that provides several features and tools for a structure-based analysis of alternative splicing events. The ProSAS database is freely accessible at http://www.bio.ifi.lmu.de/ProSAS.

Show MeSH