Non-EST based prediction of exon skipping and intron retention events using Pfam information

Most of the known alternative splice events have been detected by the comparison of expressed sequence tags (ESTs) and cDNAs. However, not all splice events are represented in EST databases since ESTs have several biases. Therefore, non-EST based approaches are needed to extend our view of a transcr...

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Main Authors:	Hiller, Michael, Huse, Klaus, Platzer, Matthias, Backofen, Rolf
Format:	Online
Language:	English
Published:	Oxford University Press 2005
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243800/

id	pubmed-1243800
recordtype	oai_dc
spelling	pubmed-12438002005-10-07 Non-EST based prediction of exon skipping and intron retention events using Pfam information Hiller, Michael Huse, Klaus Platzer, Matthias Backofen, Rolf Article Most of the known alternative splice events have been detected by the comparison of expressed sequence tags (ESTs) and cDNAs. However, not all splice events are represented in EST databases since ESTs have several biases. Therefore, non-EST based approaches are needed to extend our view of a transcriptome. Here, we describe a novel method for the ab initio prediction of alternative splice events that is solely based on the annotation of Pfam domains. Furthermore, we applied this approach in a genome-wide manner to all human RefSeq transcripts and predicted a total of 321 exon skipping and intron retention events. We show that this method is very reliable as 78% (250 of 321) of our predictions are confirmed by ESTs or cDNAs. Subsequent analyses of splice events within Pfam domains revealed a significant preference of alternative exon junctions to be located at the protein surface and to avoid secondary structure elements. Thus, splice events within Pfams are probable to alter the structure and function of a domain which makes them highly interesting for detailed biological investigation. As Pfam domains are annotated in many other species, our strategy to predict exon skipping and intron retention events might be important for species with a lower number of ESTs. Oxford University Press 2005 2005-10-04 /pmc/articles/PMC1243800/ /pubmed/16204458 http://dx.doi.org/10.1093/nar/gki870 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Hiller, Michael Huse, Klaus Platzer, Matthias Backofen, Rolf
spellingShingle	Hiller, Michael Huse, Klaus Platzer, Matthias Backofen, Rolf Non-EST based prediction of exon skipping and intron retention events using Pfam information
author_facet	Hiller, Michael Huse, Klaus Platzer, Matthias Backofen, Rolf
author_sort	Hiller, Michael
title	Non-EST based prediction of exon skipping and intron retention events using Pfam information
title_short	Non-EST based prediction of exon skipping and intron retention events using Pfam information
title_full	Non-EST based prediction of exon skipping and intron retention events using Pfam information
title_fullStr	Non-EST based prediction of exon skipping and intron retention events using Pfam information
title_full_unstemmed	Non-EST based prediction of exon skipping and intron retention events using Pfam information
title_sort	non-est based prediction of exon skipping and intron retention events using pfam information
description	Most of the known alternative splice events have been detected by the comparison of expressed sequence tags (ESTs) and cDNAs. However, not all splice events are represented in EST databases since ESTs have several biases. Therefore, non-EST based approaches are needed to extend our view of a transcriptome. Here, we describe a novel method for the ab initio prediction of alternative splice events that is solely based on the annotation of Pfam domains. Furthermore, we applied this approach in a genome-wide manner to all human RefSeq transcripts and predicted a total of 321 exon skipping and intron retention events. We show that this method is very reliable as 78% (250 of 321) of our predictions are confirmed by ESTs or cDNAs. Subsequent analyses of splice events within Pfam domains revealed a significant preference of alternative exon junctions to be located at the protein surface and to avoid secondary structure elements. Thus, splice events within Pfams are probable to alter the structure and function of a domain which makes them highly interesting for detailed biological investigation. As Pfam domains are annotated in many other species, our strategy to predict exon skipping and intron retention events might be important for species with a lower number of ESTs.
publisher	Oxford University Press
publishDate	2005
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243800/
_version_	1611378248214642688

Non-EST based prediction of exon skipping and intron retention events using Pfam information

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