I need to find genes which only use one mode of alternative splicing that is exon skipping. How can I get the list of genes which only use exon skipping as a mechanism for alternative splicing and not other mechanisms
I need to find genes which only use one mode of alternative splicing that is exon skipping. How can I get the list of genes which only use exon skipping as a mechanism for alternative splicing and not other mechanisms
Ensembl contains annotations for Alternative Splicing Events. You can get a list of genes under from Biomart, selecting the Ensembl database and filtering by splicing event.
How to do it:
Unfortunately it seems that not even Ensembl is very user friendly in this case.
There are other databases on Alternative Splicing, but I think that many are old and not maintained. In any case, the best place to start searching should be EURASNET, the European portal for Alternative Splicing.
Using biomart I'll get genes which show exon skipping event but one gene may exhibit more than one way of alternative splicing namely "alternative 3' site" or alternative 5' site or retained intron etc. I only want genes which only use exon skipping as a means of alternative splicing
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http://www.ncbi.nlm.nih.gov/pubmed/15984933 (2005) "Alternatively spliced human genes by exon skipping--a database (ASHESdb)." is down :-/