Genes Which Only Use Exon Skipping Mode For Alternative Splicing

Question

[skm770]

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

[Pierre Lindenbaum]

http://www.ncbi.nlm.nih.gov/pubmed/15984933 (2005) "Alternatively spliced human genes by exon skipping--a database (ASHESdb)." is down :-/

Answer 1

[Giovanni M Dall'Olio]

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:

• go to www.ensembl.org
• click on the Biomart link
• select the organism Dataset
• in the Filters window, expand the "Transcription Event" -> "Event Type" form
• from there you will have to select the code correspondent to Exon Skipping, from this article. Unfortunately there is not a code for "Exon Skipping". In this case I think that it is better if you look at the article by yourself and choose the code that you consider the most appropriate.
• from the Attributes window, select Transcript Event and check "Event Name" and "Event Type"

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.

[skm770]

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

[Giovanni M Dall'Olio]

The best you can do is to download the whole table, and then just filter by yourself.