I am not sure how many bps is variant within of a splicing junction can it be called splicing sites? I read some exome squencing papers, they say they found some splice site, but non of them present this number.
The shortest introns known in the literature are about ~20 bp (reference), if that is what you are looking for.
I think that if you want to make a filter, it should be at least 10 bp, considered that the splicing signals AG..Y.GT occupy at least 5 bases.
The sequence ontology definition is reasonable but this definition is not consistently used. In defining "splice site mutations" some groups may use a simpler definition. For purposes of mutation annotation, it is common to consider the 'splice sites' to be only the two intronic bases closest to each exon. The adjacent bases in the exons may change amino acid sequence even if the splicing pattern is unaffected, so these will often be classified as coding mutations instead of splicing. In reality it is of course an oversimplification. However, the 'two bases' rule is often justified by observing that these two intronic bases at each end of the intron are the most highly conserved. For example in human, a large majority of introns have a 'GT' donor and 'AG' acceptor. The remaining bases around the splice site are considerably less conserved.
A typical human Donor/Acceptor layout looks like this:
5' - Exon1 - GT .. Intron1 ... branch site ... AG - Exon2 - 3'
There are many great publications that provide more specifics on splice sites, but I particularly recommend: A general definition and nomenclature for alternative splicing events.
Figure 5 of that publication provides a 'Sequence Logo' for human. This allows you to visualize the conservation of each position of the Acceptor, Branch, and Donor sites.
In the Sequence Ontology, a splice_region_variant is defined as "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron."
Hi
I along with other coauthors has two papers in BMC research notes. We also have a ASMD (Alternative spicing mutation data base) ...
http://mco321125.meduohio.edu/~jbechtel/asmd/
The following is the link for our paper on ASMD database. You can even use the splicing potential to test different splicing enhancers and exonic mutation using these tools.
http://www.biomedcentral.com/1756-0500/1/3/about/citations-biomedcentral
Hope this helps to address your research.
Best regards,
Pankaj K. Mishra, Ph.D.
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At least 10 bp? I read some paper, some of them only 4bp.
@liyf: I personally believe that they are all sequencing errors; and even if they are not, they are probably related to some other mechanism. The splicing machinery, as we know it, needs at least two signals to carry out the splicing, so I wouldn't trust very much introns shorter than 10 bp. In any case, that is just my opinion.. By the way, can you please edit your question? I am not sure I answered what you were looking for.