I am studying alternative splicing in a mouse gene and would like to identify splicing regulatory elements that influence the splicing events. Older databases and tools concerning splicing, like ASAP II, ASTD or FAST DB, seem to be down or not maintained. Without them, my best guess is to check manually for conservation of intronic/exonic sequences between mouse and human. Is that useful for narrowing down to the likely regulatory regions? Do you know any well-maintained tools and databases that could help me further?
NNSplice (http://www.fruitfly.org/seq_tools/splice.html) and MaxEnt are precise algorithms to detect 5' and 3' splice sites. Also you can use Human Splicing Finder (http://www.umd.be/HSF3/) that contains both NNSplice and MaxEnt as well own algorithms. HSF also includes detection of splicing enhancers and silencers (ESEfinder, Rescue-ESE, PESE, etc) but they are not so accurate. In HSF you can also check the impact of mutations on splicing regulatory elements.
Regards
Eladio
Exonic splicing enhancer/silencer binding sites, are important factors in splicing as well, often overlooked.
You could use "ESEfinder" website, both for exon/intron boundaries and ESE.
or
http://astlab.tau.ac.il/index.php
altough this is only for human.
Dear Martin
ESEfinder, Rescue ESE, PESE/PESS, and other ESE/ESS algorithms are included in Human Splicing Finder. I agree with you that enhancers could be important, but, for example, we have found that
Dear Eladio,
I fully agree with you.
The only way to find out is to do the experiment, so do RT-PCR and or minigene assays with mutagenisis to find out what is the real enhancer and/or silencer binding site if present at all.
Weak donor or acceptor splice sites need help of enhancers probably. Large or small exons and large or small introns have influence as well. The distance between enhancer and exon/intron boundary might also be of influence.
PESE and PESS are putative sites, so computer derived, but ESEFinder motifs are from real known enhancer proteins derived, from which its binding motif consensus is known, still no full proof that this will always disturb splicing when mutated.
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