The intronic variations , which i have found are not at exon/intron junctions.
Hello Gurjeet Kaur
Im not sure about what you mean , but i can say that you can easily predict the effect of your variant by a good tool in Ensembl database called "Variant Effect Predictor" and this is its direct link
http://asia.ensembl.org/info/docs/tools/vep/index.html
Best regard
Hi Gurjeet
Deep intronic variations could potentially change the binding sites in intronic enhancers, or it could be in a long non coding RNA encoded by that intron (which has a separate database, I strongly recomend you to check this out in current issue of Nucleic acids research). One useful tool I have used is GWAS3D (http://jjwanglab.org/ ) whcih even calculate LD among other variants in the locus. However you may have to have the SNP IDs for that.
Best
Thank you so much for your valuable suggestions. However , i dont have SNP id for that. But the intronic variaton which i found l are not found in database. My main purpose for analyzing these intronic variation is that whether these intronic variation are affect the origin of small RNAs or Long non coding RNA in my disease case.
Hi Gurjeet,
albeit your mutations are lokated deep intronic, have you checked for an influence on splicing of your mRNA of interest?
Useful tools might be:
http://spliceport.cbcb.umd.edu/SplicingAnalyser2.html
http://www.fruitfly.org/seq_tools/splice.html
http://www.umd.be/HSF3/HSF.html
http://wangcomputing.com/assp/index.html
Best regards
Thanks Alex. Yes , i have checked whether these variations altering the mRNA splicing pattern. But unfortunately i didn't find any results. I have used fruitfly and HSFF3. I haven't used wangcomputing and spliceport. Let me try these tool .
Thanks
It's hard to give a good answer without some specifics. First, what do you mean by "deep"? It may be obvious to you, but people don't always use the same ad-hoc nomenclature. Second, are we talking about humans? That would be a pretty important thing to know. Third, is this for a specific disease? If so, is it a highly penetrant Mendelian disorder or a "complex" trait?
There are dozens, if not hundreds, of annotation tools and prediction algorithms. It's hard to know which one would be useful. There is no one-size-fits-all "bioinformatics" tool. I find that many are quite clever, but almost all or marginally useful, at best. I'd just throw your variants into ANNOVAR and see what comes up.
Dear Gurjeet Kaur,
if your aim is analyzing the potential alteration of the splicing mechanism due to your intronic mutation you can use these tools:
http://derisilab.ucsf.edu/index.php?software=105
http://web.stanford.edu/group/wonglab/SpliceMap/
Hope it's helpful =)
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