Effect Of A Deletion In Intron

Question

[Edi]

Hi,

Does anyone know how to find the effect of a deletion in intron? I found a deletion in 19 c.694+8_18del and need to find the effect.

Thank you in advance.

[Arun]

From a functional/comparative genomics perspective, this is definitely interesting and worth investing some effort. Do you know about the expression of this gene and/or its function? Are there changes in the expression pattern between the ones with and without this intron? Are there alternative transcripts? What is the expression pattern of this gene? What are its targets? There are so many questions that could be interesting to test from here on, at least in plants! :)

Edit: I just saw the LDLR in your comment. I don't know much about this. So I'll speculate. Is it possible to look at expression data and look for alternative splicing events? Is it possible to do a genome-wide DE from replicates where this gene is with the whole intron copy and with the deletions (if you already know there is a definite function and phenotypic relation for this gene).

What do you know about this gene? :)

[Vikas Bansal]

Also, can anybody suggest, if, say, this deletion is present in DGV, would you simply exclude them?

Answer 1

[friveroll]

You should check if this mutation change the splicing behavior for that gene.

Here you can check 2 links for this kind of analysis: http://www.gen2phen.org/wiki/tools-predicting-problems-mrna-splicing http://www.cbs.dtu.dk/biolinks/pserve2.php

[friveroll]

Also you can find here useful information about genomic context http://humancyc.org/HUMAN/NEW-IMAGE?type=ENZYME&object=ENSG00000130164-MONOMER

Answer 2

[Alex Paciorkowski]

What organism? Most of this non-coding stuff isn't annotated, and if it's not in a splice site, good luck. If your organism is some mammal, like human or mouse, you can use the VISTA enhancer browser to see whether there is any evidence your region of interest does anything interesting.

[friveroll]

Thanks, for that tool. A very good start, the problem could be so complex, missing metylation sites, etc...

[Edi]

This is from human and it is in LDLR low density lipoprotein receptor intronic region.

[friveroll]

I found a video tutorial http://blog.openhelix.com/?p=5814

[Arun]

Hi Alex, what do you mean "if its not in a splice site"? There are auxiliary splicing signals that enhance or suppress splicing. They might be located in the intronic regions as well. There is also evidence of chromatin marks playing part in resulting in alternative transcripts; nucleosome density as well. I think its a bit premature to stop after looking at splice signals?

[Alex Paciorkowski]

I didn't say stop looking. I said "good luck". :)

[Arun]

:) alright... :D