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Old 08-20-2013, 11:17 PM   #1
lsantome
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Default How to annotate cDNA positions of intronic SNPs?

Hi all,

For my current research I'm dealing with big amounts of intronic SNPs.

Given a list of intronic SNPs with known rs# identifiers is there any way to retrieve their position in their corresponding cDNAs???

Thank you in advance!
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Old 08-21-2013, 11:55 PM   #2
lsantome
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Default Solved!

FYI

This is the answer that I got from dbSNP user support:

For this task, NCBI does provide a service named "variation reporter", which
can be accessed here:
http://www.ncbi.nlm.nih.gov/variation/tools/reporter

You will need to convert your input data to the basic BED format with at least
three columns separated by tabs:
chr# start_pos end_pos

such as (with the forth column provided as reference for you):
chr13 28891757 28891758 rs377741993
chr6 26091101 26091102 rs377254261
chr1 23209561 23209562 rs170129


It works great
I hope it helps

Thanks!
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Old 08-22-2013, 01:25 PM   #3
swbarnes2
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How will intronic SNPs be in cDNA? Won't they be spliced away?
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Old 08-23-2013, 02:13 AM   #4
lsantome
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Quote:
Originally Posted by swbarnes2 View Post
How will intronic SNPs be in cDNA? Won't they be spliced away?
Obviously they're not in cDNA but sometimes i.e. in clinical field you may want to annotate all variants (exonic/intronic) respecting to the same reference (NM_999999.9). Moreover this annotation helps you to know how far are the intronic variants from the splice sites, giving you an extra information about its potential impact.
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