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SNPs and promoter polymorphisms

Everything on bioinformatics, the science of information technology as applied to biological research.

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Postby G-Do » Sun Oct 08, 2006 3:49 pm

The color-coding is annotated function; it tells you what the minor allele of the SNP is believed to do in terms of gene structure.

Gray: Unknown, hasn't been annotated yet
Green: Synonymous coding mutation
Red: Non-synonymous coding mutation or splice site
Blue: UTR
Black: Intron

The promoter for TGFB1 overlaps another gene, so be careful - SNPs in this region may have been annotated with the other gene's function.

As for the SNPs you could not find on NCBI, how did you get those SNPs? What search did you perform?
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Postby ermis » Mon Oct 09, 2006 8:10 pm

G-Do wrote:The color-coding is annotated function; it tells you what the minor allele of the SNP is believed to do in terms of gene structure.

1) The promoter for TGFB1 overlaps another gene, so be careful - SNPs in this region may have been annotated with the other gene's function.

2) As for the SNPs you could not find on NCBI, how did you get those SNPs? What search did you perform?


1) How can I tell searching for promoters of other genes if they overlap? Is it obvious?

2) By looking at the 2 kb snps, as I described before.
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Postby G-Do » Tue Oct 10, 2006 3:28 pm

1) I didn't say the promoters overlapped. I said that the TGFB1 gene's promoter overlaps with another gene - namely, the 3'UTR and final exon of MGC4093. This is obvious if you scroll upstream of TGFB1 in UCSC Genome Browser - if another gene occurs within 2kb of the TSS for the gene you're interested in, there is overlap.

2) The SNPs you mentioned aren't actually SNPs in the conventional sense. If you look those three SNPs up in NCBI, you'll see that they are insertion mutations, and not single nucleotide polymorphisms - that is, they represent insertions of more than one nucleotide at that spot.

It sounds like you need a primer on how to use these databases. I would recommend that you find yourself a tutorial online on (i) how to use UCSC efficiently and (ii) how to use dbSNP efficiently before asking any more questions.
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Tutorial

Postby ermis » Wed Oct 11, 2006 7:37 am

G-Do wrote:It sounds like you need a primer on how to use these databases. I would recommend that you find yourself a tutorial online on (i) how to use UCSC efficiently and (ii) how to use dbSNP efficiently before asking any more questions.


Any good suggestions?
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Postby G-Do » Wed Oct 18, 2006 2:44 am

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