Finding Exons in a gene

[Lorea]

Hi Friends,

I have been working on the hapmap data to find SNPs in a few genes of
interest which are potential in disease causing. For this i need to
know if the SNPs are in exons or introns. Can somebody tell me how one
can find exons in the gene other than using Ensembl? I have been using
the Hapmap data and this data does not seem to match with the Ensembl.
So i have to use a search method for exons other than Ensembl. If you
know how to find the exons in UCSC genome browser or the Hapmap that
would be great. Could someone help me in this regard?

Thanx in advance.

[sumera parveen]

check out the dbsnp page for that particular snp. it carries all the info about location etc. for that.

--
Sumera Parveen
M.Sc. bioinformatics
13918 Castle Blvd apt 101
Silver Spring, Maryland-20904
USA
ph: +1-662-202-6639

[Abhishek Pratap]

The quickest way to do it is to post ur query to the right mailing list. http://genome.ucsc.edu/contacts.html

They are normally very quick .

Cheers!

-A

[HARIKRISHNA REDDY]

Dear Sumera,
It is an interesting topic raised by you exons are the coding parts of
the gene and introns are noncoding parts so the possibility for
presence of SNPs only in exons. GENOMESCAN is the tool to find the
exons and introns in genome . I hope this information may useful to
you.All the best for your career . Do not hesitate to contact about
queries.

With best regards,
Harikrishnareddy,
Genovobioinfo,
Vishakapatnam,
Andhrapradesh,
India.

[Lorea]

Thank you all..your information was helpful. I was working with the
UCSC genome browser and it shows a graphical view of exons and introns
with their positions in the gene and you can even pull out the DNA
sequence at the position or range of your choice. Anyhow, Thanx to
all.

Best regards,
Lorea

On Jul 17, 5:50 am, HARIKRISHNA REDDY <harikrishnaredd...@gmail.com>
wrote:

> Dear Sumera,
> It is an interesting topic raised by you exons are the coding parts of
> the gene and introns are noncoding parts so the possibility for
> presence of SNPs only in exons. GENOMESCAN is the tool to find the
> exons and introns in genome . I hope this information may useful to
> you.All the best for your career . Do not  hesitate to contact about
> queries.
>
> With best regards,
> Harikrishnareddy,
> Genovobioinfo,
> Vishakapatnam,
> Andhrapradesh,
> India.
>

> On Thu, Jul 16, 2009 at 7:36 PM, sumera parveen<sumera...@gmail.com> wrote:
> > check out the dbsnp page for that particular snp. it carries all the info
> > about location etc. for that.
>

[Fred]

Hello,

Just to add some information related to your post.
Actually exons contains coding parts that are the open reading frame
(ORFs) and non coding parts that are the 5'UTR and and 3'UTR of the
mRNAs.
Additionally, I think that SNPs within the introns could be of
interest because some of them could be located in the sequence that
are of importance in the mRNAs splicing.

Hope this helps,

Fred

On Jul 17, 6:50 am, HARIKRISHNA REDDY <harikrishnaredd...@gmail.com>
wrote:

> Dear Sumera,
> It is an interesting topic raised by you exons are the coding parts of
> the gene and introns are noncoding parts so the possibility for
> presence of SNPs only in exons. GENOMESCAN is the tool to find the
> exons and introns in genome . I hope this information may useful to
> you.All the best for your career . Do not  hesitate to contact about
> queries.
>
> With best regards,
> Harikrishnareddy,
> Genovobioinfo,
> Vishakapatnam,
> Andhrapradesh,
> India.
>
>
>
> On Thu, Jul 16, 2009 at 7:36 PM, sumera parveen<sumera...@gmail.com> wrote:
> > check out the dbsnp page for that particular snp. it carries all the info
> > about location etc. for that.
>

> > On Tue, Jul 14, 2009 at 12:04 PM, Lorea <bhargavi2...@gmail.com> wrote:
>
> >> Hi Friends,
>
> >> I have been working on the hapmap data to find SNPs in a few genes of
> >> interest which are potential in disease causing. For this i need to
> >> know if the SNPs are in exons or introns. Can somebody tell me how one
> >> can find exons in the gene other than using Ensembl? I have been using
> >> the Hapmap data and this data does not seem to match with the Ensembl.
> >> So i have to use a search method for exons other than Ensembl. If you
> >> know how to find the exons in UCSC genome browser or the Hapmap that
> >> would be great. Could someone help me in this regard?
>
> >> Thanx in advance.
>
> > --
> > Sumera Parveen
> > M.Sc. bioinformatics
> > 13918 Castle Blvd apt 101
> > Silver Spring, Maryland-20904
> > USA

> > ph: +1-662-202-6639- Hide quoted text -
>
> - Show quoted text -

[wenhw...@gmail.com]

dear all,

Just one word of caution: differently to what has been suggested by some contributors, a SNP *can* occur in any part of a chromosome.

This means that SNPs can be found in either exons or introns. Afterall 'single nucleotide polymorphisms' doesn't imply any specific position for these. In fact, as far as I can recall, there are more SNPs in intronic regions than in exons.

Cheers,
Lee
SGC, Univ. Of Oxford

-original message-
Subject: Re: Finding Exons in a gene
From: HARIKRISHNA REDDY <harikrish...@gmail.com>
Date: 17-07-2009 06:53


Dear Sumera,
It is an interesting topic raised by you exons are the coding parts of
the gene and introns are noncoding parts so the possibility for
presence of SNPs only in exons. GENOMESCAN is the tool to find the
exons and introns in genome . I hope this information may useful to
you.All the best for your career . Do not hesitate to contact about
queries.

With best regards,
Harikrishnareddy,
Genovobioinfo,
Vishakapatnam,
Andhrapradesh,
India.

On Thu, Jul 16, 2009 at 7:36 PM, sumera parveen<sume...@gmail.com> wrote:
> check out the dbsnp page for that particular snp. it carries all the info
> about location etc. for that.
>

[Wen Hwa Lee]

Hi all -

To add to what Fred has very correctly pointed out: SNPs in introns can indeed be very interesting. Just remember that until not that long ago, all non-coding regions used to be labelled as 'junk DNA'. How wrong it is to assume that whatever we can't detect (yet) is to be 'useless and wrong'.

Several regulatory elements can be found in the non-coding regions (in addition to the splicing signals mentioned by Fred). For instance, microRNAs (miRNAs) are mostly found in either introns or even intergenic regions (!! do not mix introns and intergenic regions: introns do belong to a gene, but it is simply not translated into a protein; intergenic regions comprise everything that lay *between* different genes).

cheers,
L.