Login

Join for Free!
112112 members


How can I work out the amount of DNA coding in a region

Genetics as it applies to evolution, molecular biology, and medical aspects.

Moderator: BioTeam

How can I work out the amount of DNA coding in a region

Postby asis2 » Mon Jan 04, 2010 2:46 pm

I want to use capture technology, and I know the size and location of the region of DNA I am interested in, but I am not sure exactly how much is coding. I was wondering whether this information is available in any of the databases online like ncbi or ensembl?

I know I can guestimate that its roughly 2% of the region I have but looking for something more precise.

Cheers!

A
asis2
Garter
Garter
 
Posts: 3
Joined: Mon Jan 04, 2010 2:40 pm

Postby JackBean » Mon Jan 04, 2010 3:54 pm

You can isolate mRNA and after reverse transcription you can sequence and identify the coding regions.

What organism do you have it from? If is it sequenced, you should be able to find some list of cDNAs or something like that. Also, if you found some sequence of your gene in form of mRNA or cDNA or CDS, you will have the coding region ;)
Of course, if you new the protein sequence, you would know the coding sequence ;)
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
User avatar
JackBean
Inland Taipan
Inland Taipan
 
Posts: 5652
Joined: Mon Sep 14, 2009 7:12 pm

Re: How can I work out the amount of DNA coding in a region

Postby asis2 » Tue Jan 05, 2010 12:23 pm

Thanks JackBean, :)

Its human about half of chromosome 16 in the first instance. I do not have mRNA just the genomic DNA, though all of the coding regions are in databases which I could add up as you suggest! I was just being lazy and wondered if there was a function within the databases as for some of my other families I need to go through a lot of regions!!

Thanks again
A
asis2
Garter
Garter
 
Posts: 3
Joined: Mon Jan 04, 2010 2:40 pm


Postby JackBean » Tue Jan 05, 2010 10:17 pm

If you have human sequence, you can find easily all the info on Human Genome web page including splicing variants etc. :wink:
Do you have some locus ID or something?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
User avatar
JackBean
Inland Taipan
Inland Taipan
 
Posts: 5652
Joined: Mon Sep 14, 2009 7:12 pm

Re: How can I work out the amount of DNA coding in a region

Postby asis2 » Thu Jan 14, 2010 4:42 pm

yep - I have the names of all the genes (about 300) included as well as the coordinates of the whole region chr16:1030000-5162000.

Thanks!
asis2
Garter
Garter
 
Posts: 3
Joined: Mon Jan 04, 2010 2:40 pm


Return to Genetics

Who is online

Users browsing this forum: No registered users and 1 guest

cron