Finding the Introns, Exons, Donors, and Acceptors of a DNA Sequence ?

Question

[reeki]

I am currently working on the following sequence trying to identify exons and introns using the GT-AG rule as a marker for when an intron starts/end. How can I also identify acceptors and donors ? Is there any rule like the GT-AG rule ? Thanks for any help.

[natasha.sernova]

If I were you I would look at this scheme and a paper:

A schematic view:

here authors determine donor and acceptor sites:

http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/splicing/

Relatively old classical paper url is below:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC113136/

"It is possible that the only GT-AG, GC-AG and AT-AC pairs

can recruit the splicing machinery effectively and the other

non-canonical pairs could function exclusively in association

with a canonical pair, which shares its properties with the neighbour,

as some kind of parasitic splice sites". This is a conclusion from the paper

mentioned above.

I've found a webserver, and it looks much younger then the paper mentioned above:

http://www.ncbi.nlm.nih.gov/pubmed/19429896

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals.

You can use it.

I've found a very recent paper from 2015,

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675715/

its authors also suggest some tools, so you have a choice what to try.

I have not noticed the following post, so you can also use well-known prediction tools,

like Augustus or FGenesh. Urls for them are within the post below.

Gene Prediction

Good luck!

Answer 1

[natasha.sernova]

It's a probable answer, it is the same as my comment.

If I were you I would look at this scheme and a paper:

A schematic view:

here authors determine donor and acceptor sites:

http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/splicing/

Relatively old classical paper url is below:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC113136/

"It is possible that the only GT-AG, GC-AG and AT-AC pairs

can recruit the splicing machinery effectively and the other

non-canonical pairs could function exclusively in association

with a canonical pair, which shares its properties with the neighbour,

as some kind of parasitic splice sites". This is a conclusion from the paper

mentioned above.

I've found a webserver, and it looks much younger then the paper mentioned above:

http://www.ncbi.nlm.nih.gov/pubmed/19429896

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals.

You can use it.

I've found a very recent paper from 2015,

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675715/

its authors also suggest some tools, so you have a choice what to try.

I have not noticed the following post, so you can also use well-known prediction tools,

like Augustus or FGenesh. Urls for them are within the post below.

Gene Prediction

Good luck!