Science Buddies: "Ask an Expert"

Does anyone know how to access intron sequences on internet databases? I've tried to use BLAST to find intron sequences, but I don't really know how to use BLAST. Could someone help me use BLAST or some other database that can return intron sequences?? THANKS!

Oh, and it's really crucial that the sequences be intronic.. not exonic. Thank you again,

juggernaut4

Hi jugernaught4:

Here are some sites that might help:

http://mips.gsf.de/proj/yeast/reviews/i ... ethod.html

http://nar.oxfordjournals.org/cgi/conte ... ?ck=nck#F2

http://www.soe.ucsc.edu/pipermail/genom ... 09515.html

sounds like you are doing a really cool project. Hope it turns out well!

Best Regards,

Barrett Tomlinson

Hi juggernaut,

Basically, an intron is something that's in the DNA but not in the protein. So, what you might do is this:

Take your DNA sequence, and translate it into amino acid code (there are online tools that will do this for you).

Then, look up the actual amino acid code of the protein.

Whatever's in the DNA, but not protein, that's your introns.

Good luck.

Hello Jauggernaut,

You haven't mentioned what you would like to use the intron sequences for. Are you interested in the junctions, the entire intron sequences, the lengths or some other aspect of the introns? There are databases out there but how you use them may dictate which one might be the most appropriate.

BLAST is a sequence alignment tool. If you have a sequence to compare to then you can use BLAST to relate a second sequence to it. The issue with introns is that they tend not to be very conserved so alignments are difficult to do. The most conserved regions are at the junctions (splice donor and splice acceptor) and there is some minimal conservation at the branch point.
http://www.sumanasinc.com/webcontent/an ... icing.html
http://mips.gsf.de/proj/yeast/reviews/i ... icing.html

As far as databases go you might try the ExInt database (Exon Intron Database) which is a collection of the exon/intron structures from eukaryotic genes. This database includes intron sequences and the corresponding amino acid sequence (sequence junction boundries).
http://www.pubmedcentral.nih.gov/articl ... tid=102468
http://www.oxfordjournals.org/nar/database/summary/32

Good luck with your project!