how to find intron - (Jul/27/2005 )

Hello,

I have sequenced some PCR products. Now I want to know that it has intron or not. If it has intron, how can i find them? please teach elaborately to me. Mroeover, I would like to know about ORF. How can i find them

Thank you very much

-hyperkid-

Hi there,
There a few ways to do this
1) look for the conserver intron exon juction seq
2) manually compare a genomic seq verse the cDNA seq
or 3)use bioinformatic software like macvector or free tools like from NCBI. NCBI has some basic, but good, tools you can play with. As for an ORF finder, try

http://www.ncbi.nlm.nih.gov/gorf/gorf.html

HTH

Jeff

QUOTE (hyperkid @ Jul 27 2005, 07:05 AM)

-jeng-

Hello, Jeng
Thanks for your suggestion. I will try to do as follow your guideline.

-hyperkid-

QUOTE (hyperkid @ Jul 27 2005, 05:05 AM)

Align ESTs or cDNAs to you gene can identify introns.

-cyberpostdoc-

hi
i just thought what if there are exones but introns as well, is there a way to know where the exone end and intron begins?
cheer
chandima

-chandima-

QUOTE (chandima @ Aug 20 2005, 07:02 AM)

hi
i just thought what if there are exones but introns as well, is there a way to know where the exone end and intron begins?
cheer
chandima

Yes, if you align EST/cDNA to genomic sequence, you can identify exon/intron boundary easily, unless there are intron retention complicated cases.

Also statistics show that there are nucleotide bias at the junctions, usually is AG... GT (not sure if I remember it right, but there is a paper show that it is >80% of the cases).

-cyberpostdoc-