5.8S rRNA gene - help (Jun/06/2005 )

hi,
can anybody tell me how can I recognize the beginning of the 5.8S in a mixed seq? I mean that I've used a universal primer (Hillis & Dixon, 1991) from 3' 18S to 5' of 5.8S, and I found the beginning of the ITS1 (my target) but I'm not sure where the ITS1 finish and start the next piece of the gene, cause my original seq was not so clean, and of course the end of the seq is orrible...
thank you
caffy

5.8S -->
151
Foxv AAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAG

Fsam AAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAG


Foxv CAAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATC

Fsam CAAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATC

300
Foxv TTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGA

Fsam TTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTTCGA

This is the 5.8s sequence of a couple of different fusarium. Since the 5.8s region is fairly conserved it might help you determine where your 5.8s sequence begins depending on the organism you are looking at.

Its typically a 150 bases long and 150 bases from where ITS1 starts. But thats based on my experience when working with Fusarium and Candida. You might try the NCBI website and look up the region sequence based on your organism.

thank you so much, I'll try