Evolutionary remnants in non-coding regions

newsmgr at merrimack.edu newsmgr at merrimack.edu
Fri Oct 10 10:13:40 EST 1997

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Newsgroups: bionet.molbio.evolution
Subject: Evolutionary remnants in non-coding regions
Message-ID: <343E309E.2861C67C at bc.edu>
From: Charlie Hoffman <hoffmacs at bc.edu>
Date: Fri, 10 Oct 1997 08:41:51 -0500
Organization: Boston College
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I am well out of my area of expertise, so please forgive my ignorance. 
My lab has cloned a fission yeast gene that encodes a member of a
highly-conserved gene family.  The putative product is 44% identical to
a family members found from squid to human, however our protein lacks
the first 36 residues (about 10% of the protein) relative to all other
members.  Even so, if I look at the coding capacity of the 5'
untranslated region, I find properly placed codons for absolutely
conserved residues found in the larger proteins.  By "eyeball alignment"
using only two one-residue gaps I can produce 25% identity between the
"non-product" of the 5' UTR of our gene and the first 36 residues of a
mouse homolog.

Here are my questions.
1.  Is it valid to suggest that this indicates the fission yeast gene
arose from a larger "standard-length" precursor and that what I am
seeing is an evolutionary remnant?
2.  Are there computer programs that can ignore the fact that I have a
stop codon and produce a protein alignment that includes this region?
3.  Are there other examples of this phenomenon?  I do not consider this
to be the same as pseudogenes, since my protein is expressed.

I would greatly appreciate your comments.

Charlie Hoffman
Boston College
"I'd rather be fission."

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