Evolutionary remnants in non-coding regions

newsmgr at merrimack.edu newsmgr at merrimack.edu
Fri Oct 17 17:54:25 EST 1997

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Newsgroups: bionet.molbio.evolution
Subject: Re: Evolutionary remnants in non-coding regions
Message-ID: <bernster.1227474789A at>
From: bernster at fcrfv1.ncifcrf.gov (bernstein, rm)
Date: Fri, 17 Oct 97 11:19:09 GMT
References: <343E309E.2861C67C at bc.edu>
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In Article <343E309E.2861C67C at bc.edu>, Charlie Hoffman <hoffmacs at bc.edu> wrote:
>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.

well, i think that #1 may be a good working hypothesis; certainly 5'
irregularities arent that uncommon, especially as you proceed thru
phylogeny.  for #2, i would use the GCG package, esp the program FRAMEALIGN.
using this program, you can align your nucleic acid sequence w/ a known
protein sequence.  in my experience w/ FRAMEALIGN, it doesnt care about 1 or
2 stop codons: theyll just be gapped over.  and as to #3, the only examples
like yours that i can think of are unfort 3' examples, e.g., a readthru.   
regards, ralph

RM Bernstein
bernster at FCRFV1.NCIFCRF.GOV
Bld#29a Rm. 2b09
Bethesda Maryland 20892

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