Evolutionary remnants in non-coding regions

Arlin Stoltzfus arlin at is.dal.ca
Thu Oct 16 20:09:12 EST 1997

newsmgr at merrimack.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.

It would clearly be valid to suggest (1) if you can show that 
the nucleotide sequence or pseudo-inferred amino acid sequence 
has significantly non-random similarity to the sequences that 
you think may be homologous to it.  With respect to (2) you can 
align the aa sequences using any alignment program by replacing 
the stop codon with some dummy residue (preferably "X", just 
make sure that the alignment program won't choke on this).  
But just making an alignment doesn't tell you that the sequences 
are homologous-- even non-homologous sequences can be aligned.
Russ Doolittle has some programs for producing
randomly scrambled alignments that can be used to judge if an 
alignment is significant (= indicative of homology).  Also, 
the FASTA package has some relevant statistics for this.  

With respect to (3), there are examples of the converse, i.e., 
non-translated sequences being recruited into coding regions 
(e.g., J Mol Evol 30(6):479-488; or Science 260:91-95 (1993)).  
If my memory serves me, there are multiple cases where a shortened 
protein is produced as a developmental option implemented 
by alternative splicing (or, in the case of a mammalian 
apolipoprotein B gene, RNA editing), but these are usually 
(always?) truncated at the 3' end, not the 5'.  I can't recall 
of any cases just like yours, but perhaps someone else out there 
knows of one.  

Arlin Stoltzfus, Ph.D. (arlin at is.dal.ca)
Department of Biochemistry, Dalhousie University
Halifax, Nova Scotia B3H 4H7 CANADA
phone: 902-494-2968     fax: 902-494-1355

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