introns-exons starts and ends.

Arlin Stoltzfus arlin at is.dal.ca
Fri Aug 27 20:16:38 EST 1999

On 25 Aug 1999, Mary K. Kuhner wrote:

> I've seen the argument made that break-at-codon-boundaries introns
> are a bit more common than the other two kinds:  this is used as
> an argument in favor of introns as a shuffling mechanism.  I don't
> know if the observation has held up to additional sequences.

For the organisms most commonly represented in sequence databases, 
the proportions are something like 45% phase 0 (between codons), 35%
phase 1, 20% phase 2. There is some between-taxon heterogeneity 
in these proportions, but the numbers are based on 100's or 
1000's of introns so the non-uniformity is beyond question. 

Just about anything that has ever been observed about introns 
has been used as an argument for an ancient exon-shuffling 
theory, and this is no exception.  The argument might make 
more sense if it were shown that phase 0 introns were more 
likely to be widely distributed (thus by inference older).  

The alternative has always been that the non-uniformity of 
intron phases is a consequences of the non-uniform phase 
distribution of the sequences taht introns jump into, which 
is by consensus something like (C/A)AG^G.  The basic 
principle here is that any arbitrary target sequence, e.g., a 
HindIII site, will be non-uniformly distributed with respect 
to reading frame because nucleotides are non-uniformly distributed 
with respect to reading frame.  Long, et al. (PNAS paper 
about 1.5 years ago) ecently provided evidence for this 
target-sequence hypothesis. 


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