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