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intron position verses sequence alignment

Kristin Bilyeu lastnamefirstinitial at missouri.edu
Thu Aug 23 17:43:05 EST 2001

I am interested in understanding the evolution of a plant enzyme, but the
problem keeps getting more complex to me.  I was hoping this group might be
able to discuss the details and perhaps point me in some new directions.
The situation is this: there are seven genes that appear to code for this
enzyme in Arabidopsis, of which I know that at least four have enzymatic
activity.  Six of these seven genes have four introns at conserved positions
within the peptide sequence and the other is missing one of these introns.
The one with the missing intron appears to lack an N-terminal signal peptide
while the other six appear to contain a signal peptide.  The nucleotide
sequences do not align very well, but the peptide sequences do to a better
degree.  So my first question is how I can integrate the intron conservation
with peptide identity to understand relatedness?  Is there a generalization
for the weight of conserved intron position verses peptide identity?
Next, there are some monocot plants with versions of this gene as well.  For
instance, in maize, there is genomic sequence of an active enzyme that
shares the first and last intron with the Arabidopsis genes (plus it
contains an N-terminal signal peptide).  In rice, I have identified
sequences that have genomic organization like the arabidopsis genes, some
like the maize gene, and some look in between in terms of having/lacking
introns.  Is there any way I can put some of this information together to
get an understanding of evolution of this gene family in plants?
Suggestions or discussion would be greatly appreciated.  My apologies for
the length of this post.

Kristin Bilyeu
Department of Agronomy
201 Waters Hall
University of Missouri
Columbia, MO 65211


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