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Splice-site consensus exceptions

GORDON SIMPSON gordon.simpson at bbsrc.ac.uk
Wed May 7 10:42:53 EST 1997


To the Arabidopsis Community,

This is an "advertisement" for a new page on AtDB dedicated to
reporting Arabidopsis introns with non-canonical splice sites:

http://genome-www.stanford.edu/Arabidopsis/splice_site_excep.html

Almost all introns in Arabidopsis mRNA genes (as for all
eukaryotes) are flanked by the sequences /GT-AG/.  However, it
has recently become apparent that rare exceptions to this rule
exist.

One exception is characterised by the non-canonical splice-site
sequences /AT-AC/.  Recently, significant progress (working with
mammalian systems) has been made in dissecting the mechanism by
which these introns are processed.  It is now clear that introns
bearing the properties of AT-AC class introns are present in
Arabidopsis.

A second exception (and so far unique) is the HAC1 gene of yeast.
Here a pre-mRNA intron bearing non-canonical splice sites appears
to be processed by a novel mechanism that may involve tRNA
ligase.

I have provided details to AtDB - which David Flanders has put
onto a page - giving details of exceptions to the GT-AG rule for
splice site consensus sequences.  The page is designed to provide
a "pointer" as to what to look for if you think a gene you are
characterising has unsual intron border sequences.  I hope to
collate any such exceptions found and update the page accordingly
for ready access to the Arabidopsis community.

The page can be found in AtDB, under the "AtDB Services &
Features" section:

http://genome-www.stanford.edu/Arabidopsis/splice_site_excep.html

Gordon Simpson
The John Innes Centre
Colney
Norwich
U.K.
email:- gordon.simpson at bbsrc.ac.uk






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