intron conservation and slippage

J. David Spafford jspaffor at gpu.srv.ualberta.ca
Fri Aug 15 19:21:15 EST 1997

Hi.  I am looking for some advice.  I have cloned a voltage-gated sodium
channel gene in both its cDNA form and the full-length region covered in
genomic DNA.  I have found that the majority of the introns are conserved in
my gene and in all genes of the family.  The major differences arises in the
unconserved non-transmembranal regions of the protein.  If I do a comparison
with the sodium channel with its known ancestor, the calcium channel, I am
also finding some conservation of introns.  However, there appears to be
intron slippage, because some of the introns aren't in the exact homologous
locations.  In some cases, a poor amino-acid alignment may be the cause of
the intron slippage.  Or maybe, I am using my a priori knowledge about
kinship and trying to see a pattern of conservation that isn't present in
the data.  I have difficulty deciding whether  I should consider one to ten
bp slippage of an intron location warrant defining an intron as homologous
orb non-homologous.

Thanks in advance,

J. David Spafford
Department of Biological Sciences,
University of Alberta, Edmonton, Canada.

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