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.
