Initiation codon which is not ATG

Brian Foley btf at lanl.gov
Thu Mar 25 15:46:57 EST 1999

Neil McEwan wrote:

> Can anyone else supply evidence of additional initiation codons. 

	We have numerous HIV-1 and HIV-2 genomic sequences where
point mutations are found in the ATG start codons.  I can not
guarantee that all of them are known to be functional in vivo.
In many cases, the ATG -> ACG or similar mutation may in fact
just represent a sequencing error.  In other cases, the viral
genome that was sequenced my be defective and not produce the 
protein, or produce it in lower quantities than would be made
from an ATG start codon.

	In your case, I would recommend analyzing the similarity
between your sequence and others of this protein family and
see if it is as high between this "defective" start codon and
the next ATG, as it is in the coboxy-terminal region of the
protein.  If the DNA/protein sequence is being conserved in
this region by purifying selection, then you can assume that
either the "defective" start is being used, or that the defective
start is simply a sequencing or PCR error.

|Brian T. Foley               btf at t10.lanl.gov                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos National Lab      http://hiv-web.lanl.gov/index.html     |
|Los Alamos, NM 87544  U.S.A. http://www.t10.lanl.gov/~btf/home.html |

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