GENEALOGY-DNA-L ArchivesArchiver > GENEALOGY-DNA > 2007-07 > 1185196935
Subject: Re: [DNA] Heteroplasmy - U5s
Date: Mon, 23 Jul 2007 09:22:15 EDT
In a message dated 7/22/2007 7:58:27 PM Pacific Daylight Time,
> It is curious that the 524 location is so prone to insertions
> and deletions. I wonder if it has anything to do with the
> configuration of the molecule at that location. If there are
> deletions at 524, then there almost never are any further
> deletions and the 315.1c always seems to be present.
> Is that because the molecule would be destabilized by
> further gaps (deletions)? I wonder what makes this 524 area
> so prone to breaks. You mentioned the poly-CA.
> I see all the "caca"s present: cagcacacac acaCcgctgc.
> The upper case C is site 524.
The repeated CA motif is like Short Tandem Repeats (STRs) on the Y
chromosome, and as we know, the mutation rate for STRs is relatively high compared to
SNPs (Single Nucleotide Polymorphisms, where one base is substituted for
another). The mutation mechanism is sometimes called "replication slippage" -- as if
the enzyme loses track of how many times it's copied a pattern already. The
longer the repeat pattern, the more likely that is. Perhaps when one deletion of
a CA motif occurrs, the section is so short that slippage is less likely.
Here's an illustration:
The observation about 315.1 is true, but it's a red herring, as most
sequences have that. It is the CRS that has the rare version, with 5 C's in a row
instead the more typical 6 C's. But since we name everything relative to the CRS,
we say there's an insertion.
Get a sneak peek of the
all-new AOL at http://discover.aol.com/memed/aolcom30tour