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Odd DNA sequence

Martin Kennedy mkennedy at chmeds.ac.nz
Wed Jul 20 20:21:21 EST 1994

Hi all,

I need some advice about a peculiar DNA sequence that we have tripped over, 
while sequencing a  mouse genomic clone.  The structure we have found is a 
tandem,  directly repeated DNA sequence, of at least 30bp, that is separated 
by  a poly (AG) microsatellite sequence.

It looks something like this:

-------------------------> CTCT..(15 repeats)..CTCT ------------------->

When lined up, the direct repeats match at about 27/30 nucleosides.

Does this structure look like anything to anyone? Could it be a retroviral/DNA 
virus insertion site?  BLAST searches don't come up with much.  I'd be 
grateful for any comments/advice about what this could be, other than some 
spurious evolutionary hiccup created to confuse molecular biologists!



NNNN   NN  Martin A Kennedy (E-mail = mkennedy at chmeds.ac.nz)  ZZZZZZZ  
NN NN  NN       Cytogenetic and Molecular Oncology Unit          ZZZ
NN  NN NN           Christchurch School of Medicine            ZZZ
NN   NNNN              Christchurch, New Zealand              ZZZZZZZ
	      Phone (64-3)364-0880  Fax (64-3)364-0750

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