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From: colby@bu-bio.bu.edu (Chris Colby)
Newsgroups: sci.bio
Subject: Re: Alu locations
Keywords: alu sequences
Message-ID: <70131@bu.edu.bu.edu>
Date: 6 Dec 90 01:53:13 GMT
References: <1965@fcs280s.ncifcrf.gov>
Sender: news@bu.edu.bu.edu
Reply-To: colby@bu-bio.UUCP (Chris Colby)
Organization: Biology Dept., Bost
Lines: 27

In article <1965@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
>Hi everyone!
>
>A friend of mine, Doug Halverson, has cloned several pieces of human DNA and
>has found that they don't all have Alu sequences in them.  His question is, in
>human genes that have been mapped or sequenced so far, have stretches of DNA as
>long as 10 to 20 kb been found to be Alu free?

	Is this a trick question? Why don't you just do a restriction
digestion with the enzyme Alu1 (for which the Alu site was named I'm
led to believe). Look and see if you get any DNA larger than 20 kB.

	Of course since an Alu sequence is 300 bp long (I just opened
my copy of Watson and looked it up) Alu1 will cut at some sites that
are not Alu sequences. This is because Alu1 has a 4bp recognition
sequence. Watson sez: Alu sequences are present in more than a million
copies and represent 3 - 6 percent of the genome. Any 5000 bp segment
will probably contain one because they are widely distributed. 

>  Tom Schneider
>  National Cancer Institute
>  Laboratory of Mathematical Biology
>  Frederick, Maryland  21702-1201
>  toms@ncifcrf.gov

Chris Colby
email: colby@bu-bio.bu.edu