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closeone million copies of AluY?
Posted by aDNAn on 17 Feb 2011 at 05:26 GMT
This is a minor detail, but I think that the article contains a mistake regarding the number of AluY elements:
"AluY belongs to the primate specific class of short nucleotide elements (SINEs) and was chosen because of its abundance in the human genome (over 1 million copies [6])"
I've just double-checked, and of the 1.2 million Repeatmasker Alu annotations in hg19, only 10% are "AluY" and another 2% variants of AluY. The reference in question (Deininger and Batzer) does not mention AluY specifically.
RE: one million copies of AluY?
mlongo replied to aDNAn on 17 Feb 2011 at 17:50 GMT
Please refer to the Deininger and Batzer reference page 1460, Table 1.
RE: RE: one million copies of AluY?
mlongo replied to mlongo on 17 Feb 2011 at 18:10 GMT
As for AluY vs Alu, we used AluY because of it being a more recently mobile element in the primate lineage (knowing there weren't 1 mil AluY's but were that many Alu's). Our initial screen with the AluY was with very low stringency to catch other Alu's as well as AluY's. These were then independently examined and adjacent, nonrepetitive sequence was mapped to a single locus in the human genome.