Alu elements comprise >10% of the human genome. We have used a computationa
l biology approach to analyze the human genomic DNA sequence databases to d
etermine the impact of gene conversion on the sequence diversity of recentl
y integrated Alu elements and to identify Alu elements that were potentiall
y retroposition competent. We analyzed 269 Alu Ya5 elements and identified
23 members of a new Alu subfamily termed Ya5a2 with an estimated copy numbe
r of 35 members, including the de novo Alu insertion in the NFI gene. Our a
nalysis of Alu elements containing one to four (Ya1-Ya4) of the Ya5 subfami
ly-specific mutations suggests that gene conversion contributed as much as
10%-20% of the variation between recently integrated Alu elements. In addit
ion, analysis of the middle A-rich region of the different Alu Ya5 members
indicates a tendency toward expansion of this region and subsequent generat
ion of simple sequence repeats. Mining the databases for putative retroposi
tion-competent elements that share 100% nucleotide identity to the previous
ly reported de novo Alu insertions linked to human diseases resulted in the
retrieval of 13 exact matches to the NFI Alu repeat, three to the Alu elem
ent in BRCA2, and one to the Alu element in FGFR2 (Apert syndrome). Transie
nt transfections of the potential source gene for the Apert's Alu with its
endogenous flanking genomic sequences demonstrated the transcriptional and
presumptive transpositional competency of the element.