BACKGROUND: The vast majority of the 1.1 million Alu elements are 
retrotranspositionally inactive, where only a few loci referred to as 'source 
elements' can generate new Alu insertions. The first step in identifying the 
active Alu sources is to determine the loci transcribed by RNA polymerase III 
(pol III). Previous genome-wide analyses from normal and transformed cell lines 
identified multiple Alu loci occupied by pol III factors, making them candidate 
source elements.
FINDINGS: Analysis of the data from these genome-wide studies determined that 
the majority of pol III-bound Alus belonged to the older subfamilies Alu S and 
Alu J, which varied between cell lines from 62.5% to 98.7% of the identified 
loci. The pol III-bound Alus were further scored for estimated 
retrotransposition potential (ERP) based on the absence or presence of selected 
sequence features associated with Alu retrotransposition capability. Our 
analyses indicate that most of the pol III-bound Alu loci candidates identified 
lack the sequence characteristics important for retrotransposition.
CONCLUSIONS: These data suggest that Alu expression likely varies by cell type, 
growth conditions and transformation state. This variation could extend to where 
the same cell lines in different laboratories present different Alu expression 
patterns. The vast majority of Alu loci potentially transcribed by RNA pol III 
lack important sequence features for retrotransposition and the majority of 
potentially active Alu loci in the genome (scored high ERP) belong to young Alu 
subfamilies. Our observations suggest that in an in vivo scenario, the 
contribution of Alu activity on somatic genetic damage may significantly vary 
between individuals and tissues.