Fig. 1.

iSINEs are less abundant than dSINEs in the human genome. a The proportional distribution of genome and “Aluome” to genic, intergenic, exonic and intronic partitions and different types of exons are shown. Alu elements are almost equally distributed to genic and intergenic regions. Within genic regions, however, a strong accumulation in non-coding regions, such as introns, 3′ UTRs, or non-coding RNAs, can be observed. b Comparison of the number of Alus in the genome in genic and intergenic regions. A large fraction of Alus accumulates in clusters, which are defined as a set of neighboring Alus that are at most 300 nucleotides apart from one another. Single SINEs (sSINE) thus have no other Alu in their vicinity. Pairs are clusters of size 2 and are further divided into dSINEs (direct tandem SINEs) and iSINEs (inverted SINEs). Based on their relative orientation to one another, iSINEs are grouped into tiSINEs (tail-to-tail) and hiSINEs (head-to-head). Clearly, iSINEs are less abundant than dSINEs