Fig. 6

SVA elements in the NPLOC4 and CABIN1 genes. a Inter-species alignments of the pre-integration and SVA-containing loci in the NPLOC4 and CABIN1 genes. Only the 5′ and 3′ ends (separated by a green spacer) of the SVA elements are shown. Target site duplications (TSDs) are highlighted in yellow. The “g” highlighted in the human element is untemplated and can be attributed to capping of the SVA RNA. nleu – Nomascus leucogenys; pabe – Pongo abelii; ggor – Gorilla gorilla; hsap – Homo sapiens; mfas – Macaca fascicularis (b) Comparison of the TSDs of the elements integrated into the NPLOC4 gene to the inferred pre-integration site (PIS) and across species. 5′ and 3′ indicate the 5′ and 3’ TSDs, respectively. Mutations in the orangutan TSDs are highlighted in yellow and red. The substitution distinguishing the human/chimpanzee TSDs from the PIS is underlined. c Integration of SVAs into the NPLOC4 locus occurred close to an Alu internal A tract. In the course of evolution insertion of an AluSx was followed by retrotransposition of an AluY directly downstream of the AluSx internal A tract. A position one nucleotide downstream of the AluY internal A tract was then targeted by the SVA insertion. Only the SVA_D insertion present in humans and chimpanzees is shown. Target sites and target site duplications are shown in red