Figure 5

R2/R1 hybrid SIDEs. (A) R1 insertions in the 28S gene in Drosophila outside the melanogaster group are flanked by a 14 bp target site duplication (arrows, upper diagram). In four species (bottom diagrams), a family of insertion elements bearing R2 ribozyme sequences (blue box) upstream of sequences with identity to R1 elements (orange box) was found in the R1 site flanked by the same 14 bp target site duplication. (B) The diagrams show the extent and level of sequence identity of each hybrid SIDE to the R1 and R2 elements in the same species. In the case of the R2/R1 SIDEs from Drosophila falleni, Drosophila innubila and Drosophila immigrans sequence identity to R1 was limited to six conserved segments found in all Drosophila R1 elements (red vertical lines; see Additional file 1). A portion of the sequence between the third and fourth conserved segments in R2/R1Dim_SIDE has 75% identity to ITS-1 of D. immigrans (green box). The lengths of the R2/R1 SIDEs are shown to the right.