Junction sequences and the probable target sites of R1 elements inserted outside the 28S genes. The inferred uninserted target sequence is shown at the top of each example. Boxed sequences indicate R1, bold uppercase sequences are identical to 28S sequences, and bold lower case nucleotides are non-templated nucleotides. (a) Insertion sites in which both 5' and 3' junctions of the R1 element were recovered; 2 to14 bp target site duplications were created by the insertions and are delineated by vertical dotted lines. (b) Insertion sites in which only the 5' junction with R1 was recovered. (c) Insertion sites in which only the 3' junction with R1 was recovered. Junctions come from the following species: D. pseudoobscura, examples 1, 4 and 11; D. mojavensis, example 2; D. persimilis, examples 3 and 12; D. sechellia, examples 5, 8, 9 and 10; D. yakuba, example 6; D. ananassae A, example 7; D. virilis, example 13. M, melanogaster-type R1 elements; A, ancestral type R1 elements.
Stage and Eickbush Genome Biology 2009 10:R49 doi:10.1186/gb-2009-10-5-r49