Linear Group II Intron Retrohoming in Drosophila Figure 4. Sequences of 59-integration junctions from linear intron RNA retrohoming in wild-type and mutant strains. 59-integration junctions of DNA extracted from 80 pooled embryos for each strain were amplified by PCR, as described in Figure 3, then TOPA-TA cloned, amplified by colony PCR, and sequenced, as described in Materials and Methods. (A) wild-type w1118; (B) lig42; (C) ku702; (D) lig42; P{lig4+}; (E) wild-type Or-R; (F) polQ2. Inserted or mutant nucleotide residues are shown in lower case letters; microhomologies between intron and exon end sequences prior to ligation are shown in parentheses; and inserted sequences that match or are complementary to nearby 59-exon or intron sequences are underlined. Freq., frequency of occurrence. doi:10.1371/journal.pgen.1002534.g004 PLoS Genetics | www.plosgenetics.org 6 February 2012 | Volume 8 | Issue 2 | e1002534