Figure 4. Sequences of 5′-integration junctions from linear intron RNA retrohoming in wild-type and mutant strains.

5′-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) lig4 ⁻; (C) ku70 ⁻; (D) lig4⁻; P{lig4⁺}; (E) wild-type Or-R; (F) polQ ⁻. 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 5′-exon or intron sequences are underlined. Freq., frequency of occurrence.