| Popis: |
Additional file 2: Figure S1. Reference (hg19) and amplicon sequence of human SVA_E H8_43. Binding sites of amplification primers are highlighted in yellow; Alu-like domain and SINE-R are highlighted in green; the amplicon part marked in red could not be resolved using Sanger sequencing. Target site duplications are italicized and underlined. Figure S2. Reference and amplicon sequences of orangutan SVA OU3. Binding sites of amplification primers are highlighted in yellow; Alu-like domain and SINE-R in green. Target site duplications are italicized and underlined. The 3′ transduction is highlighted in grey (not included in the re-amplification product). Figure S3. Reference and amplicon sequences of orangutan SVA OU4. Binding sites of amplification primers are highlighted in yellow; Alu-like domain and SINE-R in green. Target site duplications are italicized and underlined. Figure S4. The minimal polyA signal used in the mneoM cassette facilitates correct polyadenylation of neo cDNA. 3′ RACE analysis to assess correct polyadenylation of the neomycin phosphotransferase gene using the minimal functional polyA signal [25]. The minimal polyA signal (pGL3-derived) was tested downstream of an SV40 promoter-driven neomycin phosphotransferase cDNA. The stop codon is shown in red; the polyA signal and GU-rich tract are underlined. The polyA signal mediating premature polyadenylation of elements upstream of the reporter cassette is italicized and underlined. The stop codon is shown in red; the polyA signal and GU-rich tract are underlined. The polyA signal mediating premature polyadenylation of elements upstream of the reporter cassette is italicized and underlined. Figure S5. Human SVA H8_43 mneoM de novo integrations. The L1 endonuclease cleavage site on the bottom strand is indicated in blue. Extra G residues at the 5′-ends of the insertions are shown in green; target site duplications in red. Neo – neomycin phosphotransferase gene. Table S6. Sequences of oligonucleotides used in amplification and re-amplification of human and orangutan SVA elements. Restriction enzyme recognition sites present in the re-amplification primers are underlined. |
