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. 2011 Nov 2;40(4):1666–1683. doi: 10.1093/nar/gkr863

Figure 6.

Figure 6.

The nucleotide profile of SVAE de novo insertion sites resembles the consensus target sequence of pre-existing human-non-LTR retrotransposons. Target sequence logos were generated by multiple sequence alignments of genomic integration sites of L1Hs-Ta, AluYa5, SVAA and SVAE insertions using the program WebLogo (35). Logos for the top strand sequence cover four nucleotides of upstream and eight nucleotides of downstream sequences relative to the L1 EN cleavage site (arrow) on the bottom strand. Numbers denote nucleotide positions relative to the nicking site. (A) Comparison of consensus target sequences of L1 and SVAE de novo insertions. Target sequence logos were generated for SVA de novo integration sites (n = 11) and for target sequences of 35 L1 de novo insertions (43). (B) Target sequence logos of 70 preexisting L1-Ta, AluYa5 and SVAE/F insertions. Integration site sequences were identified as described in the ‘Material and Methods’ section.