Alignment of recombination junctions between HIV-lhNef and AS escape variants

<p><b>Copyright information:</b></p><p>Taken from "Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1"</p><p>Nucleic Acids Research 2006;34(8):2206-2218.</p><p>Published online 2 May 2006</p><p>PMCID:PMC1456326.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> In all alignments, the upper sequence represents HIV-lhNef and the lower sequence the AS escape variant. Escape variant AS44 evolved further into AS15 and both are presented in the same alignment. The middle sequence in the AS11, AS8 and AS19 alignments is the antisense sequence of the tRNA that is inserted in the viral genome. Homologous sequences between the tRNA and HIV-lhNef are boxed in blue, the UGG sequences at recombination junctions are shaded in grey, repeated sequences at the recombination junctions of HIV-lhNef and the AS mutants are underlined. The vertical lines between the sequences indicate identity. Slashes represent sequences that are not shown. Deleted sequences are presented as dashes, asNef sequences are bold caps, Nef sequences are normal caps, tRNA sequences are bold lower-case italics. Nucleotide numbers above the upper sequence refer to the position on the genomic HIV-1 RNA transcript, with +1 being the capped G residue. Numbers in the middle sequence of the lower three panels refer to tRNA positions