Skip to main content
. 2016 Jul 27;90(16):7046–7065. doi: 10.1128/JVI.00308-16

FIG 2.

FIG 2

Genetic variation within the C-κB and Sp1III motifs of subtype C LTR. (A) Multiple-sequence alignment of the enhancer and core promoter sequences of the subtype C LTR. The LTR sequences comprising the three NF-κB sites and three Sp1 motifs of a few representative subtype C strains deposited during the years 1989 to 2010 were downloaded from http://www.hiv.lanl.gov/. The sequence of subtype C prototype Indie C1 (GenBank accession number AB023804) was used as the reference sequence. Dots and dashes represent the sequence identity and deletions, respectively. The C-κB and Sp1III motifs are highlighted by shading and the other TFBS by square boxes. (B) Position weight matrix of the C-κB motif. A total of 1,091 subtype C U3 sequences available at the HIV sequence database (http://www.hiv.lanl.gov/) were downloaded. The sequence logo was generated using the WebLogo tool (http://weblogo.berkeley.edu/logo.cgi). (C) Position weight matrix of the Sp1III motif. The sequence logo was generated as described above.