Research Paper Volume 12, Issue 16 pp 15978—15994

Figure 5. Graphical representation of MMTVenv-like amplicons compared to exogenous and endogenous betaretroviruses. The ENV1-C/ENV1-T (panel A) and ENV2 (panel B) amplicons were mapped to the HMTV env reference sequence and compared with the latter and to other reference sequences representative for exogenous and endogenous betaretrovirus env gene in a multiple nucleotide alignment. For each sequence, grey bases represent residues that were identical to the reference HMTV, while colored residues indicate single nucleotide changes to A (red), C (blue), G (yellow), and T (green). All the three amplicons presented very few nucleotide substitutions with respect to MMTV (1 discordant nucleotide for ENV1-T and 0 for both ENV1-C and ENV2) and HMTV (2 discordant nucleotides for ENV1-T, 3 for ENV1-C and 11 for ENV2). The presence of predicted functional domains in HMTV portions corresponding or near the env amplicons is also annotated: Heptad Repeats 1 and 2 (HR1 and HR2, respectively) and immunosuppressive domain (IS). N.B. in the ENV2 alignment, JSRV is not present due to the absence of any shared nucleotide sequence.