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. 2014 Apr 21;9(4):e95633. doi: 10.1371/journal.pone.0095633

Figure 1. Alignment of modern and museum koala retrovirus sequences, showing positions of proviral genes and proteins.

Figure 1

Upper Panel: Character states matching the reference sequence (AF151794) are indicated in light grey, while mismatches (position 312) or polymorphisms (all other positions) are shown as black hatch marks. The infectious clone KV522 (AB721500) is the first sequence below the reference. The aligned sequences all display open reading frames for viral gag, pol, and env regions, except that polymorphisms at three positions in the museum samples code for a stop codon that would disrupt an open reading frame; these are indicated by red hatch marks. Green lines represent polymorphisms that could be placed in phase in overlapping sequence reads. Lower Panel: The coded proteins are indicated, following the divisions proposed by Hanger et al. (2000) relative to the polymorphism alignment. The positions of the SRLPIY domain potentially involved in viral infectivity of the GAG protein and p10 domain (Gag assembly and nuclear export signal, respectively) are indicated. Likewise, the Env motif CETTG, and p15E transmembrane envelope protein are indicated. Regions known to be divergent in Japanese isolates, KoRV-B and KoRV- C, and KoRV-D [12], [40], are indicated by orange, purple, and green arrows, respectively.