Consensus pSIVgml genome. Horizontal lines above the scale-bar indicate the relative coordinates of the contigs derived from whole genome shotgun (WGS) sequences and PCR amplicons that were used to construct the consensus genome. WGS contig 2 contained a region of indeterminate sequence, indicated by a dashed line. Distinct 5 base pair target site duplication (TSD) sequences located at the 5′ and 3′ flanks of proviral insertions are shown, demonstrating the presence of at least two distinct proviruses. The schematic below the scale shows the locations of ORFs and genomic features within the consensus proviral genome sequence. Circles with inset question marks indicate the possible presence of short, spliced Rev and Tat domains toward the 5′ and 3′ ends of the env gene, respectively; the general lack of sequence similarity of these regions within lentiviruses meant that it was not possible to determine whether or not pSIVgml encodes such domains. LTR, long-terminal repeat; TAR, transactivation responsive element; PBS, primer binding site; MA, matrix; CA, capsid; NC, nucleocapsid; PR, protease; RT, reverse transcriptase; RH, RNaseH; dUTP, dUTPase; IN, integrase; SU, surface glycoprotein; TM, transmembrane; RRE, Rev responsive element.