The MLV genome. The viral RNA in Moloney MLV is 8332 nt in length [18]. “R” sequence, 68 nt in length, is identical at both ends of the RNA. The 5′ copy of R is followed by U5 sequences and then by the PBS (nt 146–163). The long 5′ untranslated region in the RNA also includes the ψ packaging signal; contained within this signal in some MLV isolates is the CUG codon at which glyco-Gag translation is initiated (nt 357). The initiation codon for the “normal” Gag protein is at nt 621. The gag and pol coding sequences are in the same frame; they are separated by a UAG termination codon, which in turn is followed immediately by a 57-base signal, including an RNA pseudoknot, inducing the inefficient translation of the UAG as glutamine. The Env protein is translated from a spliced mRNA. The polypurine tract (PPT, nt 7803–7815) is the primer for +-strand DNA synthesis and is followed by the U3 and R regions. U3 (nt 7816–8264) is placed at the 5′ end of the DNA copy of the genome synthesized during infection; it contains promoter and enhancer sequences governing the initiation of transcription at the beginning of R.
