Genome
The genome has 9,762 nucleotides and encodes 2 nonstructural polypeptides (p150 and p90) within its 5′-terminal two-thirds and 3 structural polypeptides (C, E2, and E1) within its 3′-terminal one-third. Both envelope proteins E1 and E2 are glycosylated.
There are three sites that are highly conserved in togviruses: a stem-and-loop structure at the 5' end of the genome, a 51-nucleotide conserved sequence near the 5' end of the genome and a 20-nucleotide conserved sequence at the subgenomic RNA start site. Homologous sequenes are present in the rubella genome.
The genome encodes several non-coding RNA structures; among them is the rubella virus 3' cis-acting element, which contains multiple stem-loops, one of which has been found to be essential for viral replication.
The only significant region of homology between rubella and the alphaviruses is located at the NH2 terminus of non structural protein 3. This sequence has helicase and replicase activity. In the rubella genome these occur in the opposite orientation to that found in the alphaviruses indicating that a genome rearrangement has occurred.
The genome has the highest G+C content of any currently known single stranded RNA virus (~70%). Despite this high GC content its codon use is similar to that of its human host.
Read more about this topic: Rubella Virus