A very conserved pseudoknot structure has been shown to fold in influenza virus RNA. The pseudoknot encompasses the 3′ splice site of segment 8 RNA in both influenza A and B viruses. By sequence comparison of influenza virus strains, we derive a consensus motif that defines a novel RNA pseudoknot family. The orientation of the coaxially stacked stems in the influenza pseudoknot differs from that in classical H-pseudoknots. Apart from the size of the loops, the topology of the influenza pseudoknot resembles that of some long-range pseudoknotted conformations. A seed alignment of the influenza pseudoknot family, containing representative strain sequences together with a consensus structure description, has been submitted to the RNA families (Rfam) database.

Influenza, Influenza virus A, Influenza virus B, RNA pseudoknot, RNA secondary structure, RNA virus, Splicing, article, gene sequence, nonhuman, nucleotide sequence, phylogenetic tree, protein conformation, protein motif, protein structure, virus RNA, virus gene
dx.doi.org/10.4161/rna.7.2.11287, hdl.handle.net/1765/20356
R N A Biology
Erasmus MC: University Medical Center Rotterdam

Gultyaev, A.P, & Olsthoorn, R.C.L. (2010). A family of non-classical pseudoknots in influenza A and B viruses. R N A Biology, 7(2), 125–129. doi:10.4161/rna.7.2.11287