Influenza A segment 7 splice site

The 3' splice site of the influenza A virus segment 7 pre-mRNA can adopt two different types of RNA structure: a pseudoknot and a hairpin.

This structured region was first discovered in a bioinformatics survey of influenza A based on thermodynamic folding free energy and amino acid codon suppression.

The 3' splice site region used to produce M2 was experimentally probed with structure-sensitive chemicals and enzymes and was found to adopt both the hairpin and pseudoknot conformations in solution.

This general trend in stability: avian, swine, human, roughly follows the temperatures at which the influenza virus reproduces within each host species.

This observation is a local instance of a global trend in influenza A coding sequences, where avian, swine, and human strains show different stability.

Figure 1. Diagram of the influenza segment 7 transcript showing the open reading frames for M1 and the spliced M2 proteins. Below left is the hairpin conformation while below right is the pseudoknot. The branch point is annotated in purple, the polypyrimidine tract in blue, the 3' splice site with a red arrow and the SF2/ASF exonic enhancer site in orange