Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses
Fig 8
Possible stem-loop structure in the NS intron.
Left: The displayed sequence is the H5N8 consensus sequence, with putative base pairs from manual inspection. NS1 codons 28–30 and 35–38 have high levels of constraint. The UCCU motif in the loop is complementary to the NS2 splice acceptor site; we note that some sequences contain an alternative UUCU motif (annotated in blue), which is still capable of pairing. Right: RNAalifold prediction of pairing in H7N7 sequences, using as input the region predicted by analysis of ranked constraint data. Base pairs are highlighted in deep/mid red when all/all but one sequences are capable of forming the pairs shown. Base pairs are highlighted in deep yellow when all sequences are capable of forming the pair shown or own other pair (including GU pairs). RNAalifold was used with input options disallowing lonely pairs, allowing G-quadruplexes, and with the ribosum scoring matrix enabled. The H7N7 fold was produced with the temperature set to 41°C. Other structures predicted by RNAalifold may be found in S4–S8 Figs.