Coronavirus 3' stem-loop II-like motif (s2m)

Coronavirus 3' stem-loop II-like motif (s2m)
Predicted secondary structure and sequence conservation of s2m
Identifiers
Symbol	s2m
Rfam	RF00164
Other data
RNA type	Cis-reg
Domain(s)	Eukaryota; Viruses
SO	0000233

A representation of the 3D structure of the s2m motif.^[1]

The Coronavirus 3' stem-loop II-like motif (also known as s2m) is a secondary structure motif identified in the 3'untranslated region (3'UTR) of astrovirus, coronavirus and equine rhinovirus genomes.^[2][1] Its function is unknown, but various viral 3' UTR regions have been found to play roles in viral replication and packaging.

This motif appears to be conserved in both nucleotide sequence and secondary structure folding indicating a strong evolutionary selection for its conservation. The presence of this conserved motif in these three different viral families is suggested to be the result of at least two separate recombination events.^[1]

Other RNA families identified in the coronavirus include the SL-III cis-acting replication element (CRE), the coronavirus frameshifting stimulation element, the coronavirus packaging signal and the coronavirus 3' UTR pseudoknot.

References

1. ^ ^{a b c} Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG (2005). "The structure of a rigorously conserved RNA element within the SARS virus genome". PLoS Biol. 3 (1): e5. doi:10.1371/journal.pbio.0030005. PMC 539059. PMID 15630477. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=539059. 
2. ^ Jonassen CM, Jonassen TO, Grinde B (1998). "A common RNA motif in the 3' end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus". J. Gen. Virol. 79 ( Pt 4): 715–8. PMID 9568965. 

External links

• Rfam page for Coronavirus 3' stem-loop II-like motif (s2m)
• S2M motif