Coronavirus 3′ UTR

Downstream of this pseudoknot lies the hypervariable region (HVR), which is supported by many covarying base pairs in alphacoronaviruses.

The most 5′ structure is the bulged stem-loop (BSL), starting downstream of the N gene stop codon and is essential for viral replication.

Downstream to the BSL lies the hypervariable bulged-stemloop region (HVR), containing a triple helix junction.

It is proposed that the BSL and pseudoknot act as a molecular switch that may regulate a transition during viral RNA synthesis.

Even though a nearby pseudoknot structure, which has been observed in other genera of coronaviruses, is present, its functional importance has not been established yet.

Consensus secondary structure and sequence conservation of aCoV-3UTR (Rfam RF03121 ).
Consensus secondary structure and sequence conservation of bCoV-3UTR (Rfam RF03122 ).
Consensus secondary structure and sequence conservation of dCoV-3UTR (Rfam RF03124 ).