{"rfam": {"acc": "RF03116", "id": "aCoV-5UTR", "description": "Alphacoronavirus 5'UTR", "comment": "The first 150 to 200 nucleotides within the 5' UTR of alphacoronaviruses are highly structured and shown to be conserved on the structural level among alphacoronaviruses. The 5' UTR has been predicted to contain 3 conserved stem-loops: SL1, SL2 and SL4. SL1 is important for viral replication, most likely playing a role in the template-switch of viral subgenomic RNA transcription. Mutations of the upper part of SL1 seems to have an higher impact of viral replication level. SL2 is crucial for viral viability, nucleotides are interchangeable as long as the structure remains stable. Disrupting any G-C pairing causes major defects in viral replication. SL4 is hypothesised to play a role in directing subgenomic RNA synthesis during viral replication. Downstream of SL4 lies SL5, which overlaps with the first ORF of the viral genome. The 3 terminal loops of SL5 contain a conserved sequence 5'-UUCCGU-3' and are thought to act as the packaging signal [3]. This strong level of conservation has not been observed in other genera of coronaviruses yet.", "curation": {"author": "Lamkiewicz K", "seed_source": "Lamkiewicz K", "num_seed": 17, "num_full": 31, "num_species": 37, "type": "Cis-reg;", "structure_source": "Predicted;"}, "cm": {"build_command": "cmbuild -F CM SEED", "calibrate_command": "cmcalibrate --mpi CM", "search_command": "cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB", "cutoffs": {"gathering": 70.3, "trusted": 71.6, "noise": 52.3}}, "release": {"date": "2026-01-16", "number": "15.1"}, "clan": {"acc": "CL00116", "id": "Coronavirus-5UTR"}}}