{"rfam": {"acc": "RF03546", "id": "Flavivirus-5UTR", "description": "Flavivirus 5' UTR", "comment": "The 5' UTR of flaviviruses are highly structured, has a length of approximately 100 nucleotides and harbors two conserved RNA secondary structures vital for the viral life cycle[1][2]. During replication, a long-range RNA-RNA interaction between 5' UTR and 3' UTR of the genome is formed to initiate synthesis of new viral replicates and viral protein translation. In direct adjacency to the 5' UTR, already part of the coding region, lies the cHP structure, which is essential for the viral replication[3][4]. The first structural element is termed 5'SLA and comprises three stems (S1, S2, S3) folded as Y-shaped-like stem structure, and a side structure domain (SSD). Its overall length is around 70 nucleotides. Viral replication is stopped by disruption of S1 and S2. Further, via RNA-protein interaction with NS5, SLA serves as a promoter for RNA synthesis during circularization of the viral genome[5][6]. Despite the diversity of SSD, its stable structure is essential for infectivity[3]. The second structural element is termed 5'SLB. At its top region of the stem loop lies the translation initiation codon. It further contains the 5'UAR (upstream AUG region), which is essential for the circularization of the genome[8]. The 5'UAR interacts with the 3'UAR, which is located at the 3' UTR of the genome to form the long-range RNA-RNA interaction[8]. At the start of the coding region lies the capsid-coding hairpin region (cHP), which is followed by the 5'CS (conserved sequence). The 5'CS forms an additional long-range RNA-RNA interaction with the 3' UTR (3'CS)[5]. The cHP further aids in the start codon recognition and thus in viral replication. Studies show that the function of cHP is sequence-independent but structure-dependent[9].", "curation": {"author": "Lamkiewicz K", "seed_source": "Lamkiewicz K", "num_seed": 8, "num_full": 0, "num_species": 8, "type": "Cis-reg;", "structure_source": "Predicted; LocARNA 2.0.0RC8"}, "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": 80.0, "trusted": 82.4, "noise": 62.1}}, "release": {"date": "2026-01-16", "number": "15.1"}, "clan": {"acc": "CL00129", "id": "Flavivirus-5UTR"}}}