{"rfam": {"acc": "RF03536", "id": "Flavi_TBFV_xrRNA", "description": "Tick-borne Flavivirus exoribonuclease-resistant RNA element", "comment": "The exoribonuclease-resistant RNA elements (xrRNA) are described throughout all groups of flaviviruses. Usually, each virus harbors two xrRNAs, xrRNA1 and xrRNA2, in the beginning of the 3' UTR [1]. The formation of these stem-loops, especially xrRNA1, is vital to ensure resistance against XRN1 activity [2]. The Y-shaped stem-loop is also termed SL II and SL IV, respectively. In order to function as xrRNA, the sequence downstream is needed as well, since the upper loop region forms a pseudoknot (PK) with the single-stranded region directly downstream to its respective hairpin. In some species, the region downstream also forms a small hairpin. In such cases, the PK interactions takes place between the two loop regions. Conserved formation of these structures were observed in mammalian cells but not in mosquito cells, suggesting this region has varying functions in different hosts[3][4]. In plant-viruses, xrRNA elements have been observed as well, showing some similarities to flaviviral xrRNAs[5][6]. However, plant-virus xrRNA and flaviviral xrRNA are distinguishable by their underlying three-dimensional folds[7].", "curation": {"author": "Lamkiewicz K", "seed_source": "Lamkiewicz K", "num_seed": 18, "num_full": 0, "num_species": 11, "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": 46.5, "trusted": 55.4, "noise": 43.8}}, "release": {"date": "2026-01-16", "number": "15.1"}, "clan": {"acc": null, "id": null}}}