{"rfam": {"acc": "RF02340", "id": "DENV_SLA", "description": "Dengue virus SLA", "comment": "Flavivirus stem-loop A (SLA) is a secondary structure present in the 5 prime untranslated (5'-UTR) region of viruses of the genus Flavivirus. SLA structure was first proposed from enzymatic and chemical probing methods [1,2] afterwards the 3D structure of Dengue (PDB:7LYF, 7LYG) and Zika (PDB:5U0B) SLA viruses were reported [3]. SLA interacts with the nonstructural protein 5 (NS5), where SLA functions as a promoter for viral RNA synthesis by NS5 polymerase. The SLA secondary structure includes a bottom stem-loop (previously reported as SL1 and SL2), a top stem-loop (previously reported as SL3 and TL) and a side-loop (previously proposed as side SL). The side SL variate in length between flaviviruses (Tick-borne flaviviruses present a side SL >40nt), despite the lack of sequence conservation, deletion of the side SL abolish replication in Dengue virus. It is proposed that the side SL is essential to maintain the overall fold of Flavivirus SLA [3]. SLA 3D was also reported in PDB:7UMC, 8GZP, 8GZQ [4, 5].", "curation": {"author": "Eberhardt R, Choi K, Ontiveros-Palacios N", "seed_source": "Published; PMID:19004935", "num_seed": 15, "num_full": 2, "num_species": 9, "type": "Cis-reg;", "structure_source": "Published; PMID:19004935"}, "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": 50.5, "trusted": 50.5, "noise": 40.1}}, "release": {"date": "2026-01-16", "number": "15.1"}, "clan": {"acc": "CL00129", "id": "Flavivirus-5UTR"}}}