{"rfam": {"acc": "RF01848", "id": "ACEA_U3", "description": "ACEA small nucleolar RNA U3", "comment": "Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localisation, stability and hyper-methylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.", "curation": {"author": "Gardner PP", "seed_source": "Published; PMID:19875933", "num_seed": 28, "num_full": 2156, "num_species": 132, "type": "Gene; snRNA; snoRNA; CD-box;", "structure_source": "Published; PMID:19875933"}, "cm": {"build_command": "cmbuild -F CM SEED", "calibrate_command": "cmcalibrate --mpi CM", "search_command": "cmsearch --cpu 4 --verbose --nohmmonly -T 27.68 -Z 2958934 CM SEQDB", "cutoffs": {"gathering": 55.0, "trusted": 55.0, "noise": 54.9}}, "release": {"date": "2026-01-16", "number": "15.1"}, "clan": {"acc": "CL00100", "id": "U3"}}}