snoRNABase

Overview

snoRNABase (formerly known as snoRNA-LBME-db) is a comprehensive database dedicated to human small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). The database provides detailed annotations of modification guide RNAs that direct post-transcriptional modifications of ribosomal RNAs and spliceosomal RNAs.

Database Content

Current version contains:

• 257 C/D box snoRNAs (149 unique, accounting for large clusters)
• 86 H/ACA box snoRNAs
• 18 scaRNAs (composite guide RNAs)
• Total: 361 entries

Functional Categories:

• Modification guide RNAs (targeting rRNAs and snRNAs)
• RNA chaperones (involved in pre-rRNA processing)
• Orphan snoRNAs (114 entries without documented target RNAs)

snoRNA Biology

C/D Box snoRNAs

• Guide 2’-O-ribose methylation of target RNAs
• Characterized by conserved boxes C (RUGAUGA) and D (CUGA)
• Contain 10-21 nt antisense elements upstream of D/D’ boxes
• Part of snoRNPs with NOP1/fibrillarin, NOP56, NOP58, and NHP2L1

H/ACA Box snoRNAs

• Guide pseudouridylation (isomerization of uridine to pseudouridine)
• Characterized by two hairpin structures with H box (ANANNA) and ACA motif
• Target uridine located 14-15 bp upstream of H/ACA box
• Associated with dyskerin, NOLA1 (GAR1), NOLA2 (NHP2), and NOLA3 (NOP10)

scaRNAs (Small Cajal Body-Specific RNAs)

• Composite guide RNAs with C/D and/or H/ACA domains
• Guide modifications of RNA polymerase II transcribed snRNAs (U1, U2, U4, U5, U12)
• Accumulate in Cajal bodies rather than nucleoli

Target RNAs

snoRNAs guide modifications in:

• Ribosomal RNAs: 28S, 18S, and 5.8S rRNA
• Spliceosomal RNAs: U1, U2, U4, U5, U6, and U12 snRNA

Key Features

Detailed Annotations

For each snoRNA entry:

• Sequence information and length
• GenBank accession number with hyperlink
• Host gene information and genomic location
• Target RNA(s) and nucleotide(s)
• Predicted base-pairing interactions (unique feature)
• Literature references with PubMed links
• UCSC Genome Browser integration
• FASTA format sequence download

Search Functions

Search Page: Find snoRNAs by:

• Name (e.g., U85, ACA17, mgU12-22/U4-8)
• Partial names (e.g., “mg”, “HBII-“)
• Length
• GenBank accession number
• Target RNA (e.g., “28S” for 28S guides, “no” for orphan snoRNAs)

Find Guide RNA: Interactive tool showing:

• Which snoRNAs guide modification of specific nucleotides
• Base-pairing predictions for each modification site
• Coverage for 28S, 18S, 5.8S rRNAs and U1-U6, U12 snRNAs

Browse: Select and download snoRNA sequences in FASTA format

BLAST: Sequence similarity search against human sno/scaRNA database

Reference Sequences

The database uses standardized reference sequences:

• 18S rRNA: GenBank X03205
• 28S rRNA: GenBank U13369 (nt 7935-12969)
• 5.8S rRNA: GenBank U13369 (nt 6623-6779)

UCSC Genome Browser Integration

snoRNAs from the database are included in the UCSC Genome Browser sno/miRNA track with:

• Color-coded display (C/D box, H/ACA box, scaRNAs)
• Clickable entries linking back to snoRNABase
• Integration with other genomic annotations

Genomic Organization

• Intronic localization: Most sno/scaRNAs encoded in introns of host genes
• Host gene diversity: Range from ribosome biogenesis genes to non-coding genes
• Independent transcription: Some snoRNAs (U3, U8, U13, mgU2-25/61, mgU2-19/30, mgU12-22/U4-8) transcribed independently

Special Features

Large snoRNA Clusters

• HBII-52 cluster: 47 members (SNORD115@) from imprinted locus
• HBII-85 cluster: 27 members (SNORD116@) from Prader-Willi/Angelman syndrome locus
• 14q(I) cluster: 9 members from chromosome 14 imprinted locus
• 14q(II) cluster: 31 members from chromosome 14 imprinted locus

Nomenclature

Database integrates various naming conventions:

• En, Un, ACAn, Zn nomenclature
• HBII-n, HBI-n (human orthologs of mouse snoRNAs)
• mgU-n (methylation guide) notation
• HUGO approved names for all human snoRNAs

Data Sources

Database built through:

• Comprehensive literature compilation
• Experimentally verified snoRNAs
• Human orthologs of vertebrate snoRNAs
• Bioinformatic predictions from imprinted loci

Citation

If using snoRNABase, please cite:

Lestrade, L., and Weber, M. J. (2006). snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Research, 34(Database issue), D158-162. doi:10.1093/nar/gkj002