snOPY

snOPY (snoRNA Orthological Gene Database) is a specialized database dedicated to small nucleolar RNAs (snoRNAs) and their orthologous relationships across multiple species. Developed and maintained by the Kenmochi Laboratory at the University of Miyazaki, Japan, snOPY provides comprehensive information about snoRNA sequences, gene organization, and target modifications.

Overview

Small nucleolar RNAs (snoRNAs) are a class of small non-coding RNAs that guide chemical modifications of other RNAs, primarily ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). snOPY focuses on cataloging these important regulatory molecules and their evolutionary relationships.

Database Content

snoRNA Classes

snOPY contains information about two major classes of snoRNAs:

1. Box C/D snoRNAs:
   • Contain conserved sequence motifs: Box C (TGATGA) and Box D (CTGA)
   • Guide 2’-O-methylation of target RNAs
   • Modification occurs 5 nucleotides upstream of box D or D’
   • Complementary region upstream of boxes pairs with target RNA
2. Box H/ACA snoRNAs:
   • Contain conserved sequence motifs: Box H (ANANNA) and Box ACA (ACA)
   • Guide pseudouridylation (conversion of uridine to pseudouridine)
   • Modification site located in pseudouridylation pocket
   • Formed by RNA:RNA antisense interaction with target

snoRNA Gene Organization

snOPY catalogs three types of snoRNA gene loci:

• Intronic: snoRNA gene located within intron of protein-coding host gene; transcribed using host gene promoter
• Polycistronic: Multiple snoRNA genes organized in cluster; transcribed from single promoter
• Monocistronic: Single snoRNA gene expressed using its own promoter

Target RNAs

The database provides information about:

• rRNA targets: Modified nucleotides in ribosomal RNA
• snRNA targets: Modified nucleotides in small nuclear RNA
• Orphan snoRNAs: snoRNAs whose targets remain to be determined

Species Coverage

snOPY contains snoRNA data for over 50 organisms across multiple domains of life, including:

Mammals

• Homo sapiens (760 entries)
• Mus musculus (968 entries)
• Rattus norvegicus (1,065 entries)
• Gorilla gorilla (1,083 entries)
• Macaca mulatta (655 entries)
• And many other mammalian species

Other Vertebrates

• Gallus gallus (chicken)
• Danio rerio (zebrafish)
• Xenopus tropicalis (frog)

Invertebrates

• Drosophila melanogaster (248 entries)
• Caenorhabditis elegans (91 entries)
• Ciona intestinalis and C. savignyi (tunicates)

Fungi

• Saccharomyces cerevisiae (77 entries)
• Schizosaccharomyces pombe (58 entries)

Plants

• Arabidopsis thaliana (220 entries)
• Oryza sativa (rice, 236 entries)
• Triticum aestivum (wheat, 741 entries)
• Hordeum vulgare (barley, 455 entries)
• Physcomitrium patens (moss, 75 entries)

Key Features

Ortholog Identification

snOPY uses a unique approach to identify snoRNA orthologs:

• Traditional sequence similarity methods (e.g., BLAST) often fail due to low sequence conservation between snoRNAs from different species
• Instead, snOPY focuses on conservation of target RNA sequences (rRNA, snRNA)
• Target RNAs are aligned across species using ClustalW
• Modification sites are mapped onto alignments
• If modified nucleotides align at the same position, corresponding snoRNAs are considered orthologs

This target-based approach is more reliable than direct snoRNA sequence comparison for identifying evolutionary relationships.

Data Curation

• snoRNA data collected from public databases
• Manual curation according to sequence annotation
• Curation status tracking for data quality assurance

Search and Browse Capabilities

Users can search and filter by:

• Species: Over 50 organisms
• Box type: C/D or H/ACA class
• Target RNA: Specific rRNA or snRNA targets
• Organization: Intronic, polycistronic, or monocistronic
• Keywords: Free-text search
• Curation status: Quality filtering

BLAST Interface

Sequence similarity searches against snOPY snoRNA sequences for:

• Identifying novel snoRNAs in new sequences
• Finding homologous snoRNAs across species
• Characterizing unidentified snoRNA candidates

Integration with External Resources

snOPY is integrated with RNAcentral, contributing yeast and other organism snoRNA data to this comprehensive non-coding RNA database. Updates are regularly synchronized with RNAcentral releases.

Sister Database

snOPY is part of a suite of databases from the Kenmochi Laboratory:

• RPG (Ribosomal Protein Gene Database): Complementary resource for ribosomal protein genes

Citation

If snOPY assists your research, please cite:

Yoshihama M, Nakao A, Kenmochi N (2013). “snOPY: a small nucleolar RNA orthological gene database.” BMC Research Notes, 6:426.

Copyright and Usage

• Academic users: May freely use and link to the snOPY website
• Non-academic users: May use as end users for academic purposes; other uses require permission

snOPY is an original database product, copyright Kenmochi Laboratories.

Contact

Contact address available at the snOPY website.

Developed and maintained by: Medical Biology, Faculty of Medicine, University of Miyazaki

Last Database Updates:

• 2024-06-01: Triticum dicoccoides data updated
• 2024-03-26: RNAcentral release 24 integration
• 2023-11-30: RNAcentral release 23 integration
• 2023-08-01: Triticum aestivum data updated
• 2022-12-01: Gorilla gorilla data available