Small nucleolar RNA databases | Non-coding transcript data analysis
Small nucleolar RNA (snoRNA) are a class of non-coding RNA that mediate modifications of other RNAs such as ribosomal RNAs, transfert RNAs and small nuclear RNAs. SnoRNAs can induce methylation and pseudouridylation of pre-RNA molecules. SnoRNA databases gather information on noncoding RNA sequences, structures, expression data or target modification sites.
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.
Provides information on small nucleolar RNAs from Arabidopsis and eighteen other plant species. Information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. The Arabidopsis information is divided into box C/D and box H/ACA snoRNAs, and within each of these groups, by target sites in rRNA, snRNA or unknown. Alignments of orthologous genes and gene variants from different plant species are available for many snoRNA genes. Plant snoRNA genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.
A comprehensive bioinformatics resource to archive non-coding RNA (ncRNA)-associated cell death interactions. ncRDeathDB documents a total of more than 4600 ncRNA-mediated programmed cell death (PCD) entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.
Allows studying of RNA modifications and Small nucleolar RNAs (snoRNA) gene evolution. snOPY is a database that provides three types of information: snoRNA, snoRNA gene locus, and target RNA. The database also includes manually curated orthologous gene data for each gene. Several search parameters, including species, box motif, target RNA, gene organization, curation status, and keywords are available. snOPY enables users to analyze snoRNAs and their targets and gene organization in various species.
Deals with small non-coding RNAs (sRNAs) expression information derived from eleven normal mouse tissues, from both female and male samples. This repository provides an atlas consisting of tissue-specific as well as broadly transcribed sRNA attributed to different classes. Additionnally, it also supplies information about tissues and functionnalities obtained from an analysis leaning on machine learning.
Provides a collection of noncoding RNA sequences. Rfam is an online resource where RNA sequences are grouped into “families” and “clans” on the basis of nucleotide sequence and secondary structure homology. It includes many different types of ncRNA genes, cisregulatory elements and intronic elements, all annotated in as many species as possible. This database is searched for homologous sequences.
A dedicated database containing human C/D box and H/ACA box small nucleolar RNAs (snoRNAs), and small Cajal body-specific RNAs (scaRNAs). snoRNA-LBME-db was built by a compilation of the literature, and comprises human sno/scaRNAs that were experimentally verified, as well as the human orthologs of snoRNAs that were cloned in other vertebrate species, and some snoRNAs that are predicted by bioinformatics search in loci submitted to genomic imprinting, but have not all been experimentally verified. For each entry, the database identifies the modified nucleotide(s) in the target RNA(s), indicates the corresponding predicted base pairing, gives a few pertinent references and provides a link to the position of the sno/scaRNA on the UCSC Genome Browser. The 'Find guide RNA' function allows one to find the sno/scaRNAs predicted to guide the modification of a particular nucleotide in the rRNA and spliceosomal RNA sequences. The 'Browse' function allows one to download the sequences of selected sno/scaRNAs in the FASTA format.