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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.
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.
Plant snoRNA Database
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.
NSDNA / Nervous System Disease NcRNAome Atlas
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.
DASHR / Database of small human noncoding RNAs
Contains the most comprehensive information to date on human small non-coding RNAs (sncRNA) genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). DASHR is distinct from other existing databases because it integrates annotations for all major classes of sncRNAs with baseline expression profiles in different human tissues and cell types, making it a very useful resource to the broader scientific community.
snOPY / snoRNA Orthological Gene Database
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.
uRNADB / uRNA database
Provides aligned, annotated and phylogenetically ordered sequences. The uRNADB is a database for the study of the structures and functions of various U RNAs. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, direct links to GenBank was established via the accession number. Because of limited resources, the uRNADB has not been updated since May, 1997.
A curated database for small nucleolar RNAs (snoRNAs) and small cajal body-specific RNAs (scaRNAs). Sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more.
snoRNP database / Small nucleolar ribonucleoprotein database
A web-based collection of snoRNA and snoRNA-associated protein sequences from a wide range of species. snoRNP database currently contains over 1,000 snoRNA sequences from Bacteria, Archaea, and Eukaryotes. The database search engine can support a number of different search terms but the most common ones are: Genus (i.e. Drosophila), Species (i.e. melanogaster), Accession number, snoRNA class (C/D or H/ACA), sequence, or a sequence motif such as CUGA. The type of sequences such as RNA or protein can also be chosen by the user using the radio buttons above the search box.
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