RNAcentral Expert Databases

Currently the RNAcentral Consortium is formed by 54 Expert Databases, 45 of which have already been imported into RNAcentral.

If you develop an ncRNA database and would like to join RNAcentral, please contact us.

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Database Imported Description
5SrRNAdb 5SrRNAdb is an information resource for 5S ribosomal RNAs
CRS CRS is a database of conserved RNA motifs identified computationally in multi-species vertebrate alignments using 2D structure
CRW CRW provides comparative sequence and structure information for ribosomal, intron, and other RNAs
dictyBase dictyBase is the model organism database for the social amoeba Dictyostelium discoideum
ENA ENA is a comprehensive record of the world's nucleotide sequencing information
Ensembl Ensembl is a genome browser for vertebrate genomes and model organisms that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation
Ensembl Fungi Ensembl Fungi is a genome browser for fungi genomes that complements the Ensembl database
Ensembl Metazoa Ensembl Metazoa is a genome browser for metazoan genomes that complements the Ensembl database
Ensembl Plants Ensembl Plants is a genome browser for plant genomes that complements the Ensembl database
Ensembl Protists Ensembl Protists is a genome browser for protist genomes that complements the Ensembl database
Ensembl/GENCODE GENCODE produces high quality reference gene annotation and experimental validation for human and mouse genomes
FlyBase FlyBase is a database of Drosophila genes and genomes
GeneCards GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes
Greengenes Greengenes is a database of full-length 16S rRNA gene that provides a curated taxonomy based on de novo tree inference
GtRNAdb GtRNAdb contains tRNA gene predictions on complete or nearly complete genomes
HGNC HGNC is the worldwide authority that assigns standardised nomenclature to human genes
IntAct IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions
LncBase LncBase provides experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
LncBook LncBook is a curated knowledgebase of human long non-coding RNAs
LNCipedia LNCipedia is a comprehensive compendium of human long non-coding RNAs
lncRNAdb lncRNAdb is a database providing comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs)
MalaCards MalaCards integrates manually-curated and text-mining sources to associate genes, including ncRNAs, with diseases, and lists the supporting evidence
MGI MGI is the international database resource for the laboratory mouse
miRBase miRBase contains high-quality miRNA annotations; miRBase is responsible for assigning official miRNA gene names
MirGeneDB MirGeneDB is a curated microRNA gene database covering 45 metazoan organisms
Modomics Modomics is a comprehensive database of RNA modifications
NONCODE NONCODE is an integrated knowledge database dedicated to non-coding RNAs
PDBe PDBe is the European repository of information about the 3D structures of large biological molecules. PDBe is a member of the Worldwide Protein Data Bank
piRBase piRBase is a database of various piRNA associated data to support piRNA functional study
PomBase PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe
RDP RDP provides quality-controlled, aligned and annotated rRNA sequences and a suite of analysis tools
RefSeq RefSeq is a comprehensive, integrated, non-redundant, well-annotated set of reference sequences
Rfam Rfam is a collection of non-coding RNA families, represented by manually curated sequence alignments, consensus secondary structures and predicted homologues
RGD RGD is a rat genetic and genomic research resource
SGD SGD provides comprehensive integrated biological information for the budding yeast
SILVA SILVA is a comprehensive resource for quality checked and aligned ribosomal RNA sequence data
snoDB snoDB is an interactive database of human snoRNA sequences, abundance and interactions
snOPY snOPY provides comprehensive information about snoRNAs, their gene loci, orthologues and their target RNAs
snoRNA Database The snoRNA Database is a curated collection of archaeal snoRNAs maintained by the Lowe Lab at UC Santa Cruz
SRPDB SRPDB provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP
TAIR TAIR is a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana
TarBase TarBase is a collection of manually curated experimentally validated miRNA-gene interactions
tmRNA Website tmRNA Website contains predicted tmRNA sequences from RefSeq bacterial genomes, plasmids, phages and some organelles
WormBase WormBase curates, stores and displays genomic and genetic data about nematodes with primary emphasis on C. elegans and related nematodes
ZFIN The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism
ZWD ZWD is a git-based collection of non-coding RNA alignments maintained by Dr Zasha Weinberg
miRTarBase miRTarBawse is an experimentally validated microRNA-target interactions database
NPInter NPInter contains data on experimentally determined functional interactions between ncRNAs and proteins, mRNAs or genomic DNA
PLncDB PLncDB provides comprehensive genomic view of Arabidopsis lncRNAs
RNApathwaysDB RNApathwaysDB contains RNA maturation and decay pathways
snoRNA Atlas snoRNA Atlas is a database of human snoRNAs
sRNAmap sRNAmap is a collection of sRNA sequences and interactions
tmRDB tmRDB is a collection of aligned, annotated and phylogenetically ordered sequences related to structure and function of tmRNA
tRNAdb tRNAdb is a compilation of tRNA sequences and tRNA genes.