The following are RNA databases freely accessible online.
miRBase database: a searchable database of published miRNA sequences and annotation.
miRDB is an online database for miRNA target prediction and functional annotations.
Rfam database is an annotated, open access database that contains information about non-coding RNA (ncRNA) families and other structured RNA elements.
RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases representing a broad range of organisms and RNA types. Its development is coordinated by European Bioinformatics Institute and is supported by Wellcome.
deepBase facilitates the integrative and interactive display and analysis of expression, evolution, function of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, cancer and exosome samples. It provided the most comprehensive expression analysis of sRNAs and lncRNAs, the expression patterns of tRFs and snoRNAs from thousands of cancer and normal samples, the correlations between ncRNAs and patients’ survival and the function prediction of ncRNAs in tumor tumorigenesis.
LNCipedia, of the Ghent University in Belgium, is a comprehensive compendium of human long non-coding RNAs (lncRNA), a public database for lncRNA sequence and annotation and manually curated lncRNA articles.
LncRNAWiki is a wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs).
LncBook a curated knowledgebase of human long non-coding RNAs.
NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). It collects ncRNAs data from three sources: 1) Literature mining, 2) GenBank, 3) Specialized Database such as Ensembl, RefSeq, lncRNAdb, lncipedia.
lncRNome, hosted by the CSIR Institute of Genomics and Integrative Biology of India, is a comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans. The resource hosts information on over 17000 long noncoding RNAs in Human. The resource provides information on the types, chromosomal locations, description on the biological functions and disease associations of long noncoding RNAs. In addition, it provides access to datasets on protein-lncRNA interactions and genomic variations in lncRNA loci. The resource also provides a browsable interface for the datasets.
NRED (ncRNA Expression Database) of the University of Queensland Diamantina Institute in Australia, integrates annotated expression data from various sources.
C-It-Loci is a tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms. Conserved loci are pairs of adjacent homologous protein-coding genes shared between one or more species. Expression profiles are based on RNA-seq data from many sources to derive tissue enrichment or specificity. Classifications of transcripts are based on the latest release of ENSEMBL.
NDB (Nucleic Acid Database) contains information about experimentally determined nucleic acids and complex assemblies. Use the NDB to perform searches based on annotations relating to sequence, structure, and function, and to download, analyze, and learn about nucleic acids.
ENCORI (The Encyclopedia of RNA Interactomes) is an open-source platform for studying the miRNA-ncRNA, miRNA-mRNA, ncRNA-RNA, RNA-RNA, RBP-ncRNA and RBP-mRNA interactions.
Blood Atlas is a haematopoietic transcriptomes atlas.
exoRBase is a repository of extracellular vesicles (EVs) long RNAs (exLRs) derived from RNA-seq data analyses in different human body fluids. The exLRs contain messenger RNA (mRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA).
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA modifying enzymes.
piRNAdb is a piRNA storage and search system, and with some other relevant information like alignments, tissue expression, clusters, datasets, associated genes and ontology terms of these piRNAs.
Circular RNA Databases
circRNADb is a database of circular RNA.
circBank is a comprehensive database of human circRNA.
circBase: public circRNA datasets.
CIRCpedia v2 is an updated comprehensive database containing circRNA annotations from over 180 RNA-seq datasets across six different species.
CSCD (cancer-specific circRNA database) collects available RNASeq datasets in cancer and normal samples.
TSCD (Tissue-Specific CircRNA Database) provides a global view of tissue-specific circRNA in main tissues of human and mouse.
PlantcircBase is a comprehensive database of plant circular RNAs.
circAtlas is an integrated resource of circRNAs in vertebrates.
TRCirc provides regulatory information about transcription of circRNAs.
NeuroCirc is an integrative web-based resource of circRNA expression in the human brain.
Circular RNA Interactome enables the prediction and mapping of binding sites for RBPs and miRNAs on reported circRNAs.
Circad is a manually curated database of circular RNAs associated with diseases.
GreenCircRNA is a Wiki-database of plant CircRNAs.
circVAR is a free online genetic resource for circular RNAs in human.