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miRBase is the public archive of microRNA sequences and annotations, and the registry where new microRNA genes are named. Researchers use it to look up a microRNA by accession, name or keyword, to find the microRNAs at a genomic location, and to cite the resource correctly. This guide covers what it holds, who maintains it, how its search options work, and how to cite it.
What miRBase is
miRBase describes itself as “the microRNA database” and “the archive for microRNA sequences and annotations” (mirbase.org, read 2026-11-07). Its help pages call it the home of the miRNA Sequence database and Registry. Two functions follow from that wording:
- Sequence database. It catalogs microRNA gene sequences (hairpin precursors and the mature microRNAs cut from them) and distributes them freely to the public.
- Registry. It assigns names to newly described microRNA genes. The help pages include a section on submitting miRNA sequences for naming and one on miRNA naming conventions.
If you work with small RNAs, you will often meet miRBase identifiers in papers about Argonaute proteins, in assay design (for example stem-loop primer approaches), and in broader gene-regulation topics such as epigenetics.
Who runs it and what it covers
miRBase is maintained at the University of Manchester (the site carries the Faculty of Biology, Medicine and Health logo). The primary publication lists Kozomara, Birgaoanu and Griffiths-Jones as the authors. The site announced version 23.1 as released in September 2026.
For scale, the 2019 Nucleic Acids Research paper reports the contents of release 22 (these are release 22 figures, not current ones):
| Item in release 22 | Count reported |
|---|---|
| Hairpin precursor sequences | 38,589 |
| Mature microRNAs | 48,860 |
| Organisms | 271 |
Source: Kozomara A, Birgaoanu M, Griffiths-Jones S. “miRBase: from microRNA sequences to function.” Nucleic Acids Research 2019;47(D1):D155-D162.
How to search miRBase
The home page offers several search entry points. These use the interface’s own terms as read on 2026-11-07.
- Open mirbase.org. The top navigation has Search, Browse, Help and Downloads.
- Keyword search. Type “a miRNA accession, name or keyword” into the main search box.
- Search by genomic location. Choose an organism and a chromosome, optionally enter start and end positions. Leaving the positions blank returns all miRNAs on that chromosome.
- Search by tissue expression. Choose an organism and a tissue.
- Search by sequence. This option links out to the RNAcentral sequence search rather than running inside miRBase.
- Use Browse to move through the archive without a query, and Help for the explanation of what miRBase provides, how searching works, genome assemblies and naming conventions.
- Use Downloads when you need the data in bulk.
Strengths and limits
Strengths
- It is both an archive and a naming registry, so the name used in a paper can be traced to one authoritative record.
- Searches by accession or name, genomic location and tissue expression each have a dedicated form.
- The maintainers publish annotation guidelines: “A uniform system for microRNA annotation” (RNA, 2003) and “Criteria for annotation of plant MicroRNAs” (Plant Cell, 2008).
Limits to keep in mind
- Counts change with each release. Quote the release number with any count, as above.
- Sequence similarity searching is handled by RNAcentral, not by miRBase itself.
- miRBase is a sequence and annotation archive. Experimental evidence for function needs to come from the primary data sources and papers you cite alongside it.
Alternatives and companions
| Resource | Role relative to miRBase | Source |
|---|---|---|
| RNAcentral | Where miRBase’s “By sequence” option sends you to search by sequence | mirbase.org home page, read 2026-11-07 |
For other kinds of biological reference data, see our guides to BioGRID (curated interactions) and InterPro (protein families). For depositing your own sequences, see BankIt and GenBank submission.
How to cite miRBase
The miRBase help pages name “miRBase: from microRNA sequences to function” (Kozomara, Birgaoanu and Griffiths-Jones, Nucleic Acids Research 2019, 47:D155-D162) as the primary citation, and list earlier papers from 2014, 2011, 2008 and 2006, plus the 2004 Registry paper. They ask users to cite miRBase alongside the primary data sources behind the sequences they use. State the release number you queried in your methods.
FAQ
What is miRBase?
It is the archive for microRNA sequences and annotations and the registry for naming microRNA genes, run from the University of Manchester.
Who maintains miRBase?
The 2019 paper credits Kozomara, Birgaoanu and Griffiths-Jones at the University of Manchester. The site shows the Faculty of Biology, Medicine and Health logo.
Can I search miRBase by sequence?
The “By sequence” option links to the RNAcentral search.
Can I look up microRNAs by chromosome location?
Yes. Pick an organism and chromosome, with optional start and end positions; blank positions return all miRNAs on that chromosome.
Where can I submit a new microRNA for naming?
The Help section has a page on submitting miRNA sequences for naming.
Sources
- miRBase home page, https://mirbase.org/ (read 2026-11-07)
- miRBase help, https://mirbase.org/help/ (read 2026-11-07)
- Kozomara et al. 2019, https://academic.oup.com/nar/article/47/D1/D155/5179337 (read 2026-11-07)
