MiRBase: MicroRNA Sequences, Targets and Gene Nomenclature

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Dec 31

PMID 16381832

Citations 2323

Authors

Sam Griffiths-Jones

Russell J Grocock

Stijn van Dongen

Alex Bateman

Anton J Enright

Affiliations

Soon will be listed here.

Abstract

The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at http://microrna.sanger.ac.uk/.

Citing Articles

Identification of Oncogene-Induced Senescence-Associated MicroRNAs.

Foutadakis S, Soureas K, Roupakia E, Besta S, Avgeris M, Kolettas E Methods Mol Biol. 2025; 2906:189-213.

PMID: 40082357 DOI: 10.1007/978-1-0716-4426-3_11.

miRNA-Based Diagnosis of Schizophrenia Using Machine Learning.

Heda V, Dogra S, Kouznetsova V, Kumar A, Kesari S, Tsigelny I Int J Mol Sci. 2025; 26(5).

PMID: 40076899 PMC: 11900116. DOI: 10.3390/ijms26052280.

EBAX-1/ZSWIM8 destabilizes miRNAs, resulting in transgenerational inheritance of a predatory trait.

Quiobe S, Kalirad A, Roseler W, Witte H, Wang Y, Rodelsperger C Sci Adv. 2025; 11(11):eadu0875.

PMID: 40073139 PMC: 11900880. DOI: 10.1126/sciadv.adu0875.

MiR-769-5p of macrophage exosomes induced by GRP78 promotes stemness and chemoresistance in colorectal cancer.

Tian J, Zhang L, La X, Fan X, Li Z Cell Death Dis. 2025; 16(1):156.

PMID: 40044682 PMC: 11882909. DOI: 10.1038/s41419-025-07466-7.

The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback.

Luo M, Zhao J, Merila J, Barrett R, Guo B, Hu J BMC Biol. 2025; 23(1):70.

PMID: 40038570 PMC: 11881503. DOI: 10.1186/s12915-025-02176-0.

References

Griffiths-Jones S . The microRNA Registry. Nucleic Acids Res. 2003; 32(Database issue):D109-11. PMC: 308757. DOI: 10.1093/nar/gkh023. View

Ambros V, Bartel B, Bartel D, Burge C, Carrington J, Chen X . A uniform system for microRNA annotation. RNA. 2003; 9(3):277-9. PMC: 1370393. DOI: 10.1261/rna.2183803. View

Enright A, John B, Gaul U, Tuschl T, Sander C, Marks D . MicroRNA targets in Drosophila. Genome Biol. 2004; 5(1):R1. PMC: 395733. DOI: 10.1186/gb-2003-5-1-r1. View

Weber M . New human and mouse microRNA genes found by homology search. FEBS J. 2005; 272(1):59-73. DOI: 10.1111/j.1432-1033.2004.04389.x. View

Lewis B, Burge C, Bartel D . Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005; 120(1):15-20. DOI: 10.1016/j.cell.2004.12.035. View

Kidner C, Martienssen R . The developmental role of microRNA in plants. Curr Opin Plant Biol. 2005; 8(1):38-44. DOI: 10.1016/j.pbi.2004.11.008. View

Brennecke J, Stark A, Russell R, Cohen S . Principles of microRNA-target recognition. PLoS Biol. 2005; 3(3):e85. PMC: 1043860. DOI: 10.1371/journal.pbio.0030085. View

Krek A, Grun D, Poy M, Wolf R, Rosenberg L, Epstein E . Combinatorial microRNA target predictions. Nat Genet. 2005; 37(5):495-500. DOI: 10.1038/ng1536. View

He L, Thomson J, Hemann M, Hernando-Monge E, Mu D, Goodson S . A microRNA polycistron as a potential human oncogene. Nature. 2005; 435(7043):828-33. PMC: 4599349. DOI: 10.1038/nature03552. View

10.

Lu J, Getz G, Miska E, Alvarez-Saavedra E, Lamb J, Peck D . MicroRNA expression profiles classify human cancers. Nature. 2005; 435(7043):834-8. DOI: 10.1038/nature03702. View

11.

ODonnell K, Wentzel E, Zeller K, Dang C, Mendell J . c-Myc-regulated microRNAs modulate E2F1 expression. Nature. 2005; 435(7043):839-43. DOI: 10.1038/nature03677. View

12.

Kim V . MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol. 2005; 6(5):376-85. DOI: 10.1038/nrm1644. View

13.

Filipowicz W, Jaskiewicz L, Kolb F, Pillai R . Post-transcriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol. 2005; 15(3):331-41. DOI: 10.1016/j.sbi.2005.05.006. View

14.

Rajewsky N, Socci N . Computational identification of microRNA targets. Dev Biol. 2004; 267(2):529-35. DOI: 10.1016/j.ydbio.2003.12.003. View

15.

Bartel D . MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116(2):281-97. DOI: 10.1016/s0092-8674(04)00045-5. View

16.

Sontheimer E, Carthew R . Silence from within: endogenous siRNAs and miRNAs. Cell. 2005; 122(1):9-12. DOI: 10.1016/j.cell.2005.06.030. View

17.

Stark A, Brennecke J, Russell R, Cohen S . Identification of Drosophila MicroRNA targets. PLoS Biol. 2003; 1(3):E60. PMC: 270017. DOI: 10.1371/journal.pbio.0000060. View

18.

Ambros V . The functions of animal microRNAs. Nature. 2004; 431(7006):350-5. DOI: 10.1038/nature02871. View

19.

Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R . Fast and effective prediction of microRNA/target duplexes. RNA. 2004; 10(10):1507-17. PMC: 1370637. DOI: 10.1261/rna.5248604. View

20.

Rodriguez A, Griffiths-Jones S, Ashurst J, Bradley A . Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004; 14(10A):1902-10. PMC: 524413. DOI: 10.1101/gr.2722704. View