Learn to use miRBase, an online resource for microRNA genomics. In miRBase users can find stem-loop miRNA precursor sequences, mature microRNA sequences, information about miRNA clusters, genomic coordinates, features flanking a microRNA gene, and references to original literature describing the miRNA. The resource also includes a database of computationally predicted microRNA targets. MicroRNA and target sequences are linked to annotated databases that provide additional biological knowledge. The entire contents of the database are available for free downloading. Learn to use this database, to facilitate all your microRNA research needs.

You will learn:

  • multiple ways to search the miRBase database, e.g. by name, keyword, genomic location, and by sequence
  • to navigate the microRNA entry pages
  • to access and use deep sequencing reports to interpret microRNA validity
  • to find genomic features marking the start and end of primary miRNA transcripts
  • to find all potential miRNA targets in a genome


This tutorial is a part of the tutorial group Expression resources. You might find the other tutorials in the group interesting:

Functional Glycomics Gateway: The home for Functional Glycomics research

CleanEx: A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature

Allen Mouse Brain Atlas: Mapped gene expression data in mouse brain

DBTSS: Database of Transcriptional Start Sites

Alternative Splicing and Transcript Diversity (ASTD) database: A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat

GENSAT: Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.

Gene Expression Omnibus (GEO): A gene expression/molecular abundance repository and a curated, online resource for gene expression data

ArrayExpress: A public repository for microarray gene expression data at the EBI


Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.


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Barrero A. Roberto et al., An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1428-4

Guo Yan et al., Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3470-z

Cumbo Fabio et al., TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1419-5

Capra E. et al., Small RNA sequencing of cryopreserved semen from single bull revealed altered miRNAs and piRNAs expression between High- and Low-motile sperm populations Non-human and non-rodent vertebrate genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3394-7

Rasko E.J. John et al., Nuclear microRNAs in normal hemopoiesis and cancer. Journal of Hematology Oncology (2017) doi:10.1186/s13045-016-0375-x