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MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

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Related Experiment Video

Updated: May 11, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

miRmap web: Comprehensive microRNA target prediction online.

Charles E Vejnar¹, Matthias Blum, Evgeny M Zdobnov

¹Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

Nucleic Acids Research

|May 30, 2013

Summary

The miRmap software library accurately ranks microRNA (miRNA) targets by predicting gene repression strength. Its user-friendly web application provides valuable tools for researchers studying miRNA gene regulation.

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Last Updated: May 11, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

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Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

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Area of Science:

Bioinformatics
Molecular Biology
Genomics

Background:

MicroRNAs (miRNAs) are key regulators of gene expression, posttranscriptionally repressing protein-coding genes.
Identifying miRNA targets relies on partial complementarity between miRNA and messenger RNA (mRNA) seed sequences, leading to numerous predictions.

Purpose of the Study:

To develop and present miRmap, an open-source software library and web application for ranking potential miRNA targets based on predicted repression strength.
To provide a user-friendly resource for exploring precomputed miRNA target predictions and performing custom target predictions.

Main Methods:

MiRmap integrates multiple features including thermodynamic, evolutionary, probabilistic, and sequence-based data.
It incorporates features from established miRNA target prediction tools like TargetScan, PITA, PACMIT, and miRanda.
The miRmap web application allows browsing, prediction, ranking, sorting, filtering, and exporting of miRNA target data.

Main Results:

MiRmap provides a biologically meaningful criterion (repression strength) for ranking thousands of potential miRNA targets.
The web application offers precomputed predictions for model organisms and enables custom target predictions.
Integrated features facilitate efficient data management and programmatic access for researchers.

Conclusions:

MiRmap enhances the accuracy and usability of miRNA target prediction.
The tool serves as a valuable resource for researchers investigating miRNA function and gene regulation.
MiRmap is accessible online at http://mirmap.ezlab.org.