miRBase is the authoritative online database for microRNA (miRNA) sequences and their annotations. It serves as a centralized hub, providing researchers with a consistently updated and curated collection of miRNA data. This resource acts as a uniform reference point for the global scientific community.
The database offers a standardized framework for identifying and classifying these small RNA molecules. It consolidates information from numerous studies, ensuring access to a reliable and comprehensive dataset. This centralized approach streamlines research efforts and promotes clarity in the rapidly evolving field of miRNA biology.
Core Data in miRBase
miRBase stores two types of miRNA sequences: the precursor miRNA and the mature miRNA. The precursor miRNA is the longer, hairpin-shaped RNA molecule from which the functional miRNA is processed. This precursor structure is the initial transcript that folds into a characteristic stem-loop.
From a single precursor, one or sometimes two mature miRNA sequences can be derived. These mature miRNAs are short, functional sequences, typically 18-25 nucleotides long, that regulate gene expression. The database annotates these sequences, including their genomic location within various organisms.
miRBase entries also include comprehensive annotations that link to relevant scientific literature and other external biological databases. These connections provide broader context for each miRNA, allowing researchers to explore its documented functions and interactions. The integration of sequence data with these annotations enhances the database’s utility for diverse research applications.
Navigating miRBase Nomenclature
Understanding miRBase’s naming system is important for accurate identification and communication in miRNA research. Each miRNA entry follows a structured nomenclature that conveys specific information. For instance, a name like hsa-mir-21-5p can be broken down into distinct components.
The initial three-letter prefix, such as ‘hsa’ for Homo sapiens, indicates the species. The ‘mir’ or ‘miR’ designation clarifies whether the entry refers to the precursor or mature sequence, respectively. A unique identifying number, like ’21’, is then assigned to distinguish individual miRNA families or members.
A suffix, typically ‘-5p’ or ‘-3p’, specifies which arm of the precursor hairpin the mature miRNA originates from. This distinction is important because both arms can potentially yield functional mature miRNAs, sometimes with different regulatory roles. miRBase also assigns stable accession numbers, such as ‘MI’ for precursor sequences and ‘MIMAT’ for mature sequences. These accession numbers provide persistent identifiers that remain constant across different database versions, facilitating consistent referencing.
Searching and Accessing Data
Accessing information within miRBase is straightforward. The primary method for retrieving specific miRNA data is through the search bar. Users can input a miRNA name, an accession number, or a relevant keyword to initiate a search.
Upon executing a search, the results page displays a concise overview of matching entries. This page highlights the precursor and mature miRNA sequences, their accession numbers, and direct links to their genomic context. Navigating these results allows researchers to quickly pinpoint the specific data they require.
For users needing to analyze larger datasets or integrate miRBase information into computational pipelines, the database offers bulk data access. This is primarily facilitated through an FTP (File Transfer Protocol) site, where entire releases of miRNA sequences and annotations can be downloaded. This feature supports comprehensive bioinformatic analyses, allowing researchers to process vast amounts of data offline.
The Role of miRBase in Research
miRBase provides a standardized and consistently updated reference for miRNA sequences. This standardization ensures consistency and comparability across diverse research studies. By serving as a singular, curated source, it mitigates ambiguity from disparate naming conventions or sequence variations.
The database supports reproducible science by offering a stable platform for referencing specific miRNA entries. Researchers can confidently cite miRBase accession numbers, knowing these identifiers link to precisely defined sequences and annotations. This reliability is valuable in fields where precise molecular characterization is important.
Research fields that use miRBase include cancer biology, where miRNAs are investigated as potential biomarkers or therapeutic targets. Developmental biology also relies on miRBase to understand the roles of miRNAs in organismal growth and differentiation. Its utility extends to diagnostics, where specific miRNA profiles are explored for disease detection.