About

FishmiRNA database

FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles. The Methods and data used for each species' annotation appear in the Download section and in the FishmiRNA publication. Gene orthology relationships among species were curated based on relationships previously established in five fish species. Expression patterns of mature miRNAs are provided from the analysis of selected smallRNA sequencing libraries using the software Prost! (GitHub).

General statistics

The FishmiRNA database focuses on ray-finned fishes. The most recent update () provides annotations for species and covers miRNA genes and mature miRNAs.

Explore miRNA annotations

Explore the database by searching on species, genes, mature produce names, orthologies, genomic positions or by BLAST and export data, sequences and annotations.

Explore expressions

Explore and compare expression patterns of mature miRNAs provided from the analysis of selected smallRNA sequencing libraries.

Download data

Download the current or previous FishmiRNA database (TSV, FASTA and GFF for all data or per species) and find links to annotation and expression data citations.

Partners & funding

See the list of partners and funding involved in the FishmiRNA database project.

General statistics

FishmiRNA database statistics

Last update

0

miRNA genes

0

mature miRNAs

0

Species

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Phylogenetic orders

The FishmiRNA species
Species tree extracted from Rabosky et al, 2018
Hover a species name for a summary of its annotation
Click on a species name to explore its miRNAs
miRNA genes:
mature miRNAs:

Annotations

Explore FishmiRNA database

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Configure the table below by selecting column name(s)

Number of visible columns: /.
'All' columns or 'Reset to default'.
'Remove all filters' in the search box.

Search

Filter by source and/or by position
Search by BLAST against hairpin and/or mature sequences

Export

For the filtered row(s) export data, sequences or annotations

The data. A FASTA file of the hairpin sequence(s).
A FASTA file of the mature sequence(s). A GFF file of the miRNA(s).
For the selected row(s):

Expressions

Explore expression data

Show/Hide columns

Configure the table below by selecting column name(s)

Number of visible columns: /.
'All' columns or 'Reset to default'.
'Remove all filters' in the search box.

Search

Filter by source
Search by BLAST against mature sequences

Select one or more species scientific name.
Filter by miRNA name.
Filter by FishmiRNA Mature ID.
Enter query - nucl. FASTA seq(s).
Expect value
Evalue [Real].
Max output
Max output hit [Int].
Filter query sequence(s).

Export

For the filtered row(s) export data, sequences or annotations

The data.
For the selected row(s):

Download

Download data

If you make use of the data presented in FishmiRNA, please cite the FishmiRNA paper but also the original articles for the specific annotations and/or sequencing data used in your study.
Data and citations are available for FishmiRNA as a whole or by species:

Partners & Funding

Partners

INRAE

French National Research Institute
Agriculture Food and Environment

LPGP

Fish Physiology And
Genomics - @INRAE

SIGENAE

Information System for Livestock
Genomes - @INRAE

UO

University of Oregon
Institute Of Neuroscience

Funding

ANR

French National
Research Agency

NSF

National Science
Foundation

NIH

National Institutes
of Health

USAP

United States
Antarctic Program