Ovine - Bovine - Caprine miRNA database

About

The RumimiR database contains an exhaustive in-depth description of the microRNAs from the literature for bovine, caprine and ovine species.
It provides the integration of all the pertinent public information about dairy ruminant microRNAs in a unique place.

General statistics

RumimiR database focus on bovine, caprine and ovine species. The last update () provides miRNAs.

explore miRNA

Explore the database by searching on position, source, feature... and export (data, sequence, annotation).

Partners

See the list of partners involved in the RumimiR project.

Release history

Download the current or previous RumimiR database release.

Dec2022 - 22348 miRNAs - tsv - fasta - gff
March2021 - 20095 miRNAs - tsv - fasta - gff
Jan2020 - 19847 miRNAs - tsv - fasta - gff
June2019 - 16041 miRNAs - tsv - fasta - gff

General statistics

See below some statistics about RumimiR database (several counts, distribution per species, breed and tissue, ...)
Click on the context button in the top right corner of the each chart to print and/or download
When a legend is available, click on item to show/hide the data series

Last update

Number of miRNA

Related publications

Number of miRNA

Explore

Available boxes below allow you to explore miRNA
Show/hide columns, filter by position and/or by source and/or by feature and export...

Show/hide columns

Configure the table below by selecting column name(s)

	Column name	Description
1	Chr.	Chromosome name
2	Start	Genomic position of the microRNA - Start
3	End	Genomic position of the microRNA - End
4	Multi-mapping	Number of localisations in case of multi-mapping (with 100% query cover and 100% identity)
5	Sequence	Sequence of the mature microRNA
6	Publication	Publication in which the microRNA is described
7	Name	Name assigned to the microRNA
8	IsomiRs	Name of isomiRs of the microRNA (sequence and genomic position almost identical)
9	RumimiR id	Name of the microRNA with the RumimiR nomenclature (Rum-[BTA\|CHI\|OAR]-XXXXX)
10	Family	microRNA family to which the microRNA is affiliated
11	Tissue	Tissue in which the microRNA was discovered
12	Breed	Breed used during the study
13	Study conditions	Conditions prevailing during the study
14	Lactation stages	Lactation stages of the animals studied
15	Age	Age of the animals studied
16	Species	Species of the animals studied (bovine, caprine or ovine)
17	Number	Number of novel microRNAs described in the publication
18	Cut-off	Cut-off point used in the publication to detect novel microRNAs
19	Method	Method used to detect novel microRNAs
20	Number and breed	Number of animals studied in each breed
21	Reference genome	UMD3.1.1, ARS1 or Oar v4.0
22	Bioinformatics tools used	Software used in the study for the microRNA detection
23	Condition details	Details of study conditions (i.e. number of animals per condition)
24	5p/3p	If the microRNA is 5p or 3p
25	Strand (+/-)	Strand in which the microRNA is situated
26	Star sequence	Sequence of the star microRNA
27	Matching seed	Known microRNA with the same seed
28	small RNAs	If the microRNA described is in fact part of a snoRNA, tRNA, snRNA or rRNA
29	hsa homology	Similarity with a human microRNA
30	mmu homology	Similarity with a mouse microRNA
31	FP code	Four-digit false positive code representing four positions, each with a value of “0” or “1” (0000 to 1111): “1” in first position means that the microRNA has multiple genomic locations, “1” in second position means that the microRNA is not already listed in the RumimiR database (a microRNA occurring in different publications is more likely to be a true microRNA), “1” in third position means that the microRNA has homology with small RNAs, “1” in fourth position means that the microRNA has no identity with either human or mouse microRNA present in miRBase.

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Chromosome

Focus on miRNA located on a chromosome of interest.

Start

Start position must be greater than...

End

End position must be lower than...

Species

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Breed

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Tissue

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Specific

Select tissue-specific.

Condition

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FP code

Select one or more False Positive code.

Method

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Software

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Enter query - nucl. FASTA seq(s).

Expect value

Evalue [Real].

Max output

Max output hit [Int].

Filter

Filter query sequence(s).

Export

For the filtered row(s) export...

The data. A fasta file of the miRNA sequence(s). A GFF file of the miRNA.

Partners

See below the partners involved in the RumimiR project

INRAE

French National Research Institute Agriculture Food and Environment

GABI

Animal Genetics and Integrative Biology Unit - @INRAE

GenPhySE

Genetics Physiology and Breeding Systems Unit - @INRAE

SIGENAE

Information System for Livestock Genomes - @INRAE

APIS-GENE

Investing Innovating Adding value to Ruminant Genomics Research

The bovine, caprine and ovine miRNA database

About

General statistics

explore miRNA

Partners

Release history

General statistics

Explore

Show/hide columns

Search

Export

Partners

INRAE

GABI

GenPhySE

SIGENAE

APIS-GENE