RNA Type: miRNA
Overview: miRBase is one of the central repositories of microRNA, with information based on published experimental data and in-house annotation. The database is divided into three parts: (i) miRBase Registry, which provides a nomenclature for functional annotation of miRNAs; (ii) miRBase Targets, which contains predicted miRNA target genes; and (iii) miRBase Sequence, which contains published miRNA sequences and their annotation. The release 16 contains some dataset obtained from next generation sequencing.
Search Methods:
  • Similarity: search sequences using the BLAST or SSEARCH.
  • Keyword: search by miRNA accession or name (general search); or by miRNA id, gene name, Ensembl identifier or GO term (target search).
  • TAG: search by genome or GO class.
  • Tabular: search by species.
  • Genomic Location: choosing for an organism and chromosome location.
  • Density of ncRNAs: for a cluster inter-miRNA in an organism according to different distances between each miRNA. There is also an option of genomic regions (e.g. CpG island, EST, cDNA, TFBS) surrounding miRNA precursors.
Source: Literature, Ensembl, UCSC Genome Browser.
Information Source: Experimental, In silico annotation.
Information Content: Annotation, Cluster, Evidence, Expression, Next-generation sequencing, Nomenclature of miRNA, Sequence, Structure, Target gene, Tissue.
Reference: Griffiths-Jones et al., 2008
PubmedID: 14681370, 16381832, 17991681, 20205188, 21037258.
Year: 2011;2010;2008;2006;2004
Multiple search: Yes
Download: GFF, EMBL, FASTA, Other.
Genomic Overview: No
Organism: Homo sapiens (Human), Rattus norvegicus (Norway Rat), Canis familiaris (Dog), Mus musculus (House Mouse), Danio rerio (Zebrafish), Takifugu rubripes (Fugu), Gallus gallus (Chicken), Ciona intestinalis, Drosophila melanogaster (Common Fruit Fly), Caenorhabditis elegans, Arabidopsis Thaliana (Thale Cress), Macaca mulatta (Rhesus Monkey), Bos Taurus (Cattle), Ovis aries (Sheep), Sus scrofa (Wild Boar) and 142 others.

Url: http://www.mirbase.org/
June 2018: Release 3.0