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miRBase
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
