| Database | Brief Introduction | Organism Animal (A), plant (P) |
Types I (comprehensive database), II (miRNA-target interaction database), III (miRNA annotations in specific species), IV (others) |
Publication Span | Latest Update | Aviailability | Reference |
|---|---|---|---|---|---|---|---|
| Rfam | Rfam contains information about all types of noncoding RNA (ncRNA) families, each represented by multiple sequence alignments, consensus secondary structures, etc. Current version includes over 3000 miRNA families in different organisms. | A, P | I | 2003–2018 | V14.3 (2020) |  |
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| miRBase | miRBase is the first miRNA registry and the most influential miRNA database, which collects and accepts miRNA entries from researchers and publications in all different organisms. Abundant information on miRNAs including community contribution and curation greatly extends its capacity and influence. | A, P | I | 2003–2019 | V22.1 (2018) | |
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| ASRP | Arabidopsis Small RNA Project (ASRP) database is a collection of different type small RNAs, NGS datasets of sRNAs, PARE and mutants of key genes in small RNA biogenesis pathway in model plant, Arabidopsis. | P | III | 2005–2008 | 2016 | |
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| TarBase | TarBase is devoted to the indexing of experimentally supported miRNA targets. Current version holds over 1 million entries corresponding to around 670 000 unique miRNA-target pair interactions, which are supported by more than 33 experimental methodologies. | A, P | II | 2006–2018 | V8 (2018) | |
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| PMRD/PNRD | First version of PMRD (plant microRNA database) has 8843 miRNAs in 121 plant species while its updated version, PNRD (Plant Noncoding RNA Database) collected 25 739 noncoding RNA records from 150 plant organisms. Expression profiles and putative targets are also provided. | P | I | 2010–2014 | 2016 | |
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| miSolRNA | MiSolRNAdb harbors information about miRNAs and their predicted targets mainly in fruit development model plant, tomato. It emphasizes miRNA’s functions on fruit development and metabolism. | P | IV | 2010 | 2010 | |
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| PmiRKB | PmiRKB (Plant microRNA Knowledge Base) includes the miRNAs of two model plants, Arabidopsis (A. thaliana) and rice (O. sativa). Four major functional modules such as SNPs, Pri-miR, MiR–Tar, Self-reg are included. | P | III | 2010 | 2011 | |
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| miRTarBase | miRTarBase is a database collecting the experimentally validated microRNA-target interactions (MTIs). In general, these MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. | A, P | II | 2011–2020 | V8.0 (2010) | |
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| miRNEST | miRNEST is an integrative collection of animal, plant and virus microRNA data from its own computational predictions as well as from other databases and publications. Version 2.0 includes miRNAs from 522 animal and plant species and 22 viruses. | A, P | I | 2012–2014 | V2.0 (2014) | |
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| PMTED | Plant MiRNA Target Expression Database (PMTED) retrieved and analyzed expression profiles of miRNA targets represented in the plethora of existing microarray data, and provides variable information of miRNAs’ targets such as sequences, gene ontology, and differential expression profiles. | P | IV | 2013 | 2013 | |
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| PASmiR | PASmiR is a literature-curated and web-accessible database, and provide a solid platform for collection, standardization, and searching of these miRNA-stress regulation data in plants. | P | IV | 2013 | 2015 | |
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| starBase | starBase is an open-source platform for studying the miRNA-target interactions including miRNA-ncRNA, miRNA-mRNA, and provides validations from CLIP-seq, degradome-seq and RNA–RNA interactome data. | A, P | II | 2014 | V2.0 (2020) | |
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| mirPub | mirPub is a database for searching miRNA-related publications. | A, P | IV | 2015 | 2015 | |
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| PmiRExAt | PmiRExAt is a database mainly focusing on plant miRNA expression in multiple tissues and developmental stages, and its current version includes four species, wheat, rice, maize and Arabidopsis. | P | IV | 2016 | V1.1 (2016) | |
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| mirtronDB | mirtronDB (mirtron database) specially describes mirtrons in chordates, vertebrates and plants. All type of information on mirtrons such as sequences, structure, publications, etc., is included. | A, P | IV | 2019 | 2019 | |
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| MepmiRDB | MepmiRDB is a specific database for miRNAs in medicinal plants, and it currently accommodates thousands of miRNA candidates belonging to 29 species. | P | III | 2019 | 2019 | |
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| sRNAanno | sRNAanno includes three mayor classes in plants, miRNAs, phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). The annotations of these sRNAs covers 138 plant species with sequenced genomes and sRNA-seq datasets. | P | I | 2019 | 2019 | |
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| PmiREN | PmiREN (plant miRNA encyclopedia) is a comprehensive functional plant miRNA database based on a uniform processing pipeline, followed by manual curation using newly updated plant miRNA identification criteria. Beside solid basic information, it also provides many unique features such as analyses of conservation, synteny, targets, and so on. | P | I | 2019 | V1.0 (2020) | |
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