miRNA Database

Database Brief Introduction Organism

Animal (A), plant (P)


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  2003–2018  V14.3 (2020)  gobtn gobtn
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  2003–2019  V22.1 (2018)  gobtn gobtn
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.  III  2005–2008  2016  gobtn gobtn
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)  gobtn gobtn
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.  2010–2014  2016  gobtn gobtn
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.  IV  2010  2010  gobtn gobtn
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.  III  2010  2011  gobtn gobtn
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)  gobtn gobtn
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  2012–2014  V2.0 (2014)  gobtn gobtn
miRFANs  miRFANs is a comprehensive collection of miRNA targets for A. thaliana and a highly informative miRNA-mediated genetic regulatory network.  IV  2012  2012  gobtn gobtn
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.  IV  2013  2013  gobtn gobtn
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.  IV  2013  2015  gobtn gobtn
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)  gobtn gobtn
mirPub  mirPub is a database for searching miRNA-related publications.  A, P  IV  2015  2015  gobtn gobtn
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.  IV  2016  V1.1 (2016)  gobtn gobtn
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  gobtn gobtn
MepmiRDB  MepmiRDB is a specific database for miRNAs in medicinal plants, and it currently accommodates thousands of miRNA candidates belonging to 29 species.  III  2019  2019  gobtn gobtn
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.  2019  2019  gobtn gobtn
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.  2019  V1.0 (2020)  gobtn gobtn