The aim of Medicago-MIRATdb is to provide the research community with a resource of putative M. truncatula miRNAs, their potential target genes, and other supporting information from our in-house analysis to assist in the selection of candidate miRNAs and target genes for experimental design. The database currently contains 17,175 predicted miRNAs and their 3,331 unique precursor regions as well as the 16,734 genes potentially targeted by these miRNAs. While most of these miRNAs are predicted from introns, 445 are on the exons of 88 non-coding RNA transcripts. These candidate miRNAs and their targets have three main features: (i) they are free from repetitive and low complexity elements, (ii) they meet the two-dimensional structure and energy requirements, and (iii) they have near perfect miRNA::target duplex bindings.

The database provides detailed information on the sequences of the predicted miRNAs, their precursors and target genes as well as the alignments of the miRNA::miRNA* and miRNA::target duplexes, and sequence source information such as the EST library, tissue category, and EST clone number. Information about miRNA conservation in other plant species, functional classification of the target genes, and clusters of similar miRNA are also provided. The web-interface of the database affords flexibility in both search and download choices for miRNAs or target genes of interest to assist in miRNA experimental design.

Database constuction pipeline

Access Database

List of putative miRNAs