PendoTMBase: A Database for Plant Endogenous Target Mimics

With fast-evolving next-generation sequencing technology, a great amount of plant genome and transcriptome data are becoming available. Due to the availability of mature microRNA (miRNA) sequence information from the miRBase (release 21) database, it is possible to predict endogenous target mimics (eTMs) in plant by searching seed-matched target sites. We identified a total of 2669 non-redundant eTM records in 43 plant species to create a specialized web-based database platform. The platform is named PendoTMBase, which can provide details of the eTMs. Predicted pairing structure between eTMs and their target miRNA, expression levels of eTMs pairs and associated GO annotations are also stored in the database. With evaluations performed in silico, we have found that the eTMs are representative and fit for genetic studies and high value-added plants breeding. The platform also provides a function of predicting novel eTMs based on the miRNA sequences submitted by users.