mirtronDB: a mirtron knowledge base
Abstract
Mirtrons arise from short introns with atypical cleavage by using the splicing mechanism. In the current literature, there is no repository centralizing and organizing the data available to the public. To fill this gap, we developed mirtronDB, the first knowledge database dedicated to mirtron, and it is available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB currently contains a total of 1,407 mirtron precursors and 2,426 mirtron mature sequences in 18 species. MirtronDB is a specialized resource that provides free and user- friendly access to knowledge on mirtron data; it is useful to explore mirtrons and their regulations. This pape was based the original publicaion in Bioinformatics IF: 5.481 (https://doi.org/10.1093/bioinformatics/btz153).
References
Bonnet, E. et al. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics, Bioinformatics, 26, 1566-1568.
Budak, H. and Akpinar, B. (2015) Plant miRNAs: biogenesis, organization and origins, Functional & Integrative Genomics, 15, 523-531.
Dai, X. et al. (2018) psRNATarget: a plant small RNA target analysis server (2017 release), Nucleic Acids Research.
Das, S. et al. (2018) miRwayDB: a database for experimentally validated microRNA- pathway associations in pathophysiological conditions. Database (Oxford). 2018: bay023.
Fonseca B., Domingues D., Paschoal AR. mirtronDB: a mirtron knowledge base. Bioinformatics. btz153. doi: 10.1093/bioinformatics/btz153.
Gallart, A. et al. (2015) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Research, 44, D1161-D1166.
Griffiths-Jones, S. et al. (2006) miRBase: microRNA sequences, targets and gene nomenclature, Nucleic Acids Research, 34, D140-D144.
Grzegorz, R. et al. (2018) Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods, Scientific Reports, 8(1).
Huang, B. et al. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, 2, 680-682.
Lorenzetti, A. P. R. et al. (2016) PlanTE-MIR DB: a database for transposable element- related microRNAs in plant genomes. Functional & Integrative Genomics, 1-8.
Maracaja-Coutinho, V. et al. (2019), Chapter 10: Noncoding RNAs Databases: Current Status and Trend, Book: Computational Biology of Non-Coding RNA: Methods and Protocols, Springer New York, 1th edition.
Okamura, K. et al. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila, Cell, 89-100.
Paschoal, A. R. et al. (2012) Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA Biology, 274-282.
Qu, Z. and Adelson, D. (2012) Evolutionary conservation and functional roles of ncRNA, Frontiers in Genetics, 3, 205.
Ruby, J. G. et al. (2007) Intronic microRNA precursors that bypass Drosha processing, Nature, 448, 83.
