Journal
BRIEFINGS IN BIOINFORMATICS
Volume 21, Issue 1, Pages 135-143Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bby111
Keywords
plant circRNAs; PlantcircBase; BLASTcirc; non-canonical splicing signals
Funding
- National Science Foundation of China [91740108]
- Natural Science Foundation of Zhejiang Province [LY17C130004]
- Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP)
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Circular RNA (circRNA) is a kind of covalently closed single-stranded RNA molecules that have been proved to play important roles in transcriptional regulation of genes in diverse species. With the rapid development of bioinformatics tools, a huge number (95143) of circRNAs have been identified from different plant species, providing an opportunity for uncovering the overall characteristics of plant circRNAs. Here, based on publicly available circRNAs, we comprehensively analyzed characteristics of plant circRNAs with the help of various bioinformatics tools as well as in-house scripts and workflows, including the percentage of coding genes generating circRNAs, the frequency of alternative splicing events of circRNAs, the non-canonical splicing signals of circRNAs and the networks involving circRNAs, miRNAs and mRNAs. All this information has been integrated into an upgraded online database, PlantcircBase 3.0 (http://ibi.zju.edu.cn/plantcircbase/). In this database, we provided browse, search and visualization tools as well as a web-based blast tool, BLASTcirc, for prediction of circRNAs from query sequences based on searching against plant genomes and transcriptomes.
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