Characteristics of plant circular RNAs. (15th November 2018)

• Record Type: Journal Article
• Authors: Chu, Qinjie; Bai, Panpan; Zhu, Xintian; Zhang, Xingchen; Mao, Lingfeng; Zhu, Qian-Hao; Fan, Longjiang; Ye, Chu-Yu
• Is Part Of: Briefings in bioinformatics. Volume 21:Number 1(2020)
• Page Start: 135
• Page End: 143
• Publication Date: 2018-11-15
• Subjects: plant circRNAs -- PlantcircBase -- BLASTcirc -- non-canonical splicing signals; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bby111
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: 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.