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Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline

  • Rui Dong
  • Xu-Kai Ma
  • Ling-Ling Chen
  • Li YangEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1870)

Abstract

Circular RNAs (circRNAs) derived from back-spliced exons were sporadically identified about 25 years ago, and have been recently re-discovered genome-wide across different species. Interestingly, one gene locus can generate multiple circRNAs through alternative back-splicing and/or alternative splicing, thus expanding our understanding on the diversity and complexity of transcriptomes. Precise annotation of circRNAs with their alternative back-splicing and alternative splicing events is the basis for the functional characterization of different categories of circRNAs. Here we describe a step-by-step computational scheme to annotate circRNAs from publicly available RNA sequencing datasets with the CIRCexplorer2 pipeline.

Key words

CircRNA CIRCexplorer Computational biology Alternative back-splicing Alternative splicing 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of SciencesShanghaiChina
  2. 2.State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of SciencesShanghaiChina

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