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Literature DB >> 33685493

riboCIRC: a comprehensive database of translatable circRNAs.

Huihui Li¹, Mingzhe Xie¹, Yan Wang¹, Ludong Yang¹, Zhi Xie², Hongwei Wang³.

Abstract

riboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com .

Entities: Chemical

Keywords: CircRNAs; Ribosome profiling; Translatable circRNAs; circRNA-encoded peptides

Mesh：

Substances：
Peptides
RNA, Circular

Year: 2021 PMID： 33685493 PMCID： PMC7938571 DOI： 10.1186/s13059-021-02300-7

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 13.583

46 in total

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Review 3. The biogenesis, biology and characterization of circular RNAs.

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Journal: Nat Rev Genet Date: 2019-08-08 Impact factor: 53.242

4. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1.

Authors: Kotb Abdelmohsen; Amaresh C Panda; Rachel Munk; Ioannis Grammatikakis; Dawood B Dudekula; Supriyo De; Jiyoung Kim; Ji Heon Noh; Kyoung Mi Kim; Jennifer L Martindale; Myriam Gorospe
Journal: RNA Biol Date: 2017-01-12 Impact factor: 4.652

5. Specific identification and quantification of circular RNAs from sequencing data.

Authors: Jun Cheng; Franziska Metge; Christoph Dieterich
Journal: Bioinformatics Date: 2015-11-09 Impact factor: 6.937

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Authors: Shengli Li; Yuchen Li; Bing Chen; Jingjing Zhao; Shulin Yu; Yan Tang; Qiupeng Zheng; Yan Li; Peng Wang; Xianghuo He; Shenglin Huang
Journal: Nucleic Acids Res Date: 2018-01-04 Impact factor: 16.971

Review 7. Ribosome profiling reveals the what, when, where and how of protein synthesis.

Authors: Gloria A Brar; Jonathan S Weissman
Journal: Nat Rev Mol Cell Biol Date: 2015-10-14 Impact factor: 94.444

8. NCBI BLAST: a better web interface.

Authors: Mark Johnson; Irena Zaretskaya; Yan Raytselis; Yuri Merezhuk; Scott McGinnis; Thomas L Madden
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9. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Authors: Daehwan Kim; Geo Pertea; Cole Trapnell; Harold Pimentel; Ryan Kelley; Steven L Salzberg
Journal: Genome Biol Date: 2013-04-25 Impact factor: 13.583

10. Extensive translation of circular RNAs driven by N⁶-methyladenosine.

Authors: Yun Yang; Xiaojuan Fan; Miaowei Mao; Xiaowei Song; Ping Wu; Yang Zhang; Yongfeng Jin; Yi Yang; Ling-Ling Chen; Yang Wang; Catherine Cl Wong; Xinshu Xiao; Zefeng Wang
Journal: Cell Res Date: 2017-03-10 Impact factor: 25.617

10 in total

1. Tissue- and stage-specific landscape of the mouse translatome.

Authors: Hongwei Wang; Yan Wang; Jiaqi Yang; Qian Zhao; Nan Tang; Congying Chen; Huihui Li; Chichi Cheng; Mingzhe Xie; Yang Yang; Zhi Xie
Journal: Nucleic Acids Res Date: 2021-06-21 Impact factor: 16.971

Review 2. Circular RNAs in cardiovascular diseases.

Authors: Xiaohan Mei; Shi-You Chen
Journal: Pharmacol Ther Date: 2021-09-27 Impact factor: 12.310

Review 3. Circular RNA translation, a path to hidden proteome.

Authors: Tanvi Sinha; Chirag Panigrahi; Debojyoti Das; Amaresh Chandra Panda
Journal: Wiley Interdiscip Rev RNA Date: 2021-08-02 Impact factor: 9.349

4. circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome.

Authors: Wenliang Zhang; Yang Liu; Zhuochao Min; Guodong Liang; Jing Mo; Zhen Ju; Binghui Zeng; Wen Guan; Yan Zhang; Jianliang Chen; Qianshen Zhang; Hanguang Li; Chunxia Zeng; Yanjie Wei; Godfrey Chi-Fung Chan
Journal: Nucleic Acids Res Date: 2022-01-07 Impact factor: 16.971