IRESbase


32512182	IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. [PMID: 32512182] Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang, Xuejiang Guo, Xiaofeng Song Abstract Internal ribosome entry sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA (circRNA), with no 5' cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidence will be useful for further studies. In this study, we present IRESbase, a comprehensive database of IRESs, by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNAs. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses, respectively. As IRESbase collects only IRES of minimal length with functional evidence, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and long non-coding RNAs (lncRNAs), 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequence. IRESbase is available at http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php. Genomics Proteomics Bioinformatics. 2020:() \| 37 Citations (from Europe PMC, 2025-03-15)

IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. [PMID: 32512182]

Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang, Xuejiang Guo, Xiaofeng Song

Internal ribosome entry sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA (circRNA), with no 5' cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidence will be useful for further studies. In this study, we present IRESbase, a comprehensive database of IRESs, by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNAs. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses, respectively. As IRESbase collects only IRES of minimal length with functional evidence, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and long non-coding RNAs (lncRNAs), 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequence. IRESbase is available at http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php.

Genomics Proteomics Bioinformatics. 2020:() | 37 Citations (from Europe PMC, 2025-03-15)

URL:	http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php
Full name:	Internal ribosome entry sites
Description:	A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites.
Year founded:	2020
Last update:	2020-04-01
Version:
Accessibility:	Accessible
Country/Region:	China

Data type:	RNA
Data object:	Animal Fungi Plant Virus
Database category:	Literature
Major species:	Homo sapiens Mus musculus Drosophila melanogaster Rattus norvegicus Saccharomyces cerevisiae Zea mays Aplysia californica Canis lupus Gallus gallus Mus pahari Nicotiana tabacum Ovis aries
Keywords:	Internal Ribosome Entry Sites

University/Institution:	Nanjing University of Aeronautics and Astronautics
Address:	Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
City:	Nanjing
Province/State:	Jiangsu
Country/Region:	China
Contact name (PI/Team):	Xiaofeng Song
Contact email (PI/Helpdesk):	xfsong@nuaa.edu.cn

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