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IRESbase: a Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites

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

Posted 16 Jan 2020
bioRxiv DOI: 10.1101/2020.01.15.894592 (published DOI: 10.1016/j.gpb.2020.03.001)

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, with no 5′ cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidences will be useful for further studies. In this study, we present a comprehensive database of IRESs (IRESbase) by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNA information. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses. As our database collected only IRES of minimal length with functional evidences, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and lncRNAs, 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequences. The IRESbase is available at <http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php>.

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