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iresbase:A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites

Genomics, Proteomics & Bioinformatics 2020年第2期18卷 129-139页

作者： Jian Zhao Yan Li Cong Wang Haotian Zhang Hao Zhang Bin Jiang Xuejiang Guo Xiaofeng Song Department of Biomedical Engineering Nanjing University of Aeronautics and AstronauticsNanjing 211106China State Key Laboratory of Reproductive Medicine Department of Histology and EmbryologyNanjing Medical UniversityNanjing 211166China Center of Pathology and Clinical Laboratory Sir Run Run HospitalNanjing Medical UniversityNanjing 211166China College of Automation Engineering Nanjing University of Aeronautics and AstronauticsNanjing 211106China

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 no5’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://***/cgi-bin/iresbase/index.php.

关键词： ires Circular RNA Long non-coding RNA Eukaryotic ires viral ires

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