IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites.

Genomics, Proteomics & Bioinformatics
Jian ZhaoXiaofeng 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 availab...Continue Reading

Citations

Nov 22, 2020·Pharmacological Reviews·Torsten Schöneberg, Ines Liebscher
Mar 10, 2021·Genome Biology·Huihui LiHongwei Wang
May 5, 2021·Database : the Journal of Biological Databases and Curation·Tzu-Hsien YangCheng-Tse Liu
May 21, 2021·Nature·Jessica Sook Yuin HoIvan Marazzi
Jun 8, 2021·Journal of Clinical Laboratory Analysis·Yaqin LuZhisen Shen
Aug 4, 2021·Wiley Interdisciplinary Reviews. RNA·Tanvi SinhaAmaresh Chandra Panda
Sep 28, 2021·Nucleic Acids Research·Dezhong LvYongsheng Li

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Software Mentioned

BLAST
Metascape
CPAT
IRESite
Vienna RNA package
Excel
RNAfold
Windows
circAtlas
miRanda

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