Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.
Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.
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DOI：
10.1093/nar/gkac1094
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发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
Gregory, Richard, I
中科院分区：
文献类型：
--
作者：
Liu, Qi;Peng, Xin;Shen, Mengyuan;Qian, Qian;Xing, Junlian;Li, Chen;Gregory, Richard, I
上游开放阅读框架(UORF)通常被定义为位于信使RNA(MRNAs)主要蛋白质编码序列(CDS)上游的5‘非翻译区内的翻译位点。虽然uORF广泛存在于真核生物的mRNAs中，并调节下游CDS的翻译，但目前还缺乏关于uORF的全面资源。我们开发了RiBO-uORF(http://rnainformatics.org.cn/RiboUORF))，作为基于核糖体图谱(RiBO-SEQ)数据的uORF分析的综合功能资源。Ribo-uORF目前支持六种物种：人、小鼠、大鼠、斑马鱼、果蝇和蠕虫。Ribo-uORF包括501 554个主动翻译的uORF和107 914个上游翻译起始位点(UTI)，分别从1495个Ribo-seq和77个定量翻译起始序列(QTI-seq)数据集中识别出来。我们还开发了mRNA浏览来可视化项目，如uORF、顺式调控元件、遗传变异、eQTL、基于GWAS的关联、RNA修改和RNA编辑。Ribo-uORF提供了一个非常直观的Web界面，可以方便地浏览、搜索和可视化uORF数据。最后，在Ribo-uORF中开发了uORFcan和UTR5var，利用用户上传的数据集精确识别uORFs并分析基因突变对uORFs的影响。Ribo-uORF将极大地促进uORF及其在mRNA翻译和转录后基因表达调控中的作用的研究。RIBO-uORF是一个全面的数据库，它为根据核糖体图谱数据和几个相关资源识别和表征uORF提供了宝贵的资源和分析工具。
Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5′ untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs). Although uORFs are prevalent in eukaryotic mRNAs and modulate the translation of downstream CDSs, a comprehensive resource for uORFs is currently lacking. We developed Ribo-uORF (http://rnainformatics.org.cn/RiboUORF) to serve as a comprehensive functional resource for uORF analysis based on ribosome profiling (Ribo-seq) data. Ribo-uORF currently supports six species: human, mouse, rat, zebrafish, fruit fly, and worm. Ribo-uORF includes 501 554 actively translated uORFs and 107 914 upstream translation initiation sites (uTIS), which were identified from 1495 Ribo-seq and 77 quantitative translation initiation sequencing (QTI-seq) datasets, respectively. We also developed mRNAbrowse to visualize items such as uORFs, cis-regulatory elements, genetic variations, eQTLs, GWAS-based associations, RNA modifications, and RNA editing. Ribo-uORF provides a very intuitive web interface for conveniently browsing, searching, and visualizing uORF data. Finally, uORFscan and UTR5var were developed in Ribo-uORF to precisely identify uORFs and analyze the influence of genetic mutations on uORFs using user-uploaded datasets. Ribo-uORF should greatly facilitate studies of uORFs and their roles in mRNA translation and posttranscriptional control of gene expression. Ribo-uORF is a comprehensive database that provides valuable resources and analysis tools for the identification and characterization of uORFs based on ribosome profiling data and several related resources.
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影响因子：
64.8
作者：
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通讯作者：
Pandey, Akhilesh
影响因子：
14.9
作者：
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通讯作者：
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影响因子：
12.3
作者：
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影响因子：
14.9
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Flicek P