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Transterm：一个辅助分析mRNA中调控序列的数据库。

Transterm: a database to aid the analysis of regulatory sequences in mRNAs.

作者信息

Jacobs Grant H, Chen Augustine, Stevens Stewart G, Stockwell Peter A, Black Michael A, Tate Warren P, Brown Chris M

机构信息

Biochemistry Department and Webster Centre, University of Otago, PO Box 56 and Bioinfotools, PO Box 6129, Dunedin, New Zealand.

出版信息

Nucleic Acids Res. 2009 Jan;37(Database issue):D72-6. doi: 10.1093/nar/gkn763. Epub 2008 Nov 4.

DOI:10.1093/nar/gkn763
PMID:18984623
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2686486/
Abstract

Messenger RNAs, in addition to coding for proteins, may contain regulatory elements that affect how the protein is translated. These include protein and microRNA-binding sites. Transterm (http://mRNA.otago.ac.nz/Transterm.html) is a database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation, elongation, termination) for species or strains in Genbank, processed through a standard pipeline. The second is curated descriptions of experimentally determined regulatory elements that function as translational control elements in mRNAs. Transterm focuses on protein binding sites, particularly those in 3'-untranslated regions (3'-UTR). For this release the interface has been extensively updated based on user feedback. The data is now accessible by strain rather than species, for example there are 10 Escherichia coli strains (genomes) analysed separately. In addition to providing a repository of data, the database also provides tools for users to query their own mRNA sequences. Users can search sequences for Transterm or user defined regulatory elements, including protein or miRNA targets. Transterm also provides a central core of links to related resources for complementary analyses.

摘要

信使核糖核酸（mRNA）除了编码蛋白质外，可能还含有影响蛋白质翻译方式的调控元件。这些元件包括蛋白质结合位点和微小RNA（miRNA）结合位点。Transterm（http://mRNA.otago.ac.nz/Transterm.html）是一个关于影响翻译的区域和元件的数据库，有两个主要的独特组成部分。第一个部分是通过标准流程处理的、对Genbank中物种或菌株影响翻译（起始、延伸、终止）的一般特征进行分析的综合结果。第二个部分是对经实验确定的、在mRNA中作为翻译控制元件起作用的调控元件的精心整理的描述。Transterm专注于蛋白质结合位点，尤其是那些在3'-非翻译区（3'-UTR）中的位点。对于此次发布，基于用户反馈对界面进行了广泛更新。现在可以按菌株而非物种来访问数据，例如分别分析了10株大肠杆菌菌株（基因组）。除了提供数据仓库外，该数据库还为用户提供了查询自身mRNA序列的工具。用户可以搜索Transterm或用户定义的调控元件的序列，包括蛋白质或miRNA靶点。Transterm还提供了一个核心链接集合，指向用于互补分析的相关资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/92ea22fc9518/gkn763f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/7f56c3f782cc/gkn763f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/bca78200c00a/gkn763f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/92ea22fc9518/gkn763f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/7f56c3f782cc/gkn763f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/bca78200c00a/gkn763f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f56b/2686486/92ea22fc9518/gkn763f3.jpg

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