AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
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DOI：
10.1093/nar/gkv1238
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Hofacker IL
中科院分区：
文献类型：
--
作者：
Fallmann J;Sedlyarov V;Tanzer A;Kovarik P;Hofacker IL
AREsite2是AREsite的更新版本，AREsite是一个在线资源，用于研究人类和小鼠mRNA 3'UTR序列中的富au元素（ARE）。新的更新和增强的版本允许详细调查AU， GU和富u元素（ARE， GRE， URE）在智人，小家鼠，猴，秀丽隐杆线虫和黑腹果蝇的转录组。它包含基因组位置、基因背景、RNA二级结构背景和注释基序的保存信息。改进包括不仅在3 ' utr中，而且在整个基因体内，包括内含子，额外的基因组，以及从全基因组扫描中局部稳定的二级结构的基序注释。此外，我们纳入了来自CLIP-Seq实验的数据，以突出具有验证蛋白相互作用的基序。此外，我们为有经验的用户提供了一个REST接口，以半自动化的方式与数据库进行交互。该数据库可在http://rna.tbi.univie.ac.at/AREsite上公开获取
AREsite2 represents an update for AREsite, an on-line resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3′UTR sequences. The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs. Improvements include annotation of motifs not only in 3′UTRs but in the whole gene body including introns, additional genomes, and locally stable secondary structures from genome wide scans. Furthermore, we include data from CLIP-Seq experiments in order to highlight motifs with validated protein interaction. Additionally, we provide a REST interface for experienced users to interact with the database in a semi-automated manner. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite