PlantCircRNA: a comprehensive database for plant circular RNAs.

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-08-27 DOI:10.1093/nar/gkae709

Shutian He, Jianhao Bing, Yang Zhong, Xiaoyang Zheng, Ziyu Zhou, Yifei Wang, Jiming Hu, Xiaoyong Sun

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Abstract

Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.

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PlantCircRNA：植物环状核糖核酸综合数据库。

环状 RNA（circRNA）是最近发现的新型非编码调控 RNA。虽然它们存在于许多真核生物中，但对植物 circRNA 的研究却很有限。我们开发了 PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) 来填补这一空白。PlantCircRNA 最重要的两个特点是：(i) 它根据 39 245 份 RNA 测序样本纳入了 94 种植物的 circRNA；(ii) 它导入了原始 AtCircDB 和 CropCircDB 数据库。我们对已发表文章中的所有 circRNA 进行了人工整理，并将其导入数据库。此外，我们还在数据库中添加了组织和非生物胁迫的详细信息。为了帮助用户了解这些 circRNA，数据库包括一个检测分数来衡量它们的一致性，并按照最近为真核生物提出的指南建立了一个命名系统。最后，我们为用户开发了一个综合平台，用于可视化、分析和下载有关特定 circRNA 的数据。该资源将成为植物 circRNAs 的家园，并为社区提供有关这些神秘分子的前所未有的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.