PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

被引：27
作者：
Bai, Youhuang [1 ,2 ]
Dai, Xiaozhuan [1 ,2 ]
Ye, Tiantian [2 ]
Zhang, Peijing [2 ]
Yan, Xu [2 ]
Gong, Xiaonan [2 ]
Liang, Siliang [2 ]
Chen, Ming [2 ]
机构：
[1] Fujian Agr & Forestty Univ, Coll Life Sci, Dept Bioinformat, Fuzhou 350002, Fujian, Peoples R China
[2] Zhejiang Univ, Coll Life Sci, Dept Bioinformat, State Key Lab Plant Physiol & Biochem, Hangzhou 310058, Zhejiang, Peoples R China
来源：
CURRENT BIOINFORMATICS | 2019年 / 14卷 / 07期
关键词：
Plant lncRNA prediction; RNA-protein interaction; lncRNA database; Arabidopsis thaliana; Populus trichocarpa; Zea mays; GENOME-WIDE IDENTIFICATION; LONG NONCODING RNAS; WEB SERVER; DATABASE; CHROMATIN; TRANSCRIPTS; MECHANISMS; PREDICTION; EVOLUTION; PLATFORM;
D O I：
10.2174/1574893614666190131161002
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.
引用
收藏
页码：621 / 627
页数：7
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