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

Author:

Bai Youhuang1,Dai Xiaozhuan1,Ye Tiantian1,Zhang Peijing1,Yan Xu1,Gong Xiaonan1,Liang Siliang1,Chen Ming1

Affiliation:

1. Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China

Abstract

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/.

Funder

Research Foundation of Education Bureau of Fujian Province

Natural Science Foundation of Fujian Province

National Natural Sciences Foundation of China

National Key Research and Development Progrma of China

Publisher

Bentham Science Publishers Ltd.

Subject

Computational Mathematics,Genetics,Molecular Biology,Biochemistry

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