research-article

AtNAGNAG: a comprehensive database for NAGNAG alternative splicing in Arabidopsis thaliana

Authors:

Gengxin ZhangAuthors Info & Claims

ICBDR '18: Proceedings of the 2nd International Conference on Big Data Research

Pages 33 - 37

https://doi.org/10.1145/3291801.3291840

Published: 27 October 2018 Publication History

Abstract

NAGNAG alternative splicing is widely present in animal genomes. In plants, there has been little large-scale exploration of NAGNAG splicing, even in model plants such as Arabidopsis thaliana. To address this, here we describe the first database of NAGNAG motifs and their expression ratios between two splicing sites in A. thaliana. Using 435 RNA-seq datasets, we systematically identified and quantified 1,890 unique NAGNAG motifs as well as the variation of expression ratio between two splicing sites from six tissues, including 200 motifs with two novel splicing sites and 1,208 motifs containing one novel splicing site. Using this database, it is now possible to browse, search, visualize and download Arabidopsis NAGNAG motifs. The collected information can also be used to retrieve the related tissue-specific transcript and amino acid information. The database largely expands our knowledge about NAGNAG events. Placing these data in a unified browsing platform should enable high throughput functional validation of the identified NAGNAG events and understand the regulatory role of NAGNAG splicing motifs through the variation of expression ratios. Database URL: http://deepbiology.cn/nagnag.

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Cited By

Cabezas-Fuster AMicol-Ponce RFontcuberta-Cervera SPonce M(2022) Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites Nucleic Acids Research10.1093/nar/gkac33850:10(5513-5527)Online publication date: 26-May-2022
https://doi.org/10.1093/nar/gkac338

Index Terms

AtNAGNAG: a comprehensive database for NAGNAG alternative splicing in Arabidopsis thaliana
1. Information systems
  1. Information systems applications
    1. Data mining

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ICBDR '18: Proceedings of the 2nd International Conference on Big Data Research

October 2018

221 pages

ISBN:9781450364768

DOI:10.1145/3291801

Copyright © 2018 ACM.

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Shandong Univ.: Shandong University
University of Queensland: University of Queensland
Dalian Maritime University

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Association for Computing Machinery

New York, NY, United States

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Published: 27 October 2018

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ICBDR 2018: 2018 The 2nd International Conference on Big Data Research

October 27 - 29, 2018

Weihai, China

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Cited By

Cabezas-Fuster AMicol-Ponce RFontcuberta-Cervera SPonce M(2022) Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites Nucleic Acids Research10.1093/nar/gkac33850:10(5513-5527)Online publication date: 26-May-2022
https://doi.org/10.1093/nar/gkac338

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