Animal-APAdb


32986825	Animal-APAdb: a comprehensive animal alternative polyadenylation database. [PMID: 32986825] Jin W, Zhu Q, Yang Y, Yang W, Wang D, Yang J, Niu X, Yu D, Gong J. Abstract Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that recognizes different polyadenylation signals on transcripts, resulting in transcripts with different lengths of 3' untranslated regions and thereby influencing a series of biological processes. Recent studies have highlighted the important roles of APA in human. However, APA profiles in other animals have not been fully recognized, and there is no database that provides comprehensive APA information for other animals except human. Here, by using the RNA sequencing data collected from public databases, we systematically characterized the APA profiles in 9244 samples of 18 species. In total, we identified 342 952 APA events with a median of 17 020 per species using the DaPars2 algorithm, and 315 691 APA events with a median of 17 953 per species using the QAPA algorithm in these 18 species, respectively. In addition, we predicted the polyadenylation sites (PAS) and motifs near PAS of these species. We further developed Animal-APAdb, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal-APAdb/) for data searching, browsing and downloading. With comprehensive information of APA events in different tissues of different species, Animal-APAdb may greatly facilitate the exploration of animal APA patterns and novel mechanisms, gene expression regulation and APA evolution across tissues and species. Nucleic Acids Res. 2021:49(D1) \| 8 Citations (from Europe PMC, 2025-03-22)

Animal-APAdb: a comprehensive animal alternative polyadenylation database. [PMID: 32986825]

Jin W, Zhu Q, Yang Y, Yang W, Wang D, Yang J, Niu X, Yu D, Gong J.

Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that recognizes different polyadenylation signals on transcripts, resulting in transcripts with different lengths of 3' untranslated regions and thereby influencing a series of biological processes. Recent studies have highlighted the important roles of APA in human. However, APA profiles in other animals have not been fully recognized, and there is no database that provides comprehensive APA information for other animals except human. Here, by using the RNA sequencing data collected from public databases, we systematically characterized the APA profiles in 9244 samples of 18 species. In total, we identified 342 952 APA events with a median of 17 020 per species using the DaPars2 algorithm, and 315 691 APA events with a median of 17 953 per species using the QAPA algorithm in these 18 species, respectively. In addition, we predicted the polyadenylation sites (PAS) and motifs near PAS of these species. We further developed Animal-APAdb, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal-APAdb/) for data searching, browsing and downloading. With comprehensive information of APA events in different tissues of different species, Animal-APAdb may greatly facilitate the exploration of animal APA patterns and novel mechanisms, gene expression regulation and APA evolution across tissues and species.

Nucleic Acids Res. 2021:49(D1) | 8 Citations (from Europe PMC, 2025-03-22)

URL:	http://gong_lab.hzau.edu.cn/Animal-APAdb
Full name:
Description:	A comprehensive animal alternative polyadenylation database.
Year founded:	2021
Last update:
Version:
Accessibility:	Accessible
Country/Region:	China

Data type:	RNA
Data object:	Animal
Database category:	Expression
Major species:	Homo sapiens Mus musculus Rattus nativitatis Papio anubis Gallus gallus Pan troglodytes Xenopus tropicalis Bos taurus Macaca fascicularis Drosophila melanogaster Chlorocebus sabaeus Equus caballus Sus scrofa Oryctolagus cuniculus Rattus norvegicus Macaca mulatta Ovis aries Caenorhabditis elegans Danio rerio
Keywords:	alternative polyadenylation

University/Institution:	Huazhong Agricultural University
Address:	Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.
City:	Wuhan
Province/State:	Hubei
Country/Region:	China
Contact name (PI/Team):	Jing Gong
Contact email (PI/Helpdesk):	gong.jing@mail.hzau.edu.cn

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Database Commons a catalog of worldwide biological databases