Animal-APAdb: a comprehensive animal alternative polyadenylation database
| Autor: | Jing Gong, Weiwei Jin, Debing Yu, Dongyang Wang, Xiaohui Niu, Wenqian Yang, Jiajun Yang, Yanbo Yang, Qizhao Zhu |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Untranslated region
Polyadenylation AcademicSubjects/SCI00010 education Biology Web Browser computer.software_genre 03 medical and health sciences 0302 clinical medicine mental disorders Databases Genetic Genetics Animals Humans Database Issue RNA Messenger Nucleotide Motifs 3' Untranslated Regions 030304 developmental biology Regulation of gene expression 0303 health sciences Database Mechanism (biology) Three prime untranslated region Alternative splicing RNA Computational Biology Animal Alternative Alternative Splicing 030220 oncology & carcinogenesis computer psychological phenomena and processes Software |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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