{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T12:55:57Z","timestamp":1782564957426,"version":"3.54.5"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T00:00:00Z","timestamp":1601251200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970644"],"award-info":[{"award-number":["31970644"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Huazhong Agricultural University Scientific & Technological Self-innovation Foundation","award":["11041810351"],"award-info":[{"award-number":["11041810351"]}]},{"DOI":"10.13039\/501100012431","name":"Jiangsu Agricultural Science and Technology Independent Innovation Fund","doi-asserted-by":"publisher","award":["CX (17) 3014"],"award-info":[{"award-number":["CX (17) 3014"]}],"id":[{"id":"10.13039\/501100012431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2662017JC048"],"award-info":[{"award-number":["2662017JC048"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2032 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,\u00a0we 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.<\/jats:p>","DOI":"10.1093\/nar\/gkaa778","type":"journal-article","created":{"date-parts":[[2020,9,8]],"date-time":"2020-09-08T11:11:13Z","timestamp":1599563473000},"page":"D47-D54","source":"Crossref","is-referenced-by-count":21,"title":["Animal-APAdb: a comprehensive animal alternative polyadenylation database"],"prefix":"10.1093","volume":"49","author":[{"given":"Weiwei","family":"Jin","sequence":"first","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qizhao","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanbo","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqian","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajun","family":"Yang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Niu","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debing","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1895-2993","authenticated-orcid":false,"given":"Jing","family":"Gong","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China"},{"name":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P.R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,9,28]]},"reference":[{"key":"2021010313124744200_B1","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1101\/gr.202432.115","article-title":"A comprehensive analysis of 3\u2032 end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation","volume":"26","author":"Gruber","year":"2016","journal-title":"Genome Res."},{"key":"2021010313124744200_B2","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/nrg3482","article-title":"Alternative cleavage and polyadenylation: extent, regulation and function","volume":"14","author":"Elkon","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"2021010313124744200_B3","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/nrm.2016.116","article-title":"Alternative polyadenylation of mRNA precursors","volume":"18","author":"Tian","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2021010313124744200_B4","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nmeth.2288","article-title":"Analysis of alternative cleavage and polyadenylation by 3\u2032 region extraction and deep sequencing","volume":"10","author":"Hoque","year":"2013","journal-title":"Nat. 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Rev. RNA"},{"key":"2021010313124744200_B12","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.molcel.2011.08.017","article-title":"Mechanisms and consequences of alternative polyadenylation","volume":"43","author":"Di\u00a0Giammartino","year":"2011","journal-title":"Mol. Cell"},{"key":"2021010313124744200_B13","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1126\/science.1155390","article-title":"Proliferating cells express mRNAs with shortened 3\u2032 untranslated regions and fewer microRNA target sites","volume":"320","author":"Sandberg","year":"2008","journal-title":"Science"},{"key":"2021010313124744200_B14","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s40484-018-0148-3","article-title":"Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data","volume":"6","author":"Guvenek","year":"2018","journal-title":"Quant. 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Commun."},{"key":"2021010313124744200_B29","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/bty029","article-title":"APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data","volume":"34","author":"Ye","year":"2018","journal-title":"Bioinformatics"},{"key":"2021010313124744200_B30","doi-asserted-by":"crossref","first-page":"2521","DOI":"10.1093\/bioinformatics\/bty110","article-title":"TAPAS: tool for alternative polyadenylation site analysis","volume":"34","author":"Arefeen","year":"2018","journal-title":"Bioinformatics"},{"key":"2021010313124744200_B31","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nmeth.1528","article-title":"Analysis and design of RNA sequencing experiments for identifying isoform regulation","volume":"7","author":"Katz","year":"2010","journal-title":"Nat. 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