Alternative cleavage and polyadenylation (APA) is increasingly recognized as an important regulatory mechanism in eukaryotic gene expression and is dynamically modulated in a developmental, tissue-specific, or environmentally responsive manner. Given the functional importance of APA and the rapid accumulation of APA sites in plants, a comprehensive and easily accessible APA site database is necessary for improved understanding of APA-mediated gene expression regulation. We present a database called PlantAPAdb that catalogs the most comprehensive APA site data derived from sequences from diverse 3' sequencing protocols and biological samples in plants. Currently, PlantAPAdb contains APA sites in six species, Oryza sativa (japonica and indica), Arabidopsis (Arabidopsis thaliana), Medicago truncatula, Trifolium pratense, Phyllostachys edulis, and Chlamydomonas reinhardtii APA sites in PlantAPAdb are available for bulk download and can be queried in a Google-like manner. PlantAPAdb provides rich information of the whole-genome APA sites, including genomic locations, heterogeneous cleavage sites, expression levels, and sample information. It also provides comprehensive poly(A) signals for APA sites in different genomic regions according to distinct profiles of cis-elements in plants. In addition, PlantAPAdb contains events of 3' untranslated region shortening/lengthening resulting from APA, which helps to understand the mechanisms underlying systematic changes in 3' untranslated region lengths. Additional information about conservation of APA sites in plants is also available, providing insights into the evolutionary polyadenylation configuration across species. As a user-friendly database, PlantAPAdb is a large and extendable resource for elucidating APA mechanisms, APA conservation, and gene expression regulation.

中文翻译：

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PlantAPAdb：植物中其他聚腺苷酸化位点的综合数据库。

替代切割和聚腺苷酸化（APA）越来越被认为是真核基因表达中的重要调控机制，并以发育，组织特异性或对环境敏感的方式动态调节。鉴于APA的功能重要性以及植物中APA位点的快速积累，一个全面且易于访问的APA位点数据库对于增进对APA介导的基因表达调控的了解是必要的。我们提供了一个名为PlantAPAdb的数据库，该数据库对最全面的APA站点数据进行了分类，该数据是从植物3D测序协议的序列和生物样品中获得的。目前，PlantAPAdb包含六个物种的APA位点，分别为稻（粳稻和in稻），拟南芥（拟南芥），Medi藜，Medi叶，毛竹，和PlantAPAdb中的衣藻APA站点可以批量下载，并且可以类似Google的方式查询。PlantAPAdb提供了全基因组APA位点的丰富信息，包括基因组位置，异源切割位点，表达水平和样品信息。它还根据植物中顺式元素的独特概况，为不同基因组区域中的APA位点提供了全面的poly（A）信号。此外，PlantAPAdb包含由APA引起的3'非翻译区缩短/延长事件，这有助于了解3'非翻译区长度系统变化的潜在机制。还可以获得有关植物中APA位点保守性的其他信息，从而提供了对跨物种进化的聚腺苷酸构型的见解。