Hospital Sirio-Libanes, São Paulo 01308-060, Brazil.
Interunidades em Bioinformática, Universidade de São Paulo, São Paulo 05508-000, Brazil.
Bioinformatics. 2024 Sep 2;40(9). doi: 10.1093/bioinformatics/btae530.
Gene retrocopies arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species.
Here, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtles, lizards, frogs, zebrafish, and Drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology, and transposable elements (TEs). In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species.
RCPedia is available at https://www.rcpediadb.org.
基因反转录子是由加工 mRNA 转录本的反转录和基因组插入产生的。这些元件在许多物种的进化过程中极大地促进了遗传多样性和新颖性。然而，由于缺乏针对不同物种的全面、完整和用户友好的数据库，反转录子的研究一直具有挑战性。
在这里，我们介绍了 RCPedia 的一个改进版本，这是一个精心设计的用于研究反转录子的综合数据库。RCPedia 提供了在 44 个物种中鉴定的反转录子的广泛目录，其中包括 13 种灵长类动物、4 种啮齿动物、6 种翼手目动物、12 种其他哺乳动物、4 种鸟类、海龟、蜥蜴、青蛙、斑马鱼和果蝇。该数据库提供了每个物种中最完整的反转录子汇编，同时附有详细的基因组注释、表达数据和与其他数据门户的链接。此外，RCPedia 还具有简化的数据表示形式和高效的查询系统，是基因组学、进化生物学和转座元件 (TE) 等领域研究人员的宝贵工具。总之，RCPedia 的目标是增强对反转录子及其在塑造不同物种基因组景观中的关键作用的研究。
RCPedia 可在 https://www.rcpediadb.org 上获得。
