Affiliation:
1. Hospital Sirio-Libanes , São Paulo 01308-060, Brazil
2. Interunidades em Bioinformática, Universidade de São Paulo , São Paulo 05508-000, Brazil
3. Department of Biochemistry, University of São Paulo , São Paulo, 05508-000, Brazil
Abstract
Abstract
Motivation
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.
Results
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.
Availability and implementation
RCPedia is available at https://www.rcpediadb.org.
Funder
São Paulo Research Foundation
Publisher
Oxford University Press (OUP)