RCPedia: a global resource for studying and exploring retrocopies in diverse species.

Autor:	Conceição HB; Hospital Sirio-Libanes, São Paulo 01308-060, Brazil.; Interunidades em Bioinformática, Universidade de São Paulo, São Paulo 05508-000, Brazil., Mercuri RLV; Hospital Sirio-Libanes, São Paulo 01308-060, Brazil.; Interunidades em Bioinformática, Universidade de São Paulo, São Paulo 05508-000, Brazil., de Castro MPM; Hospital Sirio-Libanes, São Paulo 01308-060, Brazil.; Department of Biochemistry, University of São Paulo, São Paulo, 05508-000, Brazil., Ohara DT; Hospital Sirio-Libanes, São Paulo 01308-060, Brazil., Guardia GDA; Hospital Sirio-Libanes, São Paulo 01308-060, Brazil., Galante PAF; Hospital Sirio-Libanes, São Paulo 01308-060, Brazil.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Sep 02; Vol. 40 (9).
DOI:	10.1093/bioinformatics/btae530
Abstrakt:	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. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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