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

Author(s)

Conceicao, Helena B. ; Mercuri, Rafael L., V ; de Castro, Matheus P. M. ; Ohara, Daniel T. ; Guardia, Gabriela D. A. ; Galante, Pedro A. F.

• Document type: Journal article
• Source: Bioinformatics; v. 40, n. 9, p. 5-pg., 2024-09-10.

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. (AU)

• FAPESP's process: 24/00078-4 - A comprehensive investigation of the interrelationship between retrocopies and cancer
• Grantee: Helena Beatriz da Conceição
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 18/15579-8 - Retroelements: a driving force generating genetic novelties in the human and mouse genome
• Grantee: Pedro Alexandre Favoretto Galante
• Support Opportunities: Research Grants - Young Investigators Grants - Phase 2
• FAPESP's process: 20/02413-4 - Intragenic retrocopies as a source of novel protein domains in humans
• Grantee: Rafael Luiz Vieira Mercuri
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 18/13613-4 - Study of the contribution of retrocopies in the origin of new genetic regions
• Grantee: Helena Beatriz da Conceição
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 17/19541-2 - Impact of RNA binding proteins on abnormal regulation of splicing in glioblastoma
• Grantee: Gabriela Der Agopian Guardia
• Support Opportunities: Scholarships in Brazil - Post-Doctoral