title: RetrogeneDB--a database of animal retrogenes.
abstract: Retrocopies of protein-coding genes, reverse transcribed and inserted into the genome copies of mature RNA, have commonly been categorized as pseudogenes with no biological importance. However, recent studies showed that they play important role in the genomes evolution and shaping interspecies differences. Here, we present RetrogeneDB, a database of retrocopies in 62 animal genomes. RetrogeneDB contains information about retrocopies, their genomic localization, parental genes, ORF conservation, and expression. To our best knowledge, this is the most complete retrocopies database providing information for dozens of species previously never analyzed in the context of protein-coding genes retroposition. The database is available at http://retrogenedb.amu.edu.pl.
authors.affiliation: Labolatory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
authors.forename: Michał
authors.initials: M
authors.lastname: Kabza
authors.affiliation: Labolatory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
authors.forename: Joanna
authors.initials: J
authors.lastname: Ciomborowska
authors.affiliation: Labolatory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland izabel@amu.edu.pl.
authors.forename: Izabela
authors.initials: I
authors.lastname: Makałowska
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D011544:Pseudogenes; D018626:Retroelements
chemical_list: D018626:Retroelements
keywords: database; gene duplication; retrogene; retroposition
references.citation: Bioinformatics. 2013 May 1;29(9):1235-7
references.pmid: 23457042
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D52-7
references.pmid: 21115458
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D749-55
references.pmid: 24316576
references.citation: Science. 1991 Feb 15;251(4995):753
references.pmid: 1990437
references.citation: BMC Bioinformatics. 2007 Aug 24;8:308
references.pmid: 17718914
references.citation: Mol Biol Evol. 2011 Jan;28(1):33-7
references.pmid: 20889727
references.citation: Mol Biol Evol. 2013 Feb;30(2):384-96
references.pmid: 23066043
references.citation: Genome Biol. 2009;10(1):R2
references.pmid: 19123937
references.citation: Nat Rev Genet. 2009 Jan;10(1):19-31
references.pmid: 19030023
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D59-66
references.pmid: 15608268
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3220-5
references.pmid: 16492757
references.citation: Nat Rev Cancer. 2001 Nov;1(2):162-8
references.pmid: 11905808
references.citation: Genome Res. 2013 Dec;23(12):2042-52
references.pmid: 24026178
references.citation: Mol Biol Evol. 2002 May;19(5):654-63
references.pmid: 11961099
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9
references.pmid: 23155063