ArticleNucleic acids research2008
The Gypsy Database (GyDB) of mobile genetic elements.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Ontogenetic Sequence of Differential Gene Expression in Predator-Induced Daphnia pulex.Molecular ecology · 2026Article
- Endogenous viral elements trace the ancient origins and early evolution of the Caulimoviridae.PLoS pathogens · 2026Article
- A comprehensive annotation of conserved protein domains in human endogenous retroviruses.NAR genomics and bioinformatics · 2026Article
- Anuran genome size evolution is driven by relatively recent retrotransposon activity and by life history.BMC genomics · 2025Article
- Telomere-to-Telomere Genome Assembly of Tibetan Medicinal MushroomJournal of fungi (Basel, Switzerland) · 2023Article
- A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane.Plant communications · 2023Article
- Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.GigaScience · 2019Article
- Homologous Capsid Proteins Testify to the Common Ancestry of Retroviruses, Caulimoviruses, Pseudoviruses, and Metaviruses.Journal of virology · 2017Article
- Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads.Scientific reports · 2015Article
- Genome-wide analysis of LTR-retrotransposons in oil palm.BMC genomics · 2015Article
- Comparative Analysis of the Shared Sex-Determination Region (SDR) among Salmonid Fishes.Genome biology and evolution · 2015Article
- Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae).Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons.Genetica · 2011Article
- Identification and characterization of jute LTR retrotransposons:: Their abundance, heterogeneity and transcriptional activity.Mobile genetic elements · 2011Article
- Article
- Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements.BMC genomics · 2011Article
- The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.Nucleic acids research · 2011Article
- Article
- A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block.BMC plant biology · 2010Article
- Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons.Mobile DNA · 2010Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es.
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