Gypsy-Integrase-Related Type 1 (GINGER1) is a recently described pool of exon-intron transposons (Bao et al. 2010), which encode for a transposase (TR) showing the occurrence of a GPY/F module (Malik & Eickbush 1999) thought to mediate multimerization (Ebina et al. 2008) at its C-terminus. GINGER1 elements also show an additional module adjacent to the GPY/F module, which depending on the element may be an ovarian tumor (OTU) cysteine protease domain, or an Ulp1 protease catalytic domain (Bao et al. 2010). The latter may also be coupled with a plant homeodomain (PHD) finger motif (Bao et al. 2010). Full-length GINGER1 elements vary from approximately 2.6-7.0 kb and are flanked by terminal inverted repeats (TIRs) of approximately 40-270 nucleotides long (Figure not to scale). For simplicity´s sake the figure below shows the genomic structure without introns.


GINGER 1 transposons give the name to a phylogenetic cluster of TRs and integrases (INTs) constituted by the own GINGER1-like transposons (Bao et al. 2010), which occupy the most basal phylogenetic position within this cluster, the two GIN-like host genes of vertebrates (Llorens & Marin 2001; Bao et al. 2010; Marin 2010), and their related GINO, GINA and GINNY transposons (Marin 2010).

There are two complementary classifications for the GINGER1 elements. Based on sequence these elements can be classified as DDE TRs and INTs. Phylogenetic analyses also relate the GINGER1 cluster with the INTs coded by the Ty3/Gypsy Athila/Tat LTR retroelements. This suggests that GINGER1 elements probably evolve from a INT ancestor excised from its Ty3/Gypsy retrotransposable carrier (for more details see the DDE phylogeny). Based on INT-like structural potential similarities, the INT coded by GINGER1 elements are members of the Retroviral Integrase Superfamily (Nowotny 2009) of nucleic acid-processing enzymes involved in: a) selfish evolution; b) replication and repair of DNA; c) recombination and gene fusion; d) RNA-mediated gene silencing; and e) oncogenesis.

Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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