rGmr1 is the counterpart of Gmr1 found in the genome of the zebrafish Danio rerio (Butler et al. 2001; Goodwin and Poulter 2002). These constitute an own clade, together with other elements from diverse vertebrates, possibly related via sequence similarity with Osvaldo clade (Butler et al. 2001; Goodwin and Poulter 2002; Llorens et al. 2009). rGmr1-like elements differ from other Ty3/Gypsy LTR retroelements in the fact that the integrase domain lies upstream of the reverse transcriptase domain, an arrangement which is characteristic of Ty1/Copia LTR retroelements (Butler et al. 2001; Goodwin and Poulter 2002).

The genomic structure of rGmr1 is 4.8 Kb in size including LTRs of 21 nt. The internal region displays a Primer Binding Site (PBS), a single Open Reading Frame (ORF) that codes for a gag-pol polyprotein, and a Polypurine Tract (PPT) adjacent to the 3´LTRs.



Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:

MA=matrix PR=protease DU or DUT=dUTPase TM=transmembrane TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
CA=capsid RT=reverse transcriptase INT=Integrase CHR=chromodomain
NC=nucleocapsid RH=RNaseH SU=surface MOV=movement protein
PPT=polypurine tract PBS=primer binding site ATF=aphid transmission factor VAP=virion associated protein

Related literature

Genbank accession: 125846079
Clade: Gmr1
Cluster or genus: Undetermined
Branch or class: Branch 2
Family: Ty3/Gypsy
System: LTR retroelements
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Danio rerio
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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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