Retrofit is a Ty1/Copia-like LTR retrotransposon found in the Xa21 disease resistance gene family of rice (Oryza longistaminata) genome (Song et al. 1997). It belongs and gives the name to the Retrofit clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009).

Retrofit full-length genome is 4866 bp in size, including two 232-bp LTRs (Peterson-Burch and Voytas 2002; Song et al. 1997). The internal region encodes for a single long Open Reading Frame (ORF) of 1445 amino acids containing the gag and pol domains typical of Ty1/Copia LTR retrotransposons: gag (with a characteristic nucleocapsid zinc finger-like motif), protease, integrase, reverse transcriptase and RNase H (Peterson-Burch and Voytas 2002).



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: 2586080
Clade: Retrofit
Cluster or genus: Undetermined
Branch or class: Branch 2
Family: Ty1/Copia
System: LTR retroelements
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Oryza longistaminata
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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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