Element:Grande1-4

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Description

Grande is a LTR retroelement originally characterized in the genome of Zea diploperennis, and known to also be widely distributed in all Mais chromosomes (Aledo et al. 1995). This element belongs to a lineage of plant LTR retrotransposons (Tat), sibling of other lineage of putative plant endogenous retroviruses (Athila), providing evidence of a shared ancestral lineage originally described as class A by Wright and Voytas (1998). The genomic structure of Grande has several subtypes, subtype 1-4 is taken as representative. The genome structure of this element is 13.8 Kb in size including LTRs of 0.6 Kb. The internal region displays a Primer Binding Site (PBS) complementary to a tRNA Arg, three Open Reading Frames (ORFs) for gag, pro, and pol genes, and downstream to the integrase domain, a non-coding region of approximately 7 Kb in size, which contains two tandem repeats and an ORF that might be transcriptionally active in reverse frame, and also, a Polypurine Tract (PPT) adjacent to the 3´LTR (Martínez-Izquierdo, García-Martínez and Vicient, 1997; García-Martínez and Martínez-Izquierdo 2003).

Structure

Grande1-4.png


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: X97604
Clade: Tat
Cluster or genus: Athila/Tat
Branch or class: Branch 2
Family: Ty3/Gypsy
System: LTR retroelements
Host:
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Zea diploperennis.gif
Zea diploperennis
Image, courtesy of Hugh D. Wilson, TAMU herbarium, Texas A&M University
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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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