Element:Gimli

Revision as of 16:46, 11 November 2009 by imported>Gydbwiki
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

Description

Gimli is a LTR retrotransposon described along with other elements in Arabidopsis. Gimli belongs to the Chromoviridae branch, term suggested (Marín and Lloréns 2000) to describe the Ty3/Gypsy elements bearing chromodomain-integrases (Malik and Eickbush 1999). The chromovirus branch is probably the most ancient phylogenetic pattern of Ty3/Gypsy retroelements (Gorinsek, Gubensek and Kordis 2004; 2005; Kordis 2005).

The genomic structure of Gimli is 5 Kb in size, including LTRs of 341 nt. The internal region displays a Primer Binding Site (PBS), a single Open Reading Frame (ORF) gag-pol, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Marín and Lloréns 2000). This element presents a detectable chromodomain at the C-terminal end of the integrase p domain. The PBS of fungi and vertebrate chromoviruses, differs significantly from that used by plant chromoviruses. While plant chromoviruses use a methionine starting tRNA (iMet), fungi and vertebrate chromoviruses use their own self-priming mechanism to start the reverse transcription (Levin 1995 ; Butler et al. 2001).

Structure

Gimli.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: AL049655 (nuc 77114-82333)
Clade: Reina
Cluster or genus: Plants
Branch or class: Chromoviruses
Family: Ty3/Gypsy
System: LTR retroelements
Host:
Explore the Tree Life Project
Arabidopsis thaliana.gif
Arabidopsis thaliana
Photo: www.knoch1.de
Browse all elements



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

Contact - Announcements - Acknowledgments - Terms of use and policy - Help - Donate
Donating legal disclaimer - Terms and conditions of the donation