Element:Cer10-1

Description

Cer10-1 is a LTR retrotransposon described in the genome of the nematode Caenorhabditis elegans (Bowen and McDonald 1999). This element tentatively belongs to the Tas clade (Copeland et al. 2005) within Branch 1 of the Bel/Pao family (Llorens et al. 2009) but depending on the protein domain phylogenetically evaulate it can fall outside to this clade. This suggests that Cer10 might constitute an own clade within the Bel/Pao phylogeny. The genome of Cer10-1 is 8 Kb in size (8097 bp in lenght), the internal coding region is disrupted by several stop codons and frameshiftings, but the different gag and pol domains of LTR retrotransposons are clearly evident in the sequence of this element (Bowen and McDonald 1999). No information about the Cer10-1 LTRs is yet available.

Structure

Cer10-1.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: 2384909
Clade: Tas
Cluster or genus: Undetermined
Branch or class: Branch 1
Family: Bel/Pao
System: LTR retroelements
Host:
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Caenorhabditis elegans.gif
Caenorhabditis elegans
Image, courtesy of Ralf J. Sommer, Max Planck Institute for Developmental Biology
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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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