Cigr-1 is a heterogeneous Ty3/Gypsy LTR retrotransposon described in the genome of the urochordate Ciona intestinalis (Simmen et al. 1998). Cigr-1 seems to be transcriptionally active and escapes DNA methylation in C.intestinalis whose genome is a stable mosaic of methylated and nonmethylated domains (Simmen et al. 1999). Although Cigr-1 has been described as an own lineage (Simmen et al. 1999; Simmen and Bird. 2000) its gag polyprotein is strongly similar to those encoded by Mag-like elements. Moreover, gag-pro-pol phylogenetic analyses indicate that Cigr-1 might be a distant Mag recombinant or a sibling lineage of Mag clade (see gag-pro-pol tree in section "phylogenies"). The genomic structure of Cigr-1 is 4.2 Kb in size including LTRs of 245 nt. The internal region of this element displays a single Open Reading Frame (ORF) coding for a gag-pol polyprotein, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Simmen et al. 1998; Simmen and Bird. 2000). Cigr-1 also exhibits, close to the 5´LTR, an unidentified putative Primer Binding Site (PBS) of 18 nt in size characterized by the following "tggccaccataaacatta" DNA motif.



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: Z83760
Clade: Cigr-1
Cluster or genus: Undetermined
Branch or class: Branch 2
Family: Ty3/Gypsy
System: LTR retroelements
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Ciona intestinalis
Courtesy of "onderwaterwereld" web site, copyright of the author Duncan van Vliet
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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.
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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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