Element:Cigr-1

Description 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. Structure 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 Mobile DNA II. (Craig et al. 2002)

Genbank accession: Z83760 Clade: Cigr-1 Cluster or genus: Undetermined Branch or class: Branch 2 Family: Ty3/Gypsy System: LTR retroelements Host: Explore the Tree Life Project Ciona intestinalis Courtesy of "onderwaterwereld" web site, copyright of the author Duncan van Vliet Browse all elements