Element:Skipper

Description Skipper is a LTR retrotransposon characterized in the slime mold Dictyostelium discoideum (Leng et al. 1998). Skipper is a distant representative of the Chromoviridae group (Marín and Lloréns 2000), 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 Skipper is 7 Kb in size, including LTRs of 400 nt. The internal region of this element displays a Primer Binding Site (PBS), three Open Reading Frames (ORFs) for gag , protease, and pol genes, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Leng et al. 1998). This element presents a detectable chromodomain at the C-terminal end of its integrase. 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 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: AF049230 Clade: Skipper Cluster or genus: Undetermined Branch or class: Chromoviruses Family: Ty3/Gypsy System: LTR retroelements Host: Explore the Tree Life Project Dictyostelium discoideum Image, courtesy of Michael Schleicher, the Ludwig-Maximilians-Universitaet Browse all elements