Element:Amn-ichi

From The Gypsy Database

Description

Amn-ichi is a LTR retrotransposon described in Anolis carolinensis (Piskurek et al. 2008). This element belongs to V-clade (Llorens et al. 2009) the chromovirus lineage of vertebrate-like Ty3/Gypsy LTR retrotransposons (Marín and Lloréns 2000) characterized by encoding for chromodomain-integrases (Malik and Eickbush 1999). The chromovirus branch has been disclosed to be the most ancient phylogenetic pattern of Ty3/Gypsy retroelements (Gorinsek, Gubensek and Kordis 2004; 2005; Kordis 2005).

The genomic structure of Amn-ichi is 6.4 Kb in size, including LTRs of 887-886 nt. The internal region of this element displays a Primer Binding site (PBS), two Open Reading Frames (ORFs) for gag, and pol genes, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Llorens et al. 2009). This element presents a detectable chromodomain at the C-terminal end of 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

Amn-ichi.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:224497847
Clade:V-clade
Cluster or genus:Fungi and vertebrates
Branch or class:Chromoviruses
Family:Ty3/Gypsy
System:LTR retroelements
Host:
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Anolis carolinensis.jpg
Anolis carolinensis
Image, courtesy of Wikipedia
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