Element:Suzu

From The Gypsy Database

Description

Suzu is a LTR retrotransposon described in the fugu fish Takifugu rubripes (Frame et al. 2001). There are 150 estimated copies of this element in the Fugu genome. Suzu belongs to the Suzu clade (Copeland et al. 2005) within Branch 2 of the Bel/Pao LTR retrotransposons family (Llorens et al. 2009). Suzu genome is about of 7.6 Kb in size (7618 bp long). The 5’- and 3’- LTRs, of respectively 726 and 724 nts long, bind a single ORF of 1884 amino acids (aa) that encodes for the typical gag and pol protein domains. The gag C-terminus shows a triple-zinc-finger-like motifs characteristic of the nucleocapsid domain of Bel/Pao LTR retrotransposons, while pol contains the typical PR, RT, RNAse H and INT domains. Unlike to other LTR retroelements Suzu PR and RNAse H present unusual functional motifs (DLA instead of the typical DS/TG catalitic PR motif), and (DGS instead of DAS in RNAse H) (Frame et al. 2001). Identical PR and RH motifs have been found in the Gabel Bel/Pao element also belonging to the Suzu clade (Llorens et al. 2009).

Structure

Suzu.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:23194331
Clade:Suzu
Cluster or genus:Undetermined
Branch or class:Branch 3
Family:Bel/Pao
System:LTR retroelements
Host:
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Takifugu rubripes.gif
Takifugu rubripes (Fugu rubripes)
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