Element:Saci-6

From The Gypsy Database

Description

Saci-6 is one of the several LTR retrotransposons characterized in the human parasite blood fluke Schistosoma mansoni in which have been estimated 20-200 copies of this retroelement (DeMarco et al. 2005). Saci-6 belongs to Sinbad clade (Copeland et al. 2005) within Branch 2 of the Bel/Pao LTR retrotransposon family (Llorens et al. 2009). The genome structure of Saci-6 is about 4.2 Kb in size (4236 bp long), including LTRs of 78 nt (5´LTR) and 177 nt (3´LTR). It is a truncated element which LTRs flanked a single ORF that encodes for gag and pol polyproteins. The gag polyprotein contains the matrix, capsid and nucleocapsid domains. The latter presents the characteristic triple-zinc-finger-like motifs (CCHC cysteine motifs), while pol only shows an intact protease domain and partial sequences showing similarity to the reverse transcriptase, RNase H and integrase domains (DeMarco et al. 2005).

Structure

Saci 6.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:67625726
Clade:Sinbad
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Bel/Pao
System:LTR retroelements
Host:
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Schistosoma mansoni.png
Schistosoma mansoni
Courtesy of Stephen J. Davies, Uniformed Services University
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