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).
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:
||DU or DUT=dUTPase
||TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
||PBS=primer binding site
||ATF=aphid transmission factor
||VAP=virion associated protein