Hydra3-1 is a LTR retrotransposon found in the genome of the simple freshwater animal Hydra magnipapillata (Llorens et al. 2009). This element belongs to the Tas clade (Copeland et al. 2005) within Branch 1 of the Bel/Pao family (Llorens et al. 2009). The genome of Hydra3-1 is 7773 bp long including LTRs of respectively 819 (5’LTR) and 809 nts (3’LTR). The size difference is due to a series of deletions within both LTR sequences. The LTRs flank a single ORF encoding for both gag and pol polyproteins which associated domains are the typical of LTR retrotransposon gag-pol domains (Llorens et al. 2009).
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