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Hydra1-1 is a Ty1/Copia LTR retrotransposon found in the genome of the simple freshwater animal Hydra magnipapillata (GenBank accession NW_002165175). It belongs and gives the name to Hydra clade within Branch 2 of the Ty1/Copia LTR retrotransposons family (Llorens et al. 2009).
The genome of Hydra1-1 is 4306 bp in size, including LTRs of 163 bp long. The LTRs flanked internal region encodes for a single long ORF that, although is broken by two stop codons, contains the typical gag-pol domains structure of Ty1/Copia LTR retrotransposons (gag, protease, integrase, reverse transcriptase and ribonuclease H).
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