Element:Hydra3-1

From The Gypsy Database

Description

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).

Structure

Hydra3-1.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:204801980
Clade:Tas
Cluster or genus:Undetermined
Branch or class:Branch 1
Family:Bel/Pao
System:LTR retroelements
Host:
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Hydra magnipapillata.jpg
Hydra magnipapillata
Wikimedia commons (image from PLoS journals), courtesy of Friederike Anton-Erxleben
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