Element:Hydra1-1

From The Gypsy Database

Description

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).

Structure

Hydra1-1.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:194993408
Clade:Hydra
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Hydra magnipapillata.jpg
Hydra Magnipapillata
Wikimedia commons (image from PLoS journals), courtesy of Friederike Anton-Erxleben
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