Element:Hydra1-2

From The Gypsy Database

Description

Hydra1-2 is a Ty1/Copia LTR retrotransposon found in the zebrafish Danio rerio (GenBank accession XM_001922068). It is closely related with other Ty1/Copia-like LTR retrotransposon - Hydra1-1 previously found in Hydra magnipapillata - and together they constitute the components of the Hydra clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009).

The genome of Hydra1-2 is 4148 bp long and encodes a single long ORF of 1336 amino acids with the typical gag-pol structure domains of Ty1/copia LTR retrotransposons (gag, protease, integrase, reverse transcriptase and ribonuclease H). Information about the LTRs of Hydra1-2 is not yet available.

Structure

Hydra1-2.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:189515648
Clade:Hydra
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Danio rerio.jpg
Danio rerio
Image, courtesy of Wikipedia
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