Element:Ty2

From The Gypsy Database

Description

Ty2 is representative of one of the four LTR retrotransposon sets (Ty1, Ty2, Ty3 and Ty4) described in the genome of yeast Saccharomyces cerevisiae (Boeke and Sandmeyer 1991). Ty2 belongs to Ty (Pseudovirus) clade one of the three original genera on which the in-progrees Pseudoviridae classification is constituted (Boeke et al 2005).

The genome of Ty2 is 5959 bp in size, including two 332-bp LTRs that flank an internal region bounded upstream and downstream by a Primer Binding Site (PBS), complementary to a tRNAiMet, and a Polypurine Tract (PPT1), respectively. Interestingly, a second sequence very similar to the PPT1 was found near the middle of the pol gene (PTT2). The coding internal region displays two overlapping Open Reading Frames (ORFs): the first contains the gag protein while the second the typical Ty1/Copia pol-polyprotein domains (protease, integrase, reverse transcriptase and ribonuclease H) (Boeke and Sandmeyer 1991). The gag-associated RNA-binding motif (CCHC) has not been identified in this element (Peterson-Burch and Voytas 2002). The central PPT2 has been demonstrated to be not essential for the element transposition (Heyman et al. 2003; Friant et al. 1996).

Structure

Ty2.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:632669 (nts 4392-10350)
Clade:Ty (Pseudovirus)
Cluster or genus:Pseudovirus
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Saccharomyces cerevisiae.gif
Saccharomyces cerevisiae
Image, Joaquin Panadero,
Copyright, GyDB, Biotech Vana
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