Element:Tma

From The Gypsy Database

Description

Tma is a LTR retrotransposon characterized from sequencing data in Arabidopsis (Wright y Voytas 1998). Tma belongs to the Chromoviridae branch, term suggested (Marín and Lloréns 2000) to describe the Ty3/Gypsy elements bearing chromodomain-integrases (Malik and Eickbush 1999). The chromovirus branch is probably the most ancient phylogenetic pattern of Ty3/Gypsy retroelements (Gorinsek, Gubensek and Kordis 2004; 2005; Kordis 2005).

At the genomic structure level Tma has several subtypes, the sequence available in the Genbank accession AC005398 is taken as a representative. This clone is 7.3 Kb in size, including LTRs of 1.1 Kb. The internal region displays a Primer Binding Site (PBS), two Open Reading Frames (ORFs) for gag, and pol genes, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Wright y Voytas 1998). This element presents a detectable chromodomain at the C-terminal end of the integrase domain. The PBS of fungi and vertebrate chromoviruses, differs significantly from that used by plant chromoviruses. While plant chromoviruses use a methionine starting tRNA (iMet), fungi and vertebrate chromoviruses use their own self-priming mechanism to start the reverse transcription (Levin 1995 ; Butler et al. 2001).

Structure

Tma.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:AC005398 (nuc; 43778-51134)
Clade:Del
Cluster or genus:Chromoviridae
Branch or class: 
Family:Ty3/Gypsy
System:LTR retroid elements
Host:
Explore the Tree Life Project
Arabidopsis thaliana.gif
Arabidopsis thaliana
Photo: www.knoch1.de
Browse all elements
Jump to: navigation, search


This website use cookies, by continuing to browse the site you are agreeing to our use of cookies. More info about our cookies here.