Element:Calypso

Description

Calypso is a LTR retroelement found in the genome Glycine max (Peterson-Burch et al. 2000). Calypso belongs to Athila clade, a lineage of possible retroviruses in plants (Wright and Voytas 2002), which is sibling of Tat clade, a lineage of plant LTR retrotransposons. Both lineages provide evidence of a shared ancestral lineage originally described as Class A by Wright and Voytas (1998). The full-length consensus for Calypso is 13 Kb in size including LTRs of 1.8 Kb. The internal region of this element displays a Primer Binding Site (PBS) complementary to a tRNAAsp, three Open Reading Frames (ORFs) for gag, pol, and env genes, and two Polypurine Tracts, PPT1 and PPT2, adjacent to the 3´LTR (Wright and Voytas 2002).

Structure

Calypso.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: AF186183(env Calypso2-1)
AF186185(5′LTR, gag Calypso4-1)
AF186186(3′LTR, pol Calypso5-1)
Clade: Athila
Cluster or genus: Athila/Tat
Branch or class: Branch 2
Family: Ty3/Gypsy
System: LTR retroelements
Host:
Explore the Tree Life Project
Glycine max.gif
Glycine max
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
Browse all elements



Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

Contact - Announcements - Acknowledgments - Terms of use and policy - Help - Donate
Donating legal disclaimer - Terms and conditions of the donation