From The Gypsy Database


Cico1 is a Ty1/Copia-like LTR retrotransposon described in the genome of the urochordate Ciona intestinalis (Terrat et al. 2008). It belongs to GalEA clade a Ty1/Copia lineage specifically found in marin animals (Terrat et al. 2008).

The genome of Cico1, of 4513 bp in size, includes 323-bp LTRs that flank an internal region containing a Primer Binding Site (PBS) complementary to a tRNAMet, a single large Open Reading Frame (ORF) (which harbors a frameshift) and a Polypurine Tract (PPT) adjacent to its 3’LTR. The ORF displays the typical gag and pol polyprotein domains of Ty1/Copia LTR retrotransposons: gag, protease, integrase, reverse transcriptase and RNase H (Terrat et al. 2008).



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:154726956
Cluster or genus:Undetermined
Branch or class:Branch 1
System:LTR retroelements
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Ciona intestinalis
Courtesy of "onderwaterwereld" web site, copyright of the author Duncan van Vliet
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