TREP, the TRansposable Elements Platform

Superfamily Copia                   RLC

Full classification: Retrotransposon, LTR, Copia

Copia elements are Class 1 transposons.

They are extremely well characterized and widespread in animals, plants and fungi. The terminal repeats usually end in TG (5' end) and CA (3' end).
Upon insertion, they create a 5 bp Target site duplication (TSD).

Structure of Copia elements

Sequence domains

LTR: Long terminal repeat
Function: Contains promoter and terminator elements (dual function).
Protein motifs:

GAG: GAG protein
Function: Required as envelope of virus-like capsid
Protein motifs: CCHC

AP: Aspartic protease
Function:
Protein motifs:

INT: Integrase
Function:
Protein motifs: HHCC DDE

RT: Reverse transcriptase
Function: Reverse transcription of mRNA to DNA, core motif is relatively variable (FY)(IAMV)DD
Protein motifs: YVDD

RH: RNAse H
Function:
Protein motifs: DEDD

LTR: Long terminal repeat
Function: Contains promoter and terminator elements (dual function).
Protein motifs:

642 Copia Download all 'RLC' elements in total_TREP database elements from the following taxa are in the total_TREP database:

Taxonomic group	Total elements
ANIMALIA	16
Chromalveolates	29
FUNGI	113
NULL	1
PLANTAE	471
Stramenopiles	12

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