Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA.

Like DNA transposable elements Retrotransposons can induce mutations by inserting near or within genes. Furthermore, Retrotransposons-induced mutations are relatively stable, because the sequence at the insertion site is retained as they transpose via the replication mechanism. Retrotransposons copy themselves to RNA and then, via reverse transcriptase, back to DNA. Most Retrotransposons are very old and through accumulated mutations, are no longer able to retro transpose.

Types of Retrotransposons

Retrotransposons, also known as class I transposable elements, consist of two sub-types, the long terminal repeat (LTR) and the non-LTR Retrotransposons.

LTR Retrotransposons

LTR Retrotransposons have direct LTRs that range from ~100 bp to over 5 kb in size.LTR Retrotransposons are further sub-classified into three

1. Ty1-Copia-like (Pseudoviridae)

These are abundant in species ranging from single-cell algae to bryophytes, gymnosperms, and angiosperms.

2. Ty3-Gypsy-like (Metaviridae)

Ty3-Gypsy Retrotransposons are also widely distributed, including both gymnosperms and angiosperms.

3. Pao-BEL-like groups

Retrotransposons Pathway

Non-LTR Retrotransposons

These consist of two sub-types, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs).


Long interspersed nuclear elements are long DNA sequences (>5kb) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase II into mRNA. LINE elements code for 2 proteins; one that has the ability to bind single-stranded RNA, and another that has known reverse transcriptase and Endonuclease activity, enabling them to copy both themselves and noncoding SINEs ,such as Alu elements A typical LINE contains a 5′ UTR (untranslated region), 2 ORFs (open reading frames), and a 3′ UTR. The 5′ UTR contains an internal polymerase II promoter sequence, while the 3′ UTR contains a polyadenylation signal (AATAAA) and a poly-A tail.


Short interspersed nuclear elements are short DNA sequences (<500 bases) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. The most common SINEs in primates are called Alu sequences. Alu elements are 280 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (thus the name).SINEs make up about 13% of the human genome. Both LINEs and SINEs have a significant role in gene evolution, structure and transcription levels. The distribution of these elements has been implicated in some genetic diseases and cancers.

Retroviruses, like HIV-1 or HTLV-1 behave like Retrotransposons and contain both reverse transcriptase and integrase. The integrase is the Retrotransposons equivalent of the transposase of DNA-transposons

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