Long terminal repeat

A long terminal repeat (LTR) is a pair of identical sequences of DNA, several hundred base pairs long, which occur in eukaryotic genomes on either end of a series of genes or pseudogenes that form a retrotransposon or an endogenous retrovirus or a retroviral provirus.

This method of dating is used by paleovirologists, though it fails to take into account confounding factors such as gene conversion and homologous recombination.

U3 and U5 has been further subdivided according to transcription factor sites and their impact on LTR activity and viral gene expression.

The multi-step process of reverse transcription results in the placement of two identical LTRs, each consisting of a U3, R, and U5 region, at either end of the proviral DNA.

The finding that both HIV LTRs can function as transcriptional promoters is not surprising since both elements are apparently identical in nucleotide sequence.