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The LTRs then mediate integration of the retroviral DNA via an LTR specific integrase into another region of the host chromosome. in length and, like other retroviral LTRs, is segmented into the U3, R, and U5 regions.

As 5' and 3' LTRs are identical upon insertion, the difference between paired LTRs can be used to estimate the age of ancient retroviral insertions.

Retroviruses such as Human Immunodeficiency Virus (HIV) use this basic mechanism.

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

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Once the provirus has been integrated, the LTR on the 5′ end serves as the promoter for the entire retroviral genome, while the LTR at the 3′ end provides for nascent viral RNA polyadenylation and, in HIV-1, HIV-2, and SIV, encodes the accessory protein, Nef.

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