Retroposons, also called retrotransposons, are related to transposons. They copy themselves to RNA and then, via reverse transcriptase, back to DNA. Many retroposons have LTRs (long terminal repeats) at their ends that can contain over 1000 base pairs each. Like transposons, they create direct repeats at their entry site, which can be used to detect them. About 40% of the human genome supposedly consists of retroposons.
- Several viruseses, like HIV-1 or HTLV-1 behave like retroposons and contain both reverse transcriptase and integrase, the retroposon equivalent of transposase.
- LINES (long interspersed elements) are long DNA sequences that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase II into mRNA (messenger RNA to be translated into protein on ribosomes). Also called pseudogenes, they do not contain introns or promoters, but can code for reverse transcriptase or integrase, enabling them to copy both themselves and other, noncoding LINES. Because LINES move by copying themselves (instead of moving, like transposons do), they enlarge the genome. The human genome, for example, contains about 500,000 LINES, which is roughly 16% of the genome. LINES are used to generate genetic fingerprints.
- SINES (short interspersed elements) are short DNA sequences that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. The most common SINES are called Alu elements. Alu elements are about 300 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (thus the name). With about 1 million copies, they make up about 11% of the human genome. Both LINES and SINES are also called "selfish DNA" or "junk DNA", because they do not serve any known purpose.