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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.

The donor site from where the transposon is excised is either degraded or repaired. Inaccurate repair methods do not restore the donor to its original sequence, often inadvertently changing its phenotype.

Imperfect excision of transposable elements leads to parts of genomic sequences being carried over with the transposon. This results in a phenomenon called exon shuffling, where two unrelated exons are positioned adjacent to each other, thereby resulting in new gene structures. Thus, transposition can not only move genes around but can also reorganize non-mobile genetic elements.

Upon insertion at the target site, transposons can alter the activity of the host genetic elements. This makes DNA transposons powerful tools in genome editing. In transgenesis, synthetic DNA transposons are used as gene vehicles to study the effects of the foreign DNA in the host organism. A widely used synthetic DNA transposon is the Sleeping beauty transposon that is inserted in the genomes of different species ranging from protozoa to small vertebrates such as fishes, frogs, and mice, to introduce new traits or discover new genes.

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