Though the effects of transposition can sometimes manifest phenotypically, and indeed, this effect led to their discovery, transposons can be difficult for the cellular machinery to detect. Many TEs contain stretches of genuine coding DNA, copied from the host, and there is no distinct structure, code, or identifying characteristic of any kind that would allow a cell to recognize the full range of transposable elements with accuracy. Even besides coding for functional proteins or RNAs, some transposons, like class II elements, contain code copied from the nearby strand, allowing them to blend in. Given that the preceding is true, it must be that transposons are recognized more by their effect than their structure. Thus, cell machinery, as detailed in the next section, exists that is capable of detecting transcripts that are atypical of host genomes, such as:
* Double-stranded RNAs (dsRNAs), which are indicative of both retroviruses and transposons
and, more specifically:
* Small interfering RNAs (siRNAs), which are processed from dsRNA transcribed from inverted repeating elements in the transposon code; a short sense and anti-sense strand are created, which form dsRNA
* MicroRNAs (miRNAs), which are similar to siRNAs, but have an imperfect base pair complement; these are usually formed as a result of shared complementarity between a transposon and a host gene mRNA transcript