Non-coding RNA genes include transfer RNA (tRNA) and ribosomal RNA (rRNA), small RNAs such as snoRNAs, microRNAs, siRNAs and piRNAs and lastly long ncRNAs that include examples such as Xist, Evf, Air, CTN and PINK (see here for a more complete list of ncRNAs). The number of ncRNAs encoded within the genome is unknown, however recent transcriptomic and microarray studies suggest the existence of over 30,000 long ncRNAs and at least as many small regulatory RNAs within the mouse genome alone. Since most of the newly identified ncRNAs have not been validated for their function, it is possible that the majority of them are meaningless (e.g. non-functional or truncated transcript).
One of the major findings of the 2007 ENCODE Pilot Project was that "nearly the entire genome may be represented in primary transcripts that extensively overlap and include many non-protein-coding regions.
There began to be signs that this was not true, e.g. with the paper by Brannan et al. (1990). Then by 2001, Mattick had claimed that in fact this applied to more than 97% of the RNA produced from DNA. (See also later works by Mattick and others.) Given this imbalance, it became clear that ncRNA must be playing other important roles; but what?
Such an action-or-memory-encoding role need not conflict with the aforementioned "regulator" role. In fact "thought" itself might be seen as a special case of internal regulation. (Moreover this connection was perhaps already implied in the 1950s by Ross Ashby when he argued that recursive elaborations to a simple homeostat could yield a brainlike system..)
The term ncRNA has been used, in addition to its above definition, to describe regions of mRNA that are functional at the RNA level, i.e. they have a biological function other than coding for protein even though they are on a protein-coding mRNA, for example riboswitches and the SECIS element.
They may even overlap with protein-coding sequence and are thus dual-functional: at the RNA level and at the protein level (e.g. SgrS RNA and RNAIII). However, these conflict with the Sequence Ontology's definition of ncRNA, which requires that a RNA does not contain any protein-coding sequence in order to be labeled ncRNA.
Several publications have started using the term functional RNA (fRNA), as opposed to ncRNA, to describe regions functional at the RNA level that may or may not be stand-alone RNA transcripts. Therefore, every ncRNA is a fRNA, but there exist fRNA (such as riboswitches, SECIS elements, and other cis-regulatory regions) that are not ncRNA. Yet the term fRNA could also include mRNA as this is RNA coding for protein and hence is functional. Additionally artificially evolved RNAs also fall under the fRNA umbrella term. Some publications state that the terms ncRNA and fRNA are nearly synonymous.
Universal primers for amplifying the complete coding sequence of cytoplasmic heat shock protein 90 (HSP90) in Lepidoptera
Jan 01, 2011; Key words. Universal primer, Lepidoptera, coding sequence, untranslated region, HSP90, RACE Abstract. Using sequence alignment, a...
Identification of the full-length [Hs1.sup.pro-1] coding sequence and preliminary evaluation of soybean cyst nematode resistance in soybean transformed with [Hs1.sup.pro-1] cDNA.(NOTE)(Report)
Apr 01, 2007; Abstract: The [Hs1.sup.pro-1] gene reportedly confers resistance to the beet cyst nematode in wild beet and sugar beet. Here, we...