List of RNAs

Ribonucleic acid (RNA) occurs in different forms within organisms and serves many different roles. Listed here are the types of RNA, grouped by role. Abbreviations for the different types of RNA are listed and explained.

By role

RNAs involved in protein synthesis

Type	Abbr.	Function	Distribution	Ref.
Messenger RNA	mRNA	Codes for protein	All organisms
Ribosomal RNA	rRNA	Translation	All organisms
Signal recognition particle RNA	7SL RNA or SRP RNA	Membrane integration	All organisms	[1]
Transfer RNA	tRNA	Translation	All organisms
Transfer-messenger RNA	tmRNA	Rescuing stalled ribosomes	Bacteria	[2]

RNAs involved in post-transcriptional modification or DNA replication

Type	Abbr.	Function	Distribution	Ref.
Small nuclear RNA	snRNA	Splicing and other functions	Eukaryotes and archaea	[3]
Small nucleolar RNA	snoRNA	Nucleotide modification of RNAs	Eukaryotes and archaea	[4]
SmY RNA	SmY	mRNA trans-splicing	Nematodes	[5]
Small Cajal body-specific RNA	scaRNA	Type of snoRNA; Nucleotide modification of RNAs
Guide RNA	gRNA	mRNA nucleotide modification	Kinetoplastid mitochondria	[6]
Ribonuclease P	RNase P	tRNA maturation	All organisms	[7]
Ribonuclease MRP	RNase MRP	rRNA maturation, DNA replication	Eukaryotes	[8]
Y RNA		RNA processing, DNA replication	Animals	[9]
Telomerase RNA Component	TERC	Telomere synthesis	Most eukaryotes	[10]
Spliced Leader RNA	SL RNA	mRNA trans-splicing, RNA processing

Regulatory RNAs

Type	Abbr.	Function	Distribution	Ref.
Antisense RNA	aRNA, asRNA	Transcriptional attenuation / mRNA degradation / mRNA stabilisation / Translation block	All organisms	[11][12]
Cis-natural antisense transcript	cis-NAT	Gene regulation
CRISPR RNA	crRNA	Resistance to parasites, by targeting their DNA	Bacteria and archaea	[13]
Long noncoding RNA	lncRNA	Regulation of gene transcription, epigenetic regulation	Eukaryotes
MicroRNA	miRNA	Gene regulation	Most eukaryotes	[14]
Piwi-interacting RNA	piRNA	Transposon defense, maybe other functions	Most animals	[15][16]
Small interfering RNA	siRNA	Gene regulation	Most eukaryotes	[17]
Short hairpin RNA	shRNA	Gene regulation	Most eukaryotes	[18]
Trans-acting siRNA	tasiRNA	Gene regulation	Land plants	[19]
Repeat associated siRNA	rasiRNA	Type of piRNA; transposon defense	Drosophila	[20]
7SK RNA	7SK	negatively regulating CDK9/cyclin T complex
Enhancer RNA	eRNA	Gene regulation		[21]

Parasitic RNAs

Type	Function	Distribution	Ref.
Retrotransposon	Self-propagating	Eukaryotes and some bacteria	[22]
Viral genome	Information carrier	Double-stranded RNA viruses, positive-sense RNA viruses, negative-sense RNA viruses, many satellite viruses and reverse transcribing viruses
Viroid	Self-propagating	Infected plants	[23]
Satellite RNA	Self-propagating	Infected cells

Other RNAs

Type	Abbr.	Function	Distribution	Ref.
Vault RNA	vRNA, vtRNA	Expulsion of xenobiotics (conjectured)		[24]

RNA abbreviations

Abbr.	Name	Family	Description	Ref.
ncRNA	non coding RNA	-
nmRNA	non messenger RNA	-	synonym of ncRNA
sRNA	small RNA	-	synonym of ncRNA
smnRNA	small non messenger RNA	-	synonym of ncRNA
tRNA	transfer RNA	RF00005
sRNA	soluble RNA	-	synonym of tRNA
mRNA	messenger RNA	-
pcRNA	protein coding RNA	-	synonym of mRNA
rRNA	ribosomal RNA	multiple families
5S rRNA	5S ribosomal RNA	RF00001
5.8S rRNA	5.8S ribosomal RNA	RF00002
SSU rRNA	small subunit ribosomal RNA	CL00111
LSU rRNA	large subunit ribosomal RNA	CL00112
NoRC RNA	nucleolar remodeling complex associated RNA	RF01518
pRNA	promoter RNA	RF01518	synonym of NoRC RNA
6S RNA	6S RNA	RF00013
SsrS RNA		RF00013	synonym of 6S RNA
aRNA	antisense RNA	-	synonym of asRNA
asRNA	antisense RNA	-
asmiRNA	antisense micro RNA	-
cis-NAT	cis-natural antisense transcript	-	Natural antisense transcripts transcribed from the same genomic locus as their target but from the opposite DNA strand and form perfect pairs
crRNA	CRISPR RNA	-
tracrRNA	trans-activating crRNA	-
CRISPR RNA	CRISPR-Cas RNA	multiple families
DD RNA	DNA damage response RNA	-	RNA that activates DNA damage response
diRNA	DSB-induced small RNAs	-
dsRNA	double stranded RNA	-
endo-siRNA	endogenous small interfering RNA	-
exRNA	extracellular RNA	-
gRNA	guide RNA	-
hc-siRNA	heterochromatic small interfering RNA	-
hcsiRNA	heterochromatic small interfering RNA	-	synonym of hc-siRNA
hnRNA	heterogeneous nuclear RNA	-	synonym for pre-mRNA (in the strict sense, it may include nuclear RNA transcripts that do not end up as cytoplasmic mRNA)
RNAi	RNA interference	-	Process in which RNA inhibit gene expression or translation, by neutralizing targeted mRNA molecules
lincRNA	long intergenic non-coding RNA	-
lncRNA	long non coding RNA	-
miRNA	micro RNA	multiple families
mrpRNA	mitochondrial RNA processing ribonuclease	-	synonym of RNase MRP
nat-siRNA	natural antisense short interfering RNA	-	synonym of natsiRNA
natsiRNA	natural antisense short interfering RNA	-	Endogenous RNA regulators, between 21 and 24 nt in length, and are generated from complementary mRNA transcripts which are further processed into siRNA
OxyS RNA	oxidative stress response RNA	RF00035	Small non coding RNA which is induced in response to oxidative stress in Escherichia coli
piRNA	piwi-interacting RNA	multiple families	Small RNAs that form RNA-protein complexes with piwi proteins in animal cells
qiRNA	QDE-2 interfering RNA	-
rasiRNA	Repeat associated siRNA	-	Small RNA that is involved in the RNA interference pathway, a type of piRNA
RNase MRP	mitochondrial RNA processing ribonuclease	RF00030
RNase P	ribonuclease P	RF00010	A type of ribonuclease which cleaves RNA
scaRNA	small Cajal body-specific RNA	RF00553
scnRNA	small-scan RNA	-
scRNA	small cytoplasmic RNA	-
scRNA	small conditional RNA	-
SgrS RNA	sugar transport-related sRNA	RF00534	Small RNA that is activated by SgrR in Escherichia coli during glucose-phosphate stress
shRNA	short hairpin RNA	-
siRNA	small interfering RNA	-
SL RNA	spliced leader RNA	multiple families
SmY RNA	mRNA trans-splicing	RF01844	Small nuclear RNAs found in some species of nematode worms, thought to be involved in mRNA trans-splicing
snoRNA	small nucleolar RNA	multiple families
snRNA	small nuclear RNA	multiple families
snRNP	small nuclear ribonucleic proteins	-
SRP RNA	signal recognition particle RNA	CL00003
ssRNA	single stranded RNA	-
stRNA	small temporal RNA	-
tasiRNA	trans-acting siRNA	-
tmRNA	transfer-messenger RNA	RF00023	Bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties
uRNA	U spliceosomal RNA	multiple families
vRNA	vault RNA	-	synonym of vtRNA
vtRNA	vault RNA	RF00006
Xist RNA	X-inactive specific transcript
Y RNA	Y RNA	RF00019	Components of the Ro60 ribonucleoprotein particle and necessary for DNA replication through interactions with chromatin and initiation proteins
NATs	natural antisense transcripts	-	Natural antisense transcripts encoded within a cell that have transcript complementarity to other RNA transcripts
pre-mRNA	precursor messenger RNA	-	Immature single strand of messenger RNA
circRNA	circular RNA	-
msRNA	multicopy, single-stranded RNA		Component of retrons	[25]
cfRNA	cell-free RNA

See also

• RNA: Types of RNA
• Non-coding RNA

References

1. Gribaldo S, Brochier-Armanet C (2006). "The origin and evolution of Archaea: a state of the art". Philos Trans R Soc Lond B Biol Sci. 361 (1470): 1007–22. doi:10.1098/rstb.2006.1841. PMC 1578729. PMID 16754611.
2. Gillet R, Felden B (2001). "Emerging views on tmRNA-mediated protein tagging and ribosome rescue". Molecular Microbiology. 42 (4): 879–85. doi:10.1046/j.1365-2958.2001.02701.x. PMID 11737633.
3. Thore S, Mayer C, Sauter C, Weeks S, Suck D (2003). "Crystal Structures of the Pyrococcus abyssi Sm Core and Its Complex with RNA". J. Biol. Chem. 278 (2): 1239–47. doi:10.1074/jbc.M207685200. PMID 12409299.
4. Kiss T (2001). "Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs". The EMBO Journal. 20 (14): 3617–22. doi:10.1093/emboj/20.14.3617. PMC 125535. PMID 11447102.
5. Jones TA, Otto W, Marz M, Eddy SR, Stadler PF (2009). "A survey of nematode SmY RNAs". RNA Biol. 6 (1): 5–8. doi:10.4161/rna.6.1.7634. PMID 19106623.
6. Alfonzo JD, Thiemann O, Simpson L (1997). "The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria". Nucleic Acids Research. 25 (19): 3751–59. doi:10.1093/nar/25.19.3751. PMC 146959. PMID 9380494.
7. Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW (1999). "RNase P RNAs from some Archaea are catalytically active". Proc Natl Acad Sci USA. 96 (14): 7803–08. Bibcode:1999PNAS...96.7803P. doi:10.1073/pnas.96.14.7803. PMC 22142. PMID 10393902.
8. Woodhams MD, Stadler PF, Penny D, Collins LJ (2007). "RNase MRP and the RNA processing cascade in the eukaryotic ancestor". BMC Evolutionary Biology. 7: S13. doi:10.1186/1471-2148-7-S1-S13. PMC 1796607. PMID 17288571.
9. Perreault J, Perreault JP, Boire G (2007). "Ro-associated Y RNAs in metazoans: evolution and diversification". Molecular Biology and Evolution. 24 (8): 1678–89. doi:10.1093/molbev/msm084. PMID 17470436.
10. Lustig AJ (1999). "Crisis intervention: The role of telomerase". Proc Natl Acad Sci USA. 96 (7): 3339–41. Bibcode:1999PNAS...96.3339L. doi:10.1073/pnas.96.7.3339. PMC 34270. PMID 10097039.
11. Brantl S (2002). "Antisense-RNA regulation and RNA interference". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1575 (1–3): 15–25. doi:10.1016/S0167-4781(02)00280-4. PMID 12020814.
12. Brantl S (2007). "Regulatory mechanisms employed by cis-encoded antisense RNAs". Curr. Opin. Microbiol. 10 (2): 102–9. doi:10.1016/j.mib.2007.03.012. PMID 17387036.
13. Brouns SJ, Jore MM, Lundgren M, et al. (August 2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes". Science. 321 (5891): 960–4. Bibcode:2008Sci...321..960B. doi:10.1126/science.1159689. PMC 5898235. PMID 18703739.
14. Lin SL, Miller JD, Ying SY (2006). "Intronic microRNA (miRNA)". Journal of Biomedicine and Biotechnology. 2006 (4): 1–13. doi:10.1155/JBB/2006/26818. PMC 1559912. PMID 17057362.
15. Horwich MD, Li C, Matranga C, Vagin V, Farley G, Wang P, Zamore PD (2007). "The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC". Current Biology. 17 (14): 1265–72. doi:10.1016/j.cub.2007.06.030. PMID 17604629.
16. Ghildiyal M, Zamore PD (February 2009). "Small silencing RNAs: an expanding universe". Nat. Rev. Genet. 10 (2): 94–108. doi:10.1038/nrg2504. PMC 2724769. PMID 19148191.
17. Ahmad K, Henikoff S (2002). "Epigenetic consequences of nucleosome dynamics". Cell. 111 (3): 281–84. doi:10.1016/S0092-8674(02)01081-4. PMID 12419239.
18. Ahmad K, Henikoff S (2002). "Epigenetic consequences of nucleosome dynamics". Cell. 111 (3): 281–84. doi:10.1016/S0092-8674(02)01081-4. PMID 12419239.
19. Vazquez F, Vaucheret H (2004). "Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs". Mol. Cell. 16 (1): 69–79. doi:10.1016/j.molcel.2004.09.028. PMID 15469823.
20. Desset S, Buchon N, Meignin C, Coiffet M, Vaury C (2008). Volff J (ed.). "In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways". PLOS ONE. 3 (2): e1526. Bibcode:2008PLoSO...3.1526D. doi:10.1371/journal.pone.0001526. PMC 2211404. PMID 18253480.
21. Li, Wenbo; Notani, Dimple; Rosenfeld, Michael G. (2016-03-07). "Enhancers as non-coding RNA transcription units: recent insights and future perspectives". Nature Reviews. Genetics. Springer Nature. 17 (4): 207–223. doi:10.1038/nrg.2016.4. ISSN 1471-0056. PMID 26948815.CS1 maint: ref=harv (link)
22. Boeke JD (2003). "The unusual phylogenetic distribution of retrotransposons: a hypothesis". Genome Research. 13 (9): 1975–83. doi:10.1101/gr.1392003. PMID 12952870.
23. Flores R, Hernández C, Martínez de Alba AE, Daròs JA, Di Serio F (2005). "Viroids and viroid-host interactions". Annual Review of Phytopathology. 43: 117–39. doi:10.1146/annurev.phyto.43.040204.140243. PMID 16078879.
24. Gopinath SC, Matsugami A, Katahira M, Kumar PK (2005). "Human vault-associated non-coding RNAs bind to mitoxantrone, a chemotherapeutic compound". Nucleic Acids Res. 33 (15): 4874–81. doi:10.1093/nar/gki809. PMC 1201340. PMID 16150923.
25. Simon, Dawn M.; Zimmerly, Steven (2008-11-12). "A diversity of uncharacterized reverse transcriptases in bacteria". Nucleic Acids Research. 36 (22): 7219–7229. doi:10.1093/nar/gkn867. ISSN 1362-4962. PMC 2602772. PMID 19004871.

External links

• Rfam database — a collection of RNA families
• European ribosomal RNA database