List of RNAs

Last updated

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.

Contents

By role

RNAs involved in protein synthesis
TypeAbbr.FunctionDistributionRef.
Messenger RNA mRNA Codes for proteinAll organisms
Ribosomal RNA rRNA Translation All organisms
Signal recognition particle RNA 7SL RNA or SRP RNAMembrane integrationAll organisms [1]
Transfer RNA tRNATranslationAll organisms
Transfer-messenger RNA tmRNARescuing stalled ribosomes Bacteria [2]
RNAs involved in post-transcriptional modification or DNA replication
TypeAbbr.FunctionDistributionRef.
Small nuclear RNA snRNASplicing and other functions Eukaryotes and archaea [3]
Small nucleolar RNA snoRNANucleotide modification of RNAsEukaryotes and archaea [4]
SmY RNA SmYmRNA trans-splicing Nematodes [5]
Small Cajal body-specific RNA scaRNAType of snoRNA; Nucleotide modification of RNAs
Guide RNA gRNAmRNA nucleotide modification Kinetoplastid mitochondria [6]
Ribonuclease P RNase PtRNA maturationAll organisms [7]
Ribonuclease MRP RNase MRPrRNA maturation, DNA replication Eukaryotes [8]
Y RNA RNA processing, DNA replication Animals [9]
Telomerase RNA Component TERC Telomere synthesisMost eukaryotes [10]
Spliced Leader RNA SL RNAmRNA trans-splicing, RNA processing
Regulatory RNAs
TypeAbbr.FunctionDistributionRef.
Antisense RNA aRNA, asRNATranscriptional attenuation / mRNA degradation / mRNA stabilisation / Translation blockAll organisms [11] [12]
Cis-natural antisense transcript cis-NATGene regulation
CRISPR RNAcrRNAResistance to parasites, by targeting their DNABacteria and archaea [13]
Long noncoding RNA lncRNARegulation of gene transcription, epigenetic regulationEukaryotes
MicroRNA miRNAGene regulationMost eukaryotes [14]
Piwi-interacting RNA piRNATransposon defense, maybe other functionsMost animals [15] [16]
Small interfering RNA siRNAGene regulationMost eukaryotes [17]
Short hairpin RNA shRNAGene regulationMost eukaryotes [18]
Trans-acting siRNA tasiRNAGene regulation Land plants [19]
Repeat associated siRNA rasiRNAType of piRNA; transposon defense Drosophila [20]
7SK RNA 7SKnegatively regulating CDK9/cyclin T complex
Enhancer RNA eRNAGene regulation [21]
Parasitic RNAs
TypeFunctionDistributionRef.
Retrotransposon Self-propagatingEukaryotes and some bacteria [22]
Viral genomeInformation carrier Double-stranded RNA viruses, positive-sense RNA viruses, negative-sense RNA viruses, many satellite viruses and reverse transcribing viruses
Viroid Self-propagatingInfected plants [23]
Satellite RNA Self-propagatingInfected cells
Other RNAs
TypeAbbr.FunctionDistributionRef.
Vault RNA vRNA, vtRNAExpulsion of xenobiotics (conjectured) [24]
GlycoRNA -Unknown

RNA abbreviations

Abbr.NameFamilyDescriptionRef.
ncRNA non coding RNA-
nmRNAnon messenger RNA-synonym of ncRNA
sRNAsmall RNA-synonym of ncRNA
smnRNAsmall non messenger RNA-synonym of ncRNA
tRNA transfer RNA RF00005
sRNAsoluble RNA-synonym of tRNA
mRNA messenger RNA-
pcRNAprotein coding RNA-synonym of mRNA
rRNA ribosomal RNAmultiple 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
pRNApromoter RNA RF01518 synonym of NoRC RNA
6S RNA 6S RNA RF00013
SsrS RNA RF00013 synonym of 6S RNA
aRNAantisense RNA-synonym of asRNA
asRNA antisense RNA-
asmiRNAantisense micro RNA-
cis-NATcis-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
crRNACRISPR RNA-
tracrRNA trans-activating crRNA-
CRISPR RNACRISPR-Cas RNAmultiple families
DD RNADNA damage response RNA-RNA that activates DNA damage response
diRNADSB-induced small RNAs-
dsRNAdouble stranded RNA-
endo-siRNAendogenous small interfering RNA-
exRNA extracellular RNA-
gRNA guide RNA-
hc-siRNAheterochromatic small interfering RNA-
hcsiRNAheterochromatic small interfering RNA-synonym of hc-siRNA
hnRNAheterogeneous 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 RNAmultiple families
mrpRNAmitochondrial RNA processing ribonuclease-synonym of RNase MRP
nat-siRNAnatural 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 RNAmultiple familiesSmall RNAs that form RNA-protein complexes with piwi proteins in animal cells
qiRNAQDE-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
scnRNAsmall-scan RNA-
scRNAsmall 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 RNAspliced leader RNAmultiple 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 RNAmultiple families
snRNA small nuclear RNAmultiple families
snRNP small nuclear ribonucleic proteins-
SPA lncRNA5' small nucleolar RNA capped and 3' polyadenylated long noncoding RNA-
SRP RNA signal recognition particle RNA CL00003
ssRNAsingle 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
uRNAU spliceosomal RNAmultiple families
vRNAvault 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
NATsnatural 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
circRNAcircular RNA-
msRNAmulticopy, single-stranded RNA-Products of a retron-encoded reverse transcriptase (RT) which form a RT-msDNA complex that acts as an anti-phage antitoxin [25] [26]
cfRNAcell-free RNA-

See also

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. S2CID   45056681.
  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. S2CID   32095624.
  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 (inactive 12 July 2025). PMC   146959 . PMID   9380494.{{cite journal}}: CS1 maint: DOI inactive as of July 2025 (link)
  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 (Suppl 1) S13. Bibcode:2007BMCEE...7S..13W. 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) 026818: 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. Bibcode:2007CBio...17.1265H. doi: 10.1016/j.cub.2007.06.030 . PMID   17604629. S2CID   18880444.
  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. S2CID   17735718.
  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. S2CID   17735718.
  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 JN (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. 17 (4). Springer Nature: 207–223. doi:10.1038/nrg.2016.4. ISSN   1471-0056. PMID   26948815. S2CID   215371.
  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 (1): 117–39. Bibcode:2005AnRvP..43..117F. 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.
  26. ↑ Bobonis, Jacob; Mitosch, Karin; Mateus, André; Karcher, Nicolai; Kritikos, George; Selkrig, Joel; Zietek, Matylda; Monzon, Vivian; Pfalz, Birgit; Garcia-Santamarina, Sarela; Galardini, Marco; Sueki, Anna; Kobayashi, Callie; Stein, Frank; Bateman, Alex (2022-09-01). "Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems" (PDF). Nature. 609 (7925): 144–150. Bibcode:2022Natur.609..144B. doi:10.1038/s41586-022-05091-4. ISSN   0028-0836. PMC   11938430 . PMID   35850148. S2CID   250643138.
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