List of RNAs
By role
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] |
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 | ||
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] | |
http://www.nature.com/nrg/journal/v17/n4/abs/nrg.2016.4.html
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 | |
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 | - |
See also
References
- ↑ 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. PMC 1578729 . PMID 16754611. doi:10.1098/rstb.2006.1841.
- ↑ Gillet R, Felden B (2001). "Emerging views on tmRNA-mediated protein tagging and ribosome rescue". Molecular Microbiology. 42 (4): 879–85. PMID 11737633. doi:10.1046/j.1365-2958.2001.02701.x.
- ↑ 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. PMID 12409299. doi:10.1074/jbc.M207685200.
- ↑ Kiss T (2001). "Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs". The EMBO Journal. 20 (14): 3617–22. PMC 125535 . PMID 11447102. doi:10.1093/emboj/20.14.3617.
- ↑ Jones TA, Otto W, Marz M, Eddy SR, Stadler PF (2009). "A survey of nematode SmY RNAs". RNA Biol. 6 (1): 5–8. PMID 19106623. doi:10.4161/rna.6.1.7634.
- ↑ 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. PMC 146959 . PMID 9380494. doi:10.1093/nar/25.19.3751.
- ↑ 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. PMC 22142 . PMID 10393902. doi:10.1073/pnas.96.14.7803.
- ↑ 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. PMC 1796607 . PMID 17288571. doi:10.1186/1471-2148-7-S1-S13.
- ↑ Perreault J, Perreault JP, Boire G (2007). "Ro-associated Y RNAs in metazoans: evolution and diversification". Molecular Biology and Evolution. 24 (8): 1678–89. PMID 17470436. doi:10.1093/molbev/msm084.
- ↑ Lustig AJ (1999). "Crisis intervention: The role of telomerase". Proc Natl Acad Sci USA. 96 (7): 3339–41. PMC 34270 . PMID 10097039. doi:10.1073/pnas.96.7.3339.
- ↑ Brantl S (2002). "Antisense-RNA regulation and RNA interference". Biochimica et Biophysica Acta. 1575 (1–3): 15–25. PMID 12020814. doi:10.1016/S0167-4781(02)00280-4.
- ↑ Brantl S (2007). "Regulatory mechanisms employed by cis-encoded antisense RNAs". Curr. Opin. Microbiol. 10 (2): 102–9. PMID 17387036. doi:10.1016/j.mib.2007.03.012.
- ↑ Brouns SJ, Jore MM, Lundgren M, et al. (August 2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes". Science. 321 (5891): 960–4. PMID 18703739. doi:10.1126/science.1159689.
- ↑ Lin SL, Miller JD, Ying SY (2006). "Intronic microRNA (miRNA)". Journal of Biomedicine and Biotechnology. 2006 (4): 1–13. PMC 1559912 . PMID 17057362. doi:10.1155/JBB/2006/26818.
- ↑ 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. PMID 17604629. doi:10.1016/j.cub.2007.06.030.
- ↑ Ghildiyal M, Zamore PD (February 2009). "Small silencing RNAs: an expanding universe". Nat. Rev. Genet. 10 (2): 94–108. PMC 2724769 . PMID 19148191. doi:10.1038/nrg2504.
- ↑ Ahmad K, Henikoff S (2002). "Epigenetic consequences of nucleosome dynamics". Cell. 111 (3): 281–84. PMID 12419239. doi:10.1016/S0092-8674(02)01081-4.
- ↑ Ahmad K, Henikoff S (2002). "Epigenetic consequences of nucleosome dynamics". Cell. 111 (3): 281–84. PMID 12419239. doi:10.1016/S0092-8674(02)01081-4.
- ↑ Vazquez F, Vaucheret H (2004). "Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs". Mol. Cell. 16: 69–79. PMID 15469823. doi:10.1016/j.molcel.2004.09.028.
- ↑ 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. PMC 2211404 . PMID 18253480. doi:10.1371/journal.pone.0001526.
- ↑ "Enhancers as non-coding RNA transcription units: recent insights and future perspectives". Nat Rev Genet. doi:10.1038/nrg.2016.4L3.
- ↑ Boeke JD (2003). "The unusual phylogenetic distribution of retrotransposons: a hypothesis". Genome Research. 13 (9): 1975–83. PMID 12952870. doi:10.1101/gr.1392003.
- ↑ 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. PMID 16078879. doi:10.1146/annurev.phyto.43.040204.140243.
- ↑ 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. PMC 1201340 . PMID 16150923. doi:10.1093/nar/gki809.
External links
- Rfam database — a collection of RNA families
- European ribosomal RNA database
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