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

Related Research Articles

<span class="mw-page-title-main">RNA</span> Family of large biological molecules

Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself or by forming a template for the production of proteins. RNA and deoxyribonucleic acid (DNA) are nucleic acids. The nucleic acids constitute one of the four major macromolecules essential for all known forms of life. RNA is assembled as a chain of nucleotides. Cellular organisms use messenger RNA (mRNA) to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome.

<span class="mw-page-title-main">Ribonuclease H</span> Enzyme family

Ribonuclease H is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/DNA substrate via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from bacteria to archaea to eukaryotes.

<span class="mw-page-title-main">Transfer RNA</span> RNA that facilitates the addition of amino acids to a new protein

Transfer RNA is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. Transfer RNA (tRNA) does this by carrying an amino acid to the protein-synthesizing machinery of a cell called the ribosome. Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code.

<span class="mw-page-title-main">Ribonuclease P</span> Class of enzymes

Ribonuclease P is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein-based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA molecules. Further, RNase P is one of two known multiple turnover ribozymes in nature, the discovery of which earned Sidney Altman and Thomas Cech the Nobel Prize in Chemistry in 1989: in the 1970s, Altman discovered the existence of precursor tRNA with flanking sequences and was the first to characterize RNase P and its activity in processing of the 5' leader sequence of precursor tRNA. Recent findings also reveal that RNase P has a new function. It has been shown that human nuclear RNase P is required for the normal and efficient transcription of various small noncoding RNAs, such as tRNA, 5S rRNA, SRP RNA and U6 snRNA genes, which are transcribed by RNA polymerase III, one of three major nuclear RNA polymerases in human cells.

Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling.

<span class="mw-page-title-main">U4 spliceosomal RNA</span> Non-coding RNA component of the spliceosome

The U4 small nuclear Ribo-Nucleic Acid is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA (pre-mRNA). It forms a duplex with U6, and with each splicing round, it is displaced from the U6 snRNA in an ATP-dependent manner, allowing U6 to re-fold and create the active site for splicing catalysis. A recycling process involving protein Brr2 releases U4 from U6, while protein Prp24 re-anneals U4 and U6. The crystal structure of a 5′ stem-loop of U4 in complex with a binding protein has been solved.

<span class="mw-page-title-main">U7 small nuclear RNA</span>

The U7 small nuclear RNA is an RNA molecule and a component of the small nuclear ribonucleoprotein complex. The U7 snRNA is required for histone pre-mRNA processing.

<span class="mw-page-title-main">IFNB1</span> Protein-coding gene in the species Homo sapiens

Interferon beta is a protein that in humans is encoded by the IFNB1 gene. The natural and recombinant protein forms have antiviral, antibacterial, and anticancer properties.

<span class="mw-page-title-main">U2 small nuclear RNA auxiliary factor 1</span> Protein-coding gene in the species Homo sapiens

Splicing factor U2AF 35 kDa subunit is a protein that in humans is encoded by the U2AF1 gene.

<span class="mw-page-title-main">CUGBP1</span> Protein-coding gene in the species Homo sapiens

CUG triplet repeat, RNA binding protein 1, also known as CUGBP1, is a protein which in humans is encoded by the CUGBP1 gene.

<span class="mw-page-title-main">POP1 (gene)</span> Protein-coding gene in the species Homo sapiens

Ribonucleases P/MRP protein subunit POP1 is a protein that in humans is encoded by the POP1 gene.

<span class="mw-page-title-main">GTF2F2</span> Protein-coding gene in the species Homo sapiens

General transcription factor IIF subunit 2 is a protein that in humans is encoded by the GTF2F2 gene.

<span class="mw-page-title-main">POP4 (gene)</span> Protein-coding gene in the species Homo sapiens

Ribonuclease P protein subunit p29 is an enzyme that in humans is encoded by the POP4 gene.

In a screen of the Bacillus subtilis genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions (IGRs) over 500 base pairs in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All the small RNAs except BsrD RNA were expressed in transformed Escherichia coli cells harboring a plasmid with PCR-amplified IGRs of B. subtilis, indicating that their own promoters independently express small RNAs. Under non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase, but undetectable during the stationary phase. Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a recognition site for RNA polymerase sigma factor σA.

In molecular biology, the SR1 RNA is a small RNA (sRNA) produced by species of Bacillus and closely related bacteria. It is a dual-function RNA which acts both as a protein-coding RNA and as a regulatory sRNA.

<span class="mw-page-title-main">Long interspersed nuclear element</span>

Long interspersed nuclear elements (LINEs) are a group of non-LTR retrotransposons that are widespread in the genome of many eukaryotes. LINEs contain an internal Pol II promoter to initiate transcription into mRNA, and encode one or two proteins, ORF1 and ORF2. The functional domains present within ORF1 vary greatly among LINEs, but often exhibit RNA/DNA binding activity. ORF2 is essential to successful retrotransposition, and encodes a protein with both reverse transcriptase and endonuclease activity.

Retrozymes are a family of retrotransposons first discovered in the genomes of plants but now also known in genomes of animals. Retrozymes contain a hammerhead ribozyme (HHR) in their sequences, although they do not possess any coding regions. Retrozymes are nonautonomous retroelements, and so borrow proteins from other elements to move into new regions of a genome. Retrozymes are actively transcribed into covalently closed circular RNAs and are detected in both polarities, which may indicate the use of rolling circle replication in their lifecycle.

<span class="mw-page-title-main">Sfold</span> RNA secondary structure prediction and application software

Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions with a focus on assessment of RNA target accessibility, for major applications to the rational design of siRNAs in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.

References

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