This is a list of ''cis''-regulatory RNAs. These are
RNA
Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
motifs which regulate
nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
regions on the same molecule, as opposed to ''trans''-acting motifs which regulate a distal molecule. Some of these RNAs are broadly distributed while others are single RNA families.
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23S methyl RNA motif
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6C RNA
A
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Actino-pnp RNA motif
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AdoCbl riboswitch
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Alfalfa mosaic virus coat protein binding (CPB) RNA
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Alfalfa mosaic virus RNA 1 5′ UTR stem-loop
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Alpha operon ribosome binding site
The alpha operon ribosome binding site in bacteria is surrounded by this complex pseudoknotted RNA structure. Translation of the mRNA produces 4 ribosomal protein products, one of which (S4) acts as a translational repressor by binding to the nes ...
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Antizyme RNA frameshifting stimulation element
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APC internal ribosome entry site (IRES)
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Aphthovirus internal ribosome entry site (IRES)
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Apolipoprotein B (apoB) 5′ UTR cis-regulatory element
*
aspS RNA motif
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AtoC RNA motif
*
atpB RNA motif
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ATPC RNA motif
*
AU-rich element
Adenylate-uridylate-rich elements (AU-rich elements; AREs) are found in the 3' untranslated region (UTR) of many messenger RNAs (mRNAs) that code for proto-oncogenes, nuclear transcription factors, and cytokines. AREs are one of the most common det ...
B
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Bacteroid-trp RNA motif
*
Bag-1 internal ribosome entry site (IRES)
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Bamboo mosaic potexvirus (BaMV) cis-regulatory element
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Bamboo mosaic virus satellite RNA cis-regulatory element
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Bovine leukaemia virus RNA packaging signal
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Burkholderiales-2 RNA motif
C
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Chlorobi-RRM RNA motif
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chrB RNA motif
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Citrus tristeza virus replication signal
*
CrcB RNA motif
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Ctgf/hcs24 CAESAR
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COG3860 RNA motif
*
Cap-independent translation element
In molecular biology, a cap-independent translation element (CITE or 3'CITE) is an RNA sequence found in the 3'UTR of many RNA plant viruses.
Eukaryotic mRNAs contain a 5' cap structure which is required for efficient binding of translation initi ...
D
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DABA-DC-AT RNA motif
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DUF1874 RNA motif
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DUF3085 RNA motif
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DUF3577 RNA motif
E
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EngA RNA motif
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Enterobacteria greA leader
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Enterobacteria rnk leader
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Enteroviral 3′ UTR element
*
Enterovirus 5′ cloverleaf cis-acting replication element
*
Enterovirus cis-acting replication element
F
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Fibro-purF RNA motif
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FIE3 (ftz instability element 3′) element
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Flavivirus capsid hairpin cHP
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Flg-Rhizobiales RNA motif
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FlpD RNA motif
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folE RNA motif
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folP RNA motif
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Freshwater-2 RNA motif
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FTHFS RNA motif
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Fusobacteriales-1 RNA motif
G
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G-CSF factor stem-loop destabilising element
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Gammaproteobacteria rimP leader
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gltS RNA motif
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GP20 RNA motif
H
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Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES)
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Hepatitis C alternative reading frame stem-loop
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Hepatitis C stem-loop IV
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Hepatitis C virus (HCV) cis-acting replication element (CRE)
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Hepatitis C virus 3'X element
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Hepatitis C virus stem-loop VII
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Hepatitis E virus cis-reactive element
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HIV gag stem loop 3 (GSL3)
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HopC RNA motif
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Human parechovirus 1 (HPeV1) cis regulatory element (CRE)
*
Human rhinovirus internal cis-acting regulatory element (CRE)
*
hya RNA motif
I
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IbpB thermometer
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ilvB-OMG RNA motif
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ilvH RNA motif
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Infectious bronchitis virus D-RNA
The Infectious bronchitis virus D-RNA is an RNA element known as defective RNA or D-RNA. This element is thought to be essential for viral replication and efficient packaging of avian infectious bronchitis virus (IBV) particles.
Coronavirus D-R ...
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ivy-DE RNA motif
J
*
JUMPstart RNA motif
L
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L17DE RNA motif
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ldcC RNA motif
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LivK RNA motif
*
Lnt RNA motif
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Luteovirus cap-independent translation element (BTE)
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lysM RNA motifs
M
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Magnesium responsive RNA element The Magnesium responsive RNA element, not to be confused with the completely distinct M-box riboswitch, is a cis-regulatory element that regulates the expression of the magnesium transporter protein MgtA. It is located in the 5' UTR of this gene. ...
*
malK RNA motifs
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Mason-Pfizer monkey virus packaging signal
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Mnt IRES
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MraW RNA motif
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MsiK RNA motif
N
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N-myc IRES
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Nanos 3′ UTR translation control element
Nanos 3′ UTR translation control element is a cis-regulatory element in the 3′ untranslated region (3′ UTR) of the messenger RNA which encodes the Nanos protein. The Nanos protein in ''Drosophila'' is required for correct morphogenesis (ant ...
*
narK RNA motif
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nhaA-II RNA motif
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NLPC-P60 RNA motif
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NuoG RNA motif
P
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P27 cis-regulatory element
The p27 cis-regulatory element is a structured G/C rich RNA element which is involved in controlling cell cycle regulated translation of the p27Kip1 protein in human cells.
The p27kip1 protein is involved in cell cycle regulation and belongs t ...
*
pemK RNA motif
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Peptidase-S11 RNA motif
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PGK RNA motif
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Potassium channel RNA editing signal
The potassium channel RNA editing signal is an RNA element found in human Kv1.1 and its homologues which directs the efficient modification of an adenosine to inosine by an adenosine deaminase acting on RNA (ADAR). The ADAR modification causes a ...
*
Potato virus X cis-acting regulatory element
The Potato virus X cis-acting regulatory element is a cis-acting regulatory element found in the 3' UTR of the Potato virus X genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA ...
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PotC RNA motif
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Poxvirus AX element late mRNA cis-regulatory element
The Poxvirus AX element late mRNA family represents a ''cis''-regulatory element present at the 3' end of poxvirus late ATI mRNA and is known as the AX element. The AX element is involved in directing the efficient production and orientation-depe ...
*
Prion pseudoknot
The prion pseudoknot is predicted RNA pseudoknot structure found in prion protein mRNA. It has been suggested that this element has a possible effect in prion protein translation. The human prion protein gene contains 5 copies of a 24 nucleotide ...
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PsbNH RNA motif
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Pseudomon-groES RNA motif
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Pseudomonas rnk leader
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Pseudomonas rpsL leader
*
PyrG leader
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PyrR binding site
R
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R2 RNA element
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RbcL 5′ UTR RNA stabilising element
*
Red clover necrotic mosaic virus translation enhancer elements
Red clover necrotic mosaic virus (RCNMV) contains several structural elements present within the 3′ and 5′ untranslated regions (UTR) of the genome that enhance translation. In eukaryotes transcription is a prerequisite for translation. During ...
*
Regulatory region of repZ gene
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Retrovirus direct repeat 1 (dr1)
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Ribosomal protein L10 leader
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Ribosomal protein L13 leader
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Ribosomal protein L19 leader
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Ribosomal protein L20 leader
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Ribosomal protein L21 leader
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Ribosomal S15 leader
S15 Ribosomal protein leaders perform an important regulatory function in ribosome biogenesis. They were used as an autoregulatory mechanism to control the concentration of ribosomal proteins S15. The structure is located in the 5′ untranslated ...
*
RNase E 5′ UTR element
*
RncO
RncO is a bacterial non-coding RNA regulatory element found in the rnc leader sequence. The rnc operon is negatively auto-regulated by transcript stability. ''rnc'', the first gene in the operon codes for RNase III which cleaves the long rncO ste ...
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Rne-II RNA motif
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Rotavirus cis-acting replication element (CRE)
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Rothia-sucC RNA motif
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Rous sarcoma virus (RSV) primer binding site (PBS)
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RtT RNA
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Rubella virus 3′ cis-acting element
S
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S-element
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SerC leader
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Simian virus 40 late polyadenylation signal (SVLPA)
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SpeF leader
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Spi-1 (PU.1) 5′ UTR regulatory element
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ssnA RNA motif
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Sxy 5′ UTR element
T
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T-box leader
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terC RNA motif
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Termite-leu RNA motif
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Thermales-rpoB RNA motif
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Togavirus 5′ plus strand cis-regulatory element
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Tombusvirus 3′ UTR region IV
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Tombusvirus 5′ UTR
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Tombusvirus internal replication element (IRE)
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Tobamovirus IRES
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Transfer RNA-like structures
Transfer RNA-like structures (tRNA-like structures) are RNA sequences, which have a similar tertiary structure to tRNA; they frequently contain a pseudoknot close to the 3' end. The presence of tRNA-like structures has been demonstrated in many pla ...
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TrkB IRES
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Turnip crinkle virus (TCV) core promoter hairpin (Pr)
*
Turnip crinkle virus (TCV) repressor of minus strand synthesis H5
U
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U1A polyadenylation inhibition element (PIE)
The U1A polyadenylation inhibition element (PIE) is an RNA element which is responsible for the regulation of the length of the polyA tail of the U1A protein pre-mRNA. The PIE is located in the U1A mRNA 3' UTR
In molecular genetics, the thre ...
*
UnaL2 LINE 3′ element
V
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Vimentin 3′ UTR protein-binding region
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Voltage-gated potassium-channel Kv1.4 IRES
W
*
Wingless localisation element 3 (WLE3)
X
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xerDC RNA motif
Y
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YbhL leader
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YdaO/yuaA leader
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YkkC-yxkD leader
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YybP-ykoY leader
The yybP-ykoY leader RNA element was originally discovered in ''E. coli'' during a large scale screen and was named SraF. This family was later found to exist upstream of related families of protein genes in many bacteria, including the yybP a ...
See also
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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
RNA ...
Cis-regulatory RNA elements
RNA
Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...