This is a list of ''cis''-regulatory RNAs. These are

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

motifs which regulate

nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...

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. {{horizontal ToC, nonum=yes

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* 23S methyl RNA motif * 6C RNA

A

Actino-pnp RNA motif The Actino-''pnp'' RNA motif is a conserved structure found in Actinomycetota that is apparently in the 5' untranslated regions of genes predicted to encode exoribonucleases. The RNA element's function is likely analogous to an RNA structure fo ...

* AdoCbl riboswitch *

Alfalfa mosaic virus coat protein binding (CPB) RNA The Alfalfa mosaic virus (AMV) coat protein binding (CPB) RNA is an RNA element which is found in the 3′ UTR of the genome. AMV CPB can stimulate the translation of AMV RNA Ribonucleic acid (RNA) is a polymeric molecule essential in vari ...

Alfalfa mosaic virus RNA 1 5′ UTR stem-loop The Alfalfa mosaic virus RNA 1 5′ UTR stem-loop represents a putative stem-loop structure found in the 5′ UTR in RNA 1 of alfalfa mosaic virus. RNA 1 is responsible for encoding the viral replicase protein P1. This family is required for negat ...

* Alpha operon ribosome binding site * Antizyme RNA frameshifting stimulation element * APC internal ribosome entry site (IRES) * Aphthovirus internal ribosome entry site (IRES) *

Apolipoprotein B (apoB) 5′ UTR cis-regulatory element The apolipoprotein B (apoB) 5′ UTR cis regulatory element is an RNA element located in the 5′ UTR of the human apoB mRNA. This structured element increases translation Translation is the communication of the Meaning (linguistic), me ...

AtoC RNA motif The ''atoC'' RNA motif is a conserved RNA-like structure identified by bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data ...

* 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 d ...

B

* Bag-1 internal ribosome entry site (IRES) * Bamboo mosaic potexvirus (BaMV) cis-regulatory element * Bamboo mosaic virus satellite RNA cis-regulatory element *

Bovine leukaemia virus RNA packaging signal This family represents the bovine leukaemia virus RNA encapsidation (packaging) signal, which is essential for efficient viral replication. Discovery Before its discovery, the location of the encapsidation (packaging) signal within the bovine le ...

C

* Citrus tristeza virus replication signal *

CrcB RNA motif The fluoride riboswitch (formerly called the ''crcB'' RNA motif) is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. These RNAs were later shown to function as riboswitches that sense fluoride io ...

Ctgf/hcs24 CAESAR ctgf/hcs24 CAESAR is the name given to the cis-acting RNA element identified in the 3' untranslated region (3'UTR) of the human connective tissue growth factor (CTGF) messenger RNA. This gene is also known as hypertrophic chondrocyte Chondro ...

* Cap-independent translation element

E

* Enterobacteria greA leader * Enterobacteria rnk leader * Enteroviral 3′ UTR element * Enterovirus 5′ cloverleaf cis-acting replication element * Enterovirus cis-acting replication element

F

FIE3 (ftz instability element 3′) element The FIE3 (ftz instability element 3′) element is an RNA element found in the 3′ UTR of the fushi tarazu mRNA. The fushi tarazu gene is essential for the establishment of the Drosophila embryonic body plan. When first expressed in early embry ...

Flavivirus capsid hairpin cHP The Flavivirus capsid hairpin cHP is a conserved RNA hairpin structure identified within the capsid coding region of several flavivirus genomes. These positive strand RNA genomes are translated as a single polypeptide and subsequently cleaved into ...

* Flg-Rhizobiales RNA motif

G

* G-CSF factor stem-loop destabilising element * Gammaproteobacteria rimP leader

H

* Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) * Hepatitis C alternative reading frame stem-loop * Hepatitis C stem-loop IV * Hepatitis C virus (HCV) cis-acting replication element (CRE) * Hepatitis C virus 3'X element * Hepatitis C virus stem-loop VII * Hepatitis E virus cis-reactive element * HIV gag stem loop 3 (GSL3) *

HopC RNA motif The ''hopC'' RNA motif is a predicted cis-regulatory element identified by a bioinformatic screen for conserved RNA secondary structures. ''hopC'' RNAs are exclusively found within bacteria classified within the genus '' Helicobacter'', some ...

* Human parechovirus 1 (HPeV1) cis regulatory element (CRE) * Human rhinovirus internal cis-acting regulatory element (CRE)

I

IbpB thermometer The IbpB thermometer is an RNA thermometer element found in the ''ibpAB'' operon. The operon contains two heat-shock genes, encoding inclusion body binding proteins A and B (IbpA/B), and is the most drastically upregulated operon under heat-shock ...

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 ...

J

JUMPstart RNA motif The JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements. The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis. The ...

L

Luteovirus cap-independent translation element (BTE) The Barley yellow dwarf virus-like cap-independent translation element (BTE) is an RNA element found in the 3' UTR of some luteoviruses. This element mediates translation of genomic RNA and subgenomic RNA1 (sgRNA1). BTEs have a consensus seque ...

M

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. ...

Mason-Pfizer monkey virus packaging signal ''Mason-Pfizer monkey virus (M-PMV)'', formerly Simian retrovirus (SRV), is a species of retroviruses that usually infect and cause a fatal immune deficiency in Asian macaques. The ssRNA virus appears sporadically in mammary carcinoma of captive ...

* Mnt IRES * MraW RNA motif

N

* N-myc IRES *

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 (a ...

P

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 p27kip protein in human cells. The p27kip1 protein is involved in cell cycle regulation and belongs to ...

* Potassium channel RNA editing signal *

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. This element has been found to be required for minus strand RNA accumulation and is essential for efficient vi ...

PotC RNA motif The ''potC'' RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria. Thus, this RNA is present in environmen ...

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 contains 5 copies of a 24 nucleotide repeat ...

* Pseudomonas rnk leader * Pseudomonas rpsL leader * PyrR binding site

R

R2 RNA element R, or r, is the eighteenth letter of the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages and others worldwide. Its name in English is ''ar'' (pronounced ), plural ''ars'', or in Irela ...

* 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 * Retrovirus direct repeat 1 (dr1) *

Ribosomal protein L10 leader This family is a putative ribosomal protein leader autoregulatory structure found in ''B. subtilis'' and other low-GC Gram-positive bacteria. It is located in the 5′ untranslated regions of mRNAs encoding ribosomal proteins L10 and L12 (rplJ-r ...

Ribosomal protein L13 leader L13 ribosomal protein leaders play a role in ribosome biogenesis as part of an autoregulatory mechanism to control the concentration of ribosomal proteins L13. Three structural classes of L13 ribosomal protein leaders were detected by different ...

* Ribosomal protein L19 leader *

Ribosomal protein L20 leader L20 ribosomal protein leader is a ribosomal protein leader involved in the ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of ribosomal proteins L20. The structure is typically located in the 5′ unt ...

Ribosomal protein L21 leader A ribosomal protein L21 leader is a ribosomal protein leader autoregulatory structure that regulates mRNAs containing a gene that encodes ribosomal protein L21. An RNA motif was predicted to function as an L21 leader in a bioinformatics study, ...

* Ribosomal S15 leader *

RNase E 5′ UTR element In molecular biology, the RNase E 5′ UTR element is a cis-acting element located in the 5′ UTR of ribonuclease (RNase) E messenger RNA (mRNA). RNase E is a key regulatory enzyme in the pathway of mRNA degradation in ''Escherichia coli''. It i ...

* RncO * Rne-II RNA motif * Rotavirus cis-acting replication element (CRE) *

Rous sarcoma virus (RSV) primer binding site (PBS) This family represents a structured region around the Rous sarcoma virus (RSV) primer binding site (PBS). This region is known to be required for the efficient initiation of reverse transcription A reverse transcriptase (RT) is an enzyme used ...

* RtT RNA *

Rubella virus 3′ cis-acting element The Rubella virus 3′ cis-acting element RNA family represents a ''cis''-acting element found at the 3′ UTR in the rubella virus. This family contains three conserved step loop structures. Calreticulin (CAL), which is known to bind calcium in ...

S

* S-element *

SerC leader SerC leader is a putative regulatory RNA structure found upstream of the serC-serA operon in some alpha-proteobacteria Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and ...

Simian virus 40 late polyadenylation signal (SVLPA) SV40 is an abbreviation for simian vacuolating virus 40 or simian virus 40, a polyomavirus that is found in both monkeys and humans. Like other polyomaviruses, SV40 is a DNA virus that has the potential to cause tumors in animals, but most often ...

SpeF leader SpeF is a putative ''cis''-acting element identified in several gram negative alpha proteobacteria. It is proposed to be involved in regulating expression of genes involved in polyamide biosynthesis. SpeF is one of five putative regulatory eleme ...

* Spi-1 (PU.1) 5′ UTR regulatory element *

Sxy 5′ UTR element The Sxy 5′ UTR element is an RNA element that controls expression of the sxy gene in ''H. influenzae''. The sxy gene is a transcription factor (also known as TfoX) that regulates competence which is the ability of bacteria to take up DNA from t ...

T

* T-box leader *

Togavirus 5′ plus strand cis-regulatory element The Togavirus 5′ plus strand cis-regulatory element is an RNA element which is thought to be essential for both plus and minus strand RNA synthesis. Genus Alphavirus belongs to the family Togaviridae. Alpha viruses contain secondary structu ...

* Tombusvirus 3′ UTR region IV * Tombusvirus 5′ UTR * Tombusvirus internal replication element (IRE) * Tobamovirus IRES * Transfer RNA-like structures * TrkB IRES *

Turnip crinkle virus (TCV) core promoter hairpin (Pr) The turnip crinkle virus (TCV) core promoter hairpin (Pr) is an RNA element located in the 3' UTR In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the transl ...

Turnip crinkle virus (TCV) repressor of minus strand synthesis H5 The TCV hairpin 5 (H5) is an RNA element found in the turnip crinkle virus. This RNA element is composed of a stem-loop that contains a large symmetrical internal loop (LSL). H5 can repress minus-strand synthesis when the 3' side of the LSL pa ...

U

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

* Vimentin 3′ UTR protein-binding region *

Voltage-gated potassium-channel Kv1.4 IRES This family represents the Kv1.4 voltage-gated potassium channel internal ribosome entry site ( IRES). This region has been shown to mediate internal ribosome entry in cells derived from brain, heart, and skeletal muscle; tissues known to expres ...

W

* Wingless localisation element 3 (WLE3)

Y

YbhL leader The YbhL leader is a putative structured RNA element that is found upstream of the uncharacterized YbhL membrane protein in alpha-proteobacteria. Other non-coding RNAs uncovered in the same analysis include: speF, suhB ''suhB'', also known ...

* YdaO/yuaA leader * YkkC-yxkD leader *

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 and ...

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See also