This is a list of ''cis''-regulatory RNAs. These are RNA motifs which regulate nucleic acid 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 * 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 by between 50 and 100-fold. This family contains at least two coat p ...

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 Alfalfa mosaic virus (AMV), also known as ''Lucerne mosaic virus'' or ''Potato calico virus'', i ...

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 ...

* 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 * AtoC RNA motif * 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 de ...

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

C

* Citrus tristeza virus replication signal * CrcB RNA motif * Ctgf/hcs24 CAESAR *

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 ini ...

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 * Flavivirus capsid hairpin cHP * 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) The heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) is an RNA element that allows cap independent translation during conditions such as heat shock and stress. It has been shown that the 216 nucleotide Nucleotides are organ ...

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

I

* IbpB thermometer * Infectious bronchitis virus D-RNA

J

* JUMPstart RNA motif

L

* Luteovirus cap-independent translation element (BTE)

M

* Magnesium responsive RNA element * Mason-Pfizer monkey virus packaging signal * Mnt IRES *

MraW RNA motif The ''mraW'' RNA motif is a conserved, structured RNA found in certain bacteria. Specifically, it is predicted in many, though not all, species of actinobacteria, and especially within the genus ''Mycobacterium''. Structurally, the motif co ...

N

* N-myc IRES * Nanos 3′ UTR translation control element

P

* P27 cis-regulatory element *

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 ...

* Potato virus X cis-acting regulatory element *

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 environm ...

* Poxvirus AX element late mRNA cis-regulatory element * Prion pseudoknot * Pseudomonas rnk leader * Pseudomonas rpsL leader * PyrR binding site

R

* R2 RNA element * RbcL 5′ UTR RNA stabilising element * Red clover necrotic mosaic virus translation enhancer elements * Regulatory region of repZ gene * Retrovirus direct repeat 1 (dr1) * Ribosomal protein L10 leader * Ribosomal protein L13 leader * Ribosomal protein L19 leader * Ribosomal protein L20 leader * Ribosomal protein L21 leader * Ribosomal S15 leader * 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 ...

Rne-II RNA motif The ''rne''-II RNA motif is a conserved RNA structure identified using bioinformatics. It is detected only in species classified within the family Pseudomonadaceae, a group of gammaproteobacteria. ''rne''-II RNAs are consistently located in ...

* Rotavirus cis-acting replication element (CRE) * Rous sarcoma virus (RSV) primer binding site (PBS) * RtT RNA * Rubella virus 3′ cis-acting element

S

* S-element * SerC leader * Simian virus 40 late polyadenylation signal (SVLPA) * SpeF leader * Spi-1 (PU.1) 5′ UTR regulatory element * Sxy 5′ UTR element

T

* T-box leader * Togavirus 5′ plus strand cis-regulatory element * Tombusvirus 3′ UTR region IV * Tombusvirus 5′ UTR * Tombusvirus internal replication element (IRE) * Tobamovirus IRES *

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 pl ...

* 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 of the viral genome that is required for minus strand RNA synthesis Transcription is the process of copying a segment of DNA into RNA. The seg ...

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) * UnaL2 LINE 3′ element

V

* Vimentin 3′ UTR protein-binding region * Voltage-gated potassium-channel Kv1.4 IRES

W

* Wingless localisation element 3 (WLE3)

Y

* YbhL leader * YdaO/yuaA leader *

YkkC-yxkD leader The ykkC/yxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in ''Bacillus subtilis'' and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that i ...

* YybP-ykoY leader

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H

I

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M

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Y

See also