List of cis-regulatory RNA elements

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.

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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
 * Alfalfa mosaic virus RNA 1 5′ UTR stem-loop
 * 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
 * AtoC RNA motif
 * ATPC RNA motif
 * AU-rich element

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

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)
 * 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

N

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

P

 * P27 cis-regulatory element
 * Potassium channel RNA editing signal
 * Potato virus X cis-acting regulatory element
 * PotC RNA motif
 * Poxvirus AX element late mRNA cis-regulatory element
 * Prion pseudoknot
 * Pseudomonas rnk leader
 * Pseudomonas rpsL leader
 * PyrG 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
 * Rne-II RNA motif
 * 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
 * TrkB IRES
 * Turnip crinkle virus (TCV) core promoter hairpin (Pr)
 * Turnip crinkle virus (TCV) repressor of minus strand synthesis H5

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
 * YybP-ykoY leader