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.
# 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 aspS RNA motif AtoC RNA motif atpB RNA motif ATPC RNA motif AU-rich element
B Bacteroid-trp RNA motif 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 Burkholderiales-2 RNA motif
C Chlorobi-RRM RNA motif chrB RNA motif Citrus tristeza virus replication signal CrcB RNA motif Ctgf/hcs24 CAESAR COG3860 RNA motif Cap-independent translation element
D DABA-DC-AT RNA motif DUF1874 RNA motif DUF3085 RNA motif DUF3577 RNA motif
E EngA RNA motif Enterobacteria greA leader Enterobacteria rnk leader Enteroviral 3′ UTR element Enterovirus 5′ cloverleaf cis-acting replication element Enterovirus cis-acting replication element
F Fibro-purF RNA motif FIE3 (ftz instability element 3′) element Flavivirus capsid hairpin cHP Flg-Rhizobiales RNA motif FlpD RNA motif folE RNA motif folP RNA motif Freshwater-2 RNA motif FTHFS RNA motif Fusobacteriales-1 RNA motif
G G-CSF factor stem-loop destabilising element Gammaproteobacteria rimP leader gltS RNA motif GP20 RNA motif
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) hya RNA motif
I IbpB thermometer ilvB-OMG RNA motif ilvH RNA motif Infectious bronchitis virus D-RNA ivy-DE RNA motif
J JUMPstart RNA motif
L L17DE RNA motif ldcC RNA motif LivK RNA motif Lnt RNA motif Luteovirus cap-independent translation element (BTE) lysM RNA motifs
M Magnesium responsive RNA element malK RNA motifs Mason-Pfizer monkey virus packaging signal Mnt IRES MraW RNA motif MsiK RNA motif
N N-myc IRES Nanos 3′ UTR translation control element narK RNA motif nhaA-II RNA motif NLPC-P60 RNA motif NuoG RNA motif
P P27 cis-regulatory element pemK RNA motif Peptidase-S11 RNA motif PGK RNA motif 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 PsbNH RNA motif Pseudomon-groES RNA motif 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) Rothia-sucC RNA motif 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 ssnA RNA motif Sxy 5′ UTR element
T T-box leader terC RNA motif Termite-leu RNA motif Thermales-rpoB RNA motif 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)
X xerDC RNA motif
Y YbhL leader YdaO/yuaA leader YkkC-yxkD leader YybP-ykoY leader
See also List of RNAs