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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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
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
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