# 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.
* 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