List
edit- 6A RNA motif
- Acido-1 RNA motif
- Acido-Lenti-1 RNA motif
- Actinomyces-1 RNA motif
- AlgC RNA motif
- Anti-hemB RNA motif
- ARRPOF RNA motif
- Asd RNA motif
- AspS RNA motif
- AtpB RNA motif
- ATPC RNA motif
- Bacillaceae-1 RNA motif
- Bacilli-1 RNA motif
- Bacillus-plasmid RNA motif
- Bacteroidales-1 RNA motif
- Bacteroidales-2 RNA motif
- Bacteroides-1 RNA motif
- Betaproteobacteria-1 RNA motif
- Burkholderiales-2 RNA motif
- BZIP intron RNA motif
- CaiA RNA motif
- Che1 RNA motif
- Chlorobi-1 RNA motif
- Chloroflexi-1 RNA motif
- Chloroflexus-1 RNA motif
- ChrB RNA motif
- Clostridiales-1 RNA motif
- Clostridiales-2 RNA motif
- Clostridiales-3 RNA motif
- Clostridium-PBP RNA motif
- COG2827 RNA motif
- COG2908 RNA motif
- COG3610-DE RNA motif
- COG3860 RNA motif
- COG3943 RNA motif
- Cold-seep-1 RNA motif
- Collinsella-1 RNA motif
- Corio-PBP RNA motif
- Cow-rumen RNA motif
- Cupriavidus-1 RNA motif
- Cyano-2 RNA motif
- CyVA-1 RNA motif
- D12-methyl RNA motif
- DABA-DC-AT RNA motif
- DfrA-dnaX RNA motif
- Dictyoglomi-1 RNA motif
- DinG RNA motif
- Drum RNA motif
- DUF805 RNA motif
- DUF1646 RNA motif
- DUF1874 RNA motif
- DUF2693 RNA motif
- DUF2693-FD RNA motif
- DUF2800 RNA motif
- DUF3085 RNA motif
- DUF3268 RNA motif
- DUF3577 RNA motif
- EFASI RNA motif
- EGFOA RNA motif
- EmrB-Lactobacillus RNA motif
- EngA RNA motif
- Enterococcus-1 RNA motif
- Fibro-purF RNA motif
- Fibrobacter-1 RNA motif
- Flavo-1 RNA motif
- Flavobacterium-1 RNA motif
- FolE RNA motif
- FolP RNA motif
- Freshwater-1 RNA motif
- Freshwater-2 RNA motif
- FTHFS RNA motif
- FtsZ-DE RNA motif
- FuFi-1 RNA motif
- Fusobacteriales-1 RNA motif
- GA-cis RNA motif
- Gamma-150 RNA motif
- GEBRO RNA motif
- GltS RNA motif
- GntR-DTE RNA motif
- GOLLD RNA motif
- GP20 RNA motif
- Gut-1 RNA motif
- Gut-2 RNA motif
- HEARO RNA motif
- HOLDH RNA motif
- HTH-XRE RNA motif
- Hya RNA motif
- IlvB-OMG RNA motif
- IlvH RNA motif
- IMES-1 RNA motif
- IMES-2 RNA motif
- IMES-3 RNA motif
- IMES-4 RNA motif
- IMES-5 RNA motif
- IMPDH RNA motif
- Int-alpA RNA motif
- Ivy-DE RNA motif
- KDPG-aldolase RNA motif
- Lactis-plasmid RNA motif
- Lacto-2 RNA motif
- Lacto-3 RNA motif
- Lacto-phage-1 RNA motif
- Lacto-usp RNA motif
- LdcC RNA motif
- LeuA-Halobacteria RNA motif
- LOOT RNA motif
- M23 RNA motif
- Mahella-1 RNA motif
- McrA RNA motif
- MDR-NUDIX RNA motif
- Methylobacterium-1 RNA motif
- Methylophilales-1 RNA motif
- Methylosinus-1 RNA motif
- MISL RNA motif
- Mu-gpT-DE RNA motif
- NadA RNA motif
- NarK RNA motif
- NhaA-I RNA motif
- NhaA-II RNA motif
- NLPC-P60 RNA motif
- NMT1 RNA motif
- NqrA-Marinomonas RNA motif
- NrdJ RNA motif
- Ocean-V RNA motif
- Ocean-VII RNA motif
- OsmY RNA motif
- OTKONC RNA motif
- PAGEV RNA motif
- Parabacteroides-1 RNA motif
- Pedo-repair RNA motif
- PemK RNA motif
- Peptidase-S11 RNA motif
- PGK RNA motif
- Polynucleobacter-1 RNA motif
- Poplar-1 RNA motif
- PorB RNA motif
- Poribacteria-1 RNA motif
- Prevotella-2 RNA motif
- Proteo-phage-1 RNA motif
- ProV RNA motif
- Pseudomon-1 RNA motif
- Pseudomonadales-1 RNA motif
- Pyrobac-1 RNA motif
- QueA RNA motif
- RaiA RNA motif
- RaiA-hairpin RNA motif
- Rhizobiales-2 RNA motif
- Rhodo-rpoB RNA motif
- RMF RNA motif
- ROOL RNA motif
- Rothia-sucC RNA motif
- RpfG RNA motif
- Saliva-tongue-1 RNA motif
- Salivarius-1 RNA motif
- SbcC RNA motif
- Skipping-rope RNA motif
- SsnA RNA motif
- SsNA-helicase RNA motif
- Staphylococcus-1 RNA motif
- STAXI RNA motif
- Streptomyces-atpC RNA motif
- Streptomyces-metKH RNA motif
- Sul1 RNA motif
- TD-2 RNA motif
- TerC RNA motif
- Termite-leu RNA motif
- Thermales-rpoB RNA motif
- Throat-1 RNA motif
- TraJ-II RNA motif
- Transposase-1 RNA motif
- Transposase-2 RNA motif
- TwoAYGGAY RNA motif
- Uup RNA motif
- UxuA RNA motif
- Whalefall-1 RNA motif
- XerDC RNA motif
- Zeta-pan RNA motif
Sample data
editName: pemK RNA motif [1]
Diagram: 
Symbol: pemK
Found in: organisms within the phylum Bacillota
Comments: pemK motif RNAs likely function as cis-regulatory elements, in view of their positions upstream of protein-coding genes. Indeed, the RNAs are upstream of multiple genes that encode non-homologous proteins. If all examples of the RNA were upstream of homologous genes, there is the possibility that the RNAs were conserved in that position simply by inheritance. The non-homology of the genes downstream of pemK RNAs makes this scenario less likely.
cis-regulatory RNAs such as riboswitches in Bacillota are often followed by Rho-independent transcription terminators, and they use these transcription terminators as part of a regulatory mechanism. Specifically, depending on the regulatory state of the cis-regulatory RNA, formation of the transcription terminator is either prevented or allowed via alternate secondary structures. pemK RNAs, however, are very rarely followed by a transcription terminator. This fact could raise the possibility that these RNAs are not cis-regulatory, but rather function as small RNAs. However, there are some cis-regulatory RNAs in Bacillota that do not use Rho-independent transcription terminations as a regulatory mechanism, e.g., the yjdF RNA motif.
References
edit- ^ Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.