User:A. B./List RNA motifs

List

 * 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
Name: pemK RNA motif

Diagram:

Symbol: pemK

Rfam: RF02913

RNA type: Cis-reg

SO: SO:0005836

PDB structures: PDBe

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.