The YdaO/YuaA leader is a conserved RNA structure found upstream of the ydaO and yuaA genes in Bacillus subtilis and related genes in other bacteria. Its secondary structure and gene associations were predicted by bioinformatics.
The ykkC/yxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that it may function to switch on efflux pumps and detoxification systems in response to harmful environmental molecules. The Thermoanaerobacter tengcongensis sequence AE013027 overlaps with that of purine riboswitch suggesting that the two riboswitches may work in conjunction to regulate the upstream gene which codes for TTE0584 (Q8RC62), a member of the permease family.
The c4 antisense RNA is a non-coding RNA used by certain phages that infect bacteria. It was initially identified in the P1 and P7 phages of E. coli. The identification of c4 antisense RNAs solved the mystery of the mechanism for regulation of the ant gene, which is an anti-repressor.
The Methylobacterium-1 RNA motif is a conserved RNA structure discovered using bioinformatics. Almost all known examples of this RNA are found in DNA extracted from marine bacteria. However, one instance is predicted in Methylobacterium sp. 4-46, a species of alphaproteobacteria. The motif is presumed to function as a non-coding RNA.
The twister ribozyme is a catalytic RNA structure capable of self-cleavage. The nucleolytic activity of this ribozyme has been demonstrated both in vivo and in vitro and has one of the fastest catalytic rates of naturally occurring ribozymes with similar function. The twister ribozyme is considered to be a member of the small self-cleaving ribozyme family which includes the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), and glmS ribozymes.
The twister sister ribozyme (TS) is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. The twister sister ribozyme was discovered by a bioinformatics strategy as an RNA Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH.
The pistol ribozyme is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. The pistol ribozyme was discovered through comparative genomic analysis. Subsequent biochemical analysis determined further biochemical characteristics of the ribozyme. This understanding was further advanced by an atomic-resolution crystal structure of a pistol ribozyme
Background: The hatchet ribozyme is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. Hatchet ribozymes were discovered by a bioinformatics strategy as RNAs Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH.
Non-coding RNAs have been discovered using both experimental and bioinformatic approaches. Bioinformatic approaches can be divided into three main categories. The first involves homology search, although these techniques are by definition unable to find new classes of ncRNAs. The second category includes algorithms designed to discover specific types of ncRNAs that have similar properties. Finally, some discovery methods are based on very general properties of RNA, and are thus able to discover entirely new kinds of ncRNAs.
The Actinomyces-1 RNA motif is a conserved RNA structure that was discovered by bioinformatics. Actinomyces-1 motifs are found in the genus Actinomyces, in the phylum Actinomycetota. Actinomyces-1 RNAs likely function in trans as sRNAs. In terms of their secondary structure, Actinomyces-1 RNAs consist of a multistem junction with many conserved GA dinucleotides.
The COG2827 RNA motif is a conserved RNA structure that was discovered by bioinformatics. COG2827 motifs are found in Clostridiales.
The drum RNA motif is a conserved RNA structure that was discovered by bioinformatics. Drum motifs are found in Bacillota, Bacteroidota, Pseudomonadota, and Spirochaetota, and exhibit multiple highly conserved nucleotide positions, despite their widespread distribution.
The DUF3268 RNA motif is a conserved RNA structure that was discovered by bioinformatics. DUF3268 motifs are found in Bacillota and Clostridia.
The engA RNA motif is a conserved RNA structure that was discovered by bioinformatics. engA motifs are found in bacteria within the genus Prevotella.
The folE RNA motif, now known as the THF-II riboswitch, is a conserved RNA structure that was discovered by bioinformatics. folE motifs are found in Alphaproteobacteria.
The FuFi-1 RNA motif is a conserved RNA structure that was discovered by bioinformatics. Such RNA "motifs" are often the first step to elucidating the biological function of a novel RNA. FuFi-1 motif RNAs are found in Bacillota AND Fusobacteriota.
The ivy-DE RNA motif is a conserved RNA structure that was discovered by bioinformatics. ivy-DE motifs are found in the genus Pseudomonas.
The uup RNA motif is a conserved RNA structure that was discovered by bioinformatics. uup motif RNAs are found in Bacillota and Gammaproteobacteria.
The Zeta-pan RNA motif is a conserved RNA structure that was discovered by bioinformatics. Zeta-pan motif RNAs are found in Zetaproteobacteria.
An RNA motif is a description of a group of RNAs that have a related structure. RNA motifs consist of a pattern of features within the primary sequence and secondary structure of related RNAs. Thus, it extends the concept of a sequence motif to include RNA secondary structure. The term "RNA motif" can refer both to the pattern and to the RNA sequences that match it.
