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STAXI RNA Motif
The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif (STAXI RNA motif) is a conserved RNA-like structure identified using bioinformatics. STAXI RNAs are located near to genes encoding proteins that interact with DNA ( Ssbp, topoisomerase, XerDC integrase) or are associated with such proteins ( antirestriction proteins, which inhibit restriction enzymes). This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during DNA replication or DNA repair. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple pseudoknot structure that is repeated two or more times (see diagram). A number of other RNAs were identified in the same study, including: * Bacteroidales-1 RNA motif * Chlorobi-1 RNA motif * JUMPstart RNA motif * Lactis-plasmid RNA motif *Ocea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enterobacteriales
Enterobacterales is an order of Gram-negative bacteria, Gram-negative, non-spore forming, Facultative anaerobic organism, facultatively anaerobic, rod-shaped bacteria with the class Gammaproteobacteria. The type genus of this order is ''Enterobacter.'' The name Enterobacterales is derived from the Latin term ''Enterobacter'', referring the type genus of the order and the suffix "-ales", an ending used to denote an order. Together, Enterobacterales refers to an order whose nomenclatural type is the genus ''Enterobacter''. Historical Identification and Systematics Enterobacterales was proposed in 2005 under the name "Enterobacteriales". However, the name "Enterobacteriales" was not validated according to the rules of the ''International Code of Nomenclature of Prokaryotes,'' thus it lacked standing in nomenclature, so the name was written in parentheses. "Enterobacteriales" was a monotypic order, containing only the family ''Enterobacteriaceae'', and shared its type genus ''Esch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudoknot
__NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. Prediction and identification The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or "overlapping" nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursive scoring system to identify paired stems and consequently, most cannot detect non-nested base pairs. The newer method of stochastic context-free grammars su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TwoAYGGAY RNA Motif
The TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence (Y refers to either a C or U nucleotide) found in the motif's two terminal loops (see diagram). The RNAs are found in sequences derived from DNA extracted from uncultivated bacteria present in the human gut, as well as some bacteria in the classes Clostridia and Gammaproteobacteria Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically imp .... References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PsaA RNA Motif
The ''psaA'' RNA motif describes a class of RNAs with a common secondary structure. ''psaA'' RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operons formed of ''psaA'' and ''psaB'' genes. For this reason, it was hypothesized that ''psaA'' RNAs function as cis-regulatory elements of these genes. The ''psaAB'' genes encode proteins that form subunits in the photosystem I structure used for photosynthesis. ''psaA'' RNAs have been detected only in cyanobacteria, which is consistent with their association with photosynthesis. ''psaAB'' genes are known to be regulated in species of cyanobacteria that do not use ''psaA'' RNAs, and this system of regulation involves transcription factor proteins. In this system, the expression of ''psaAB'' genes is increased when cells are growing with limited amount of light, presumably to maximize their energy from the limited resource. On the other hand, the genes' expression is reduced when l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PotC RNA Motif
The ''potC'' RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria. Thus, this RNA is present in environmental samples, but not yet found in any cultivated organism. ''potC'' RNAs are located in the presumed 5' untranslated regions of genes predicted to encode either membrane transport proteins or peroxiredoxins. Therefore, it was hypothesized that ''potC'' RNAs are cis-regulatory elements, but their detailed function is unknown. A number of other RNAs were identified in the same study, including: *Lacto-usp RNA motif *mraW RNA motif *Ocean-V RNA motif *psaA RNA motif *Pseudomon-Rho RNA motif *rne-II RNA motif *STAXI RNA motif *TwoAYGGAY RNA motif *Whalefall-1 RNA motif *wcaG RNA motif *ykkC-yxkD leader The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ocean-V RNA Motif
The Ocean-V RNA motif is a conserved RNA structure discovered using bioinformatics. Only a few Ocean-V RNA sequences have been detected, all in sequences derived from DNA that was extracted from uncultivated bacteria found in ocean The ocean (also the sea or the world ocean) is the body of salt water that covers approximately 70.8% of the surface of Earth and contains 97% of Earth's water. An ocean can also refer to any of the large bodies of water into which the wo ... water. As of 2010, no Ocean-V RNA has been detected in any known, cultivated organism. References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lactis-plasmid RNA Motif
The ''lactis''-plasmid RNA motif is a conserved RNA structure identified by bioinformatics. The RNAs are restricted to lactic acid bacteria, and are especially common in '' Lactococcus lactis''. They typically lie near to ''repB'' genes, and are almost found in plasmids. This data suggested that ''lactis''-plasmid RNAs participate in the control of plasmid abundance. However, many of the plasmids that carry ''lactis''-plasmid RNAs also carry ctRNA In molecular biology ctRNA (counter-transcribed RNA) is a plasmid encoded noncoding RNA that binds to the mRNA of repB and causes translation (genetics), translational inhibition. ctRNA is encoded by plasmids and functions in rolling circle repl ...-pND324 RNAs, which are involved in plasmid copy count regulation. Therefore ''lactis''-plasmid RNAs might have a different function. See also * R1162-like plasmid antisense RNA References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JUMPstart RNA Motif
The JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements. The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis. The JUMPstart element has been shown to function as an RNA, and is present in the 5' untranslated regions of the genes it regulates. JUMPstart sequences include an ops element, which is an acronym for "operon-polarity suppressor" and has the nucleotide consensus GGCGGUAG. The ops element acts in concert with the RfaH protein to improve transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ... of genes downstream of the ops element, especially genes far away within long operons. References External links * Cis-regulatory RNA el ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chlorobi-1 RNA Motif
The Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobiota (formerly Chlorobi), a phylum of bacteria. The motif consists of two stem-loops that are followed by an apparent rho-independent transcription terminator. The motif is presumed to function as an independently transcribed non-coding RNA. A number of other RNAs were identified in the same study, including: * Bacteroidales-1 RNA motif * CrcB RNA Motif * Gut-1 RNA motif *JUMPstart RNA motif *Lactis-plasmid RNA motif The ''lactis''-plasmid RNA motif is a conserved RNA structure identified by bioinformatics. The RNAs are restricted to lactic acid bacteria, and are especially common in '' Lactococcus lactis''. They typically lie near to ''repB'' genes, and ... * Lacto-usp RNA motif * MraW RNA motif * Ocean-V RNA motif * PsaA RNA motif * Pseudomon-Rho RNA motif * Rne-II RNA motif References External links * Non-coding RNA {{m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteroidales-1 RNA Motif
The Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order (biology) Bacteroidales. Its presumed length is marked by a promoter on one end that conforms to an alternate consensus sequence that is common in the phylum Bacteroidota, and its 3′ end is indicated by predicted transcription terminators. It is often located downstream of a gene that encodes the L20 ribosomal subunit, although it is unclear whether there is a functional reason underlying this apparent association. Bacteroidales-1 RNA motif has been reported as a 6S RNA homologue by a report of ''Bacteroides thetaiotaomicron'' transcriptome map. The existence of small product RNAs (pRNAs) that rescue sequestered RNA polymerases In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG, in which the N could be either uracil, adenine, cytosine, or guanine, and the R is either guanine or adenine. These three sequences form stable and conserved tetraloops that play an important role in structural stability and biological function of 16S rRNA. * GNRA ** The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3' to the helix. Tetraloops with the sequence UMAC have essentially the same backbone fold as the GNRA tetraloop, but may be less likely to form tetraloop-receptor interactions. They may therefore be a better choice for closing stems when designing artificial RNAs. ** The presence of the GNRA tetraloop provides an exceptional ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
