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RNA Motif
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. Descriptions of RNAs motifs RNA motifs can be described in two main forms: a multiple sequence alignment or an explicit search pattern. An alignment is usually augmented with a consensus secondary structure, i.e. the structure that is common to all or most RNAs. The sequences in the alignment then implicitly define a pattern of conservation that can, for example, be used to find additional examples of the RNA. This search strategy is implemented by, among others, the Infernal software package. The Rfam database is a collection of multiple sequence alignments that define a large subset of reliably known RNA motifs an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue''. Overview When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein. Nevertheless, motifs need not be associated with a distinctive secondary structure. " Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). Outside of gene exons, there exist regulatory sequence motifs and motifs within the " junk", such as satellite DNA. Some of these are believed to affect the shape of nucleic acids (see for example RN ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rfam
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information. Rfam researchers also contribute to Wikipedia's RNA WikiProject. Uses The Rfam database can be used for a variety of functions. For each ncRNA fa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of 'junk' DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions have been annotated. The International Human Genome Project reported the sequence of the genome for ''Homo sapiens'' in 200The Human Genome Project although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequenci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
T-box
T-box refers to a group of transcription factors involved in embryonic limb and heart development. Every T-box protein has a relatively large DNA-binding domain, generally comprising about a third of the entire protein that is both necessary and sufficient for sequence-specific DNA binding. All members of the T-box gene family bind to the "T-box", a DNA consensus sequence of TCACACCT. Members T-boxes are especially important to the development of embryos, found in zebrafish oocyte by Bruce et al 2003 and ''Xenopus laevis'' oocyte by Xanthos et al 2001. They are also expressed in later stages, including adult mouse and rabbit studied by Szabo et al 2000. Mutations in the first one found caused short tails in mice, and thus the protein encoded was named brachyury, Greek for "short-tail". In mice this gene is named ''Tbxt'', and in humans it is named ''TBXT''. Brachyury has been found in all bilaterian animals that have been screened, and is also present in the cnidaria. The mou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Riboswitch
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules. The original definition of the term "riboswitch" specified that they directly sense small-molecule metabolite concentrations. Although this definition remains in common use, some biologists have used a broader definition that includes other cis-regulatory RNAs. However, this article will discuss only metabolite-binding riboswitches. Most known riboswitches occur in bac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Adenosylcobalamin
Adenosylcobalamin (AdoCbl), also known as coenzyme B12, cobamamide, and dibencozide, is, along with methylcobalamin (MeCbl), one of the biologically active forms of vitamin B12. Adenosylcobalamin participates as a cofactor in radical-mediated 1,2-carbon skeleton rearrangements. These processes require the formation of the deoxyadenosyl radical through homolytic dissociation of the carbon-cobalt bond. This bond is exceptionally weak, with a bond dissociation energy of 31 kcal/mol, which is further lowered in the chemical environment of an enzyme active site. An enzyme that uses adenosylcobalamin as a cofactor is methylmalonyl-CoA mutase (MCM). Further experimentation has also determined adenosylcobalamin's role in regulating expression of some bacterial genes. By binding to CarH, AdoCbl can modulate carotenoid genes, which confer warm colors onto various plants. Carotenoid transcription is activated by sunlight, due to the response from AdoCbl. There are other photoreceptors acros ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cobalamin Riboswitch
Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' UTR, 5' untranslated regions of vitamin B12, vitamin B12 (Cobalamin) related genes in bacteria. Vitamin B12, Cobalamin (vitamin B12, coenzyme B12 ) riboswitches are structured RNA elements that regulate adjacent genes related to cobalamin metabolism in response to cobalamin binding. Riboswitches are RNA-based genetic regulatory elements present in the Five prime untranslated region, 5’ untranslated region (5'UTR) of primarily bacterial RNA. These switches bind to a ligand, which is generally a metabolite, with high affinity and specificity. Ligand binding mediates allosteric rearrangement of mRNA structure, and this results in modulation of gene expression or Translation (genetics), translation of mRNA to yield a protein. The cobalamin riboswitch, along with most other riboswitches, are Cis-regulatory element, cis-regulatory. This means they regulate genes involved in the same metabolic pathways a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
6C RNA
6C RNA is a class of non-coding RNA present in actinomycetes. 6C RNA was originally discovered as a conserved RNA structure having two stem-loops each containing six or more cytosine (C) residues. Later work revealed that 6C RNAs in ''Streptomyces coelicolor'' and ''Streptomyces avermitilis'' have predicted intrinsic termination, rho-independent transcription terminators, and microarray and Reverse transcription polymerase chain reaction, reverse-transcriptase PCR experiments indicate that the ''S. coelicolor'' version is transcribed as RNA. Transcription of the ''S. coelicolor'' RNA increases during sporulation, and three transcripts were detected that overlap the 6C motif, but have different apparent start and stop sites. Additional work established that 6C RNAs regulate a variety of protein-coding genes by acting as ''trans''-acting antisense RNAs. Among the genes regulated by 6C RNAs, many are involved in DNA replication and the export of proteins. Bacteria in other studi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribozyme
Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalysis, catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems. The most common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation of RNA and DNA and peptide bond formation. For example, the smallest ribozyme known (GUGGC-3') can aminoacylate a GCCU-3' sequence in the presence of PheAMP. Within the ribosome, ribozymes function as part of the large subunit ribosomal RNA to link amino acids during Translation (biology), protein synthesis. They also participate in a variety of RNA processing reactions, including RNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Twister Ribozyme
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. Discovery In contrast to ''in vitro'' selection methods, which have aided in identifying several classes of catalytic RNA motifs, the twister ribozyme was discovered by a bioinformatics approach as a conserved RNA structure of unknown function. The hypothesis that it functions as a self-cleaving ribozyme was suggested by the similarity between genes nearby to twister ribozymes and genes nearby to hammerhead ribozymes, Indeed, the genes located nearby to these two self-cleaving ribozyme classes overlap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
