PotC RNA motif
Encyclopedia
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 gene
s predicted to encode either membrane transport proteins or peroxiredoxin
s. Therefore, it was hypothesized that potC RNAs are cis-regulatory element
s, but their detailed function is unknown.
A number of other RNAs were identified in the same study, including:
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure discovered using bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. The RNA is detected only in genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
sequences derived from DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
that was extracted from uncultivated marine
Marine (ocean)
Marine is an umbrella term. As an adjective it is usually applicable to things relating to the sea or ocean, such as marine biology, marine ecology and marine geology...
bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
. Thus, this RNA is present in environmental samples
RNAs present in environmental samples
A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area...
, but not yet found in any cultivated organism.
potC RNAs are located in the presumed 5' untranslated regions of gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s predicted to encode either membrane transport proteins or peroxiredoxin
Peroxiredoxin
Peroxiredoxins are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels and thereby mediate signal transduction in mammalian cells.- Classification :...
s. Therefore, it was hypothesized that potC RNAs are cis-regulatory element
Cis-regulatory element
A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...
s, but their detailed function is unknown.
A number of other RNAs were identified in the same study, including:
- Lacto-usp RNA motifLacto-usp RNA motifThe Lacto-usp RNA motif is a conserved RNA structure identified in bacteria by bioinformatics. Lacto-usp RNAs are found exclusively in lactic acid bacteria, and exclusively in the possible 5' untranslated regions of operons that contain a hypothetical gene and a usp gene. The usp gene encodes...
- MraW RNA motifMraW RNA motifThe mraW RNA motif is a conserved, structured RNA found in certain bacteria. Specifically, it is predicted in many, though not all, species of actinobacteria, and especially within the genus Mycobacterium. Structurally, the motif consists of a hairpin with a highly conserved terminal loop sequence...
- Ocean-V RNA motifOcean-V RNA motifThe 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 water. As of 2010, no Ocean-V RNA has been detected in any known,...
- PsaA RNA motifPsaA RNA motifThe 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...
- Pseudomon-Rho RNA motifPseudomon-Rho RNA motifThe Pseudomon-Rho RNA motif refers to a conserved RNA structure that was discovered using bioinformatics. The RNAs that conform to this motif are found in species within the genus Pseudomonas, as well as the related Azotobacter vinelandii...
- Rne-II RNA motifRne-II RNA motifThe rne-II RNA motif is a conserved RNA structure identified using bioinformatics. It is detected only in species classified within the family Pseudomonadaceae, a group of gammaproteobacteria. rne-II RNAs are consistently located in the presumed 5' untranslated regions of genes that encode...
- STAXI RNA motifSTAXI RNA motifThe Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif is a conserved RNA-like structure identified using bioinformatics. STAXI RNAs are located near to genes encoding proteins that interact with DNA or are associated with such proteins...
- TwoAYGGAY RNA motifTwoAYGGAY RNA motifThe TwoAYGGAY RNA motif is a conserved RNA structure identified by bioinformatics. Its name refers to the conserved AYGGAY nucleotide sequence found in the motif's two terminal loops...
- Whalefall-1 RNA motifWhalefall-1 RNA motifThe Whalefall-1 RNA motif refers to a conserved RNA structure that was discovered using bioinformatics. Structurally, the motif consists of two stem-loops , the second of which is often terminated by a CUUG tetraloop, which is an energetically favorable RNA sequence...
- WcaG RNA motifWcaG RNA motifThe wcaG RNA motif is an RNA structure conserved in some bacteria that was detected by bioinformatics. wcaG RNAs are found in certain phages that infect cyanobacteria. Most known wcaG RNAs were found in sequences of DNA extracted from uncultivated marine bacteria...
- YkkC-yxkD leaderYkkC-yxkD leaderThe 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 although it has been suggested that it may function to switch on efflux pumps and detoxification systems in...