Chlorobi-1 RNA motif
Encyclopedia
The Chlorobi-1 RNA motif is a conserved RNA
secondary structure identified by bioinformatics
. It is predicted to be used only by Chlorobi, a phylum
of bacteria
. The motif consists of two stem-loop
s 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:
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
secondary structure identified by 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...
. It is predicted to be used only by Chlorobi, a phylum
Phylum
In biology, a phylum The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." is a taxonomic rank below kingdom and above class. "Phylum" is equivalent to the botanical term division....
of 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...
. The motif consists of two stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
s that are followed by an apparent rho-independent transcription terminator
Intrinsic termination
Intrinsic termination is a mechanism in prokaryotes that causes mRNA transcription to be stopped. In this mechanism, the mRNA contains a sequence that can base pair with itself to form a stem-loop structure 7-20 base pairs in length that is also rich in cytosine-guanine base pairs...
. The motif is presumed to function as an independently transcribed non-coding RNA
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
.
A number of other RNAs were identified in the same study, including:
- Bacteroidales-1 RNA motifBacteroidales-1 RNA motifThe Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order Bacteroidales...
- CrcB RNA MotifCrcB RNA MotifThe crcB RNA motif is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. The motif exhibits the rigid or almost perfect conservation of the nucleotide identity at several positions across two domains of life...
- Gut-1 RNA motifGut-1 RNA motifThe Gut-1 RNA motif is a conserved RNA structure identified by bioinformatics. These RNAs are present in environmental sequences, and as of 2010 are not known to be present in any species that has been grown under laboratory conditions. Gut-1 RNA is exclusively found in DNA from uncultivated...
- JUMPstart RNA motifJUMPstart RNA motifThe 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...
- Lactis-plasmid RNA motifLactis-plasmid RNA motifThe 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...
- 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...