Ocean-VII RNA motif: Difference between revisions
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| ⚫ | The '''Ocean-VII RNA motif''' is a conserved [[RNA]] structure that was [[Bioinformatics discovery of non-coding RNAs|discovered by bioinformatics]].<ref name="Weinberg2017b">{{cite journal |vauthors=Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR |title=Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions |journal=Nucleic Acids Res. |volume=45 |issue=18 |pages=10811–10823 |date=October 2017 |pmid=28977401 |pmc=5737381 |doi=10.1093/nar/gkx699 |
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| ⚫ | Ocean-VII motifs are found in [[metagenomic]] sequences isolated from various [[Ocean|marine]] environments, and are not yet (as of 2018) known in any classified organism. This environmental context is similar to other marine RNAs that were found previously by predominantly bioinformatic<ref name="Weinberg2009">{{cite journal |vauthors=Weinberg Z, Perreault J, Meyer MM, Breaker RR |title=Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis |journal=Nature |volume=462 |issue=7273 |pages= |
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| Name = Ocean-VII |
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| image = RF03092.svg |
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| caption = Consensus [[secondary structure]] and [[sequence conservation]] of Ocean-VII RNA |
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| Symbol = Ocean-VII |
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| Rfam = RF03092 |
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| RNA_type = [[Gene]]; [[Small RNA|sRNA]] |
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| SO = {{SO|0001263}} |
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| ⚫ | The '''Ocean-VII RNA motif''' is a conserved [[RNA]] structure that was [[Bioinformatics discovery of non-coding RNAs|discovered by bioinformatics]].<ref name="Weinberg2017b">{{cite journal |vauthors=Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR |title=Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions |journal=Nucleic Acids Res. |volume=45 |issue=18 |pages=10811–10823 |date=October 2017 |pmid=28977401 |pmc=5737381 |doi=10.1093/nar/gkx699 }}</ref> |
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| ⚫ | Ocean-VII motifs are found in [[metagenomic]] sequences isolated from various [[Ocean|marine]] environments, and are not yet (as of 2018) known in any classified organism. This environmental context is similar to other marine RNAs that were found previously by predominantly bioinformatic<ref name="Weinberg2009">{{cite journal |vauthors=Weinberg Z, Perreault J, Meyer MM, Breaker RR |title=Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis |journal=Nature |volume=462 |issue=7273 |pages=656–659 |date=December 2009 |pmid=19956260 |doi=10.1038/nature08586 |pmc=4140389}}</ref> or experimental<ref name="Shi2009">{{cite journal |vauthors=Shi Y, Tyson GW, DeLong EF |title=Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column |journal=Nature |volume=459 |issue=7244 |pages=266–269 |date=May 2009 |pmid=19444216 |doi=10.1038/nature08055 |s2cid=4340144 }}</ref> methods. |
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The [[contig]]s in which Ocean-VII RNAs are quite small. Consequently, it is ambiguous whether Ocean-VII RNAs function as [[cis-regulatory element]]s or whether they operate in ''trans'' as [[small RNA]]s. |
The [[contig]]s in which Ocean-VII RNAs are quite small. Consequently, it is ambiguous whether Ocean-VII RNAs function as [[cis-regulatory element]]s or whether they operate in ''trans'' as [[small RNA]]s. |
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==References== |
==References== |
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{{reflist}} |
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<references/> |
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[[Category:Non-coding RNA]] |
[[Category:Non-coding RNA]] |
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Latest revision as of 09:56, 27 January 2023
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| Ocean-VII | |
|---|---|
 Consensus secondary structure and sequence conservation of Ocean-VII RNA | |
| Identifiers | |
| Symbol | Ocean-VII |
| Rfam | RF03092 |
| Other data | |
| RNA type | Gene; sRNA |
| SO | SO:0001263 |
| PDB structures | PDBe |
The Ocean-VII RNA motif is a conserved RNA structure that was discovered by bioinformatics.[1] Ocean-VII motifs are found in metagenomic sequences isolated from various marine environments, and are not yet (as of 2018) known in any classified organism. This environmental context is similar to other marine RNAs that were found previously by predominantly bioinformatic[2] or experimental[3] methods.
The contigs in which Ocean-VII RNAs are quite small. Consequently, it is ambiguous whether Ocean-VII RNAs function as cis-regulatory elements or whether they operate in trans as small RNAs.
References[edit]
- ^ Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.
- ^ Weinberg Z, Perreault J, Meyer MM, Breaker RR (December 2009). "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656–659. doi:10.1038/nature08586. PMC 4140389. PMID 19956260.
- ^ Shi Y, Tyson GW, DeLong EF (May 2009). "Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column". Nature. 459 (7244): 266–269. doi:10.1038/nature08055. PMID 19444216. S2CID 4340144.