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- Downstream-peptide_motif abstract "The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera Synechococcus and Prochlorococcus and one phage that infects such bacteria. It was also detected in marine samples of DNA from uncultivated bacteria, which are presumably other species of cyanobacteria.Downstream-peptide RNAs are found upstream of short open reading frames (ORFs) that are predicted to encode short peptides (usually between 17 and 100 amino acids). One of the ORFs is apparently down-regulated when cells are grown with an insufficient supply of nitrogen sources. Downstream-peptide RNAs overlap a predicted non-coding RNA called yfr6 that is over 200 nucleotides in length, but it was proposed that only the upstream region (corresponding to the Downstream-peptide motif) functions as an RNA structure. A distinct predicted non-coding RNA called yfr14 overlaps both yfr6 and Downstream-peptide RNAs. However, no experimental data has been published to resolve the question of which and how many of these RNAs are functional.The Downstream-peptide motif has a structural resemblance to a different candidate RNA structure called the glnA RNA motif. The most striking similarity is the nucleotide conservation within the P1 stem of both motifs, and this and other similarities was discussed previously.It was hypothesized that Downstream-peptide RNAs correspond to riboswitches, based on multiple lines of evidence. First, glnA RNAs are often located in the presumed 5' untranslated regions of multiple classes of genes involved in nitrogen metabolism. This, and other evidence, suggests that glnA RNAs are riboswitches, and their structural similarity to Downstream-peptide RNAs in turn suggests that Downstream-peptide RNAs are also riboswitches. Second, Downstream-peptides are consistently positioned in a place that is consistent with a cis-regulatory role in regulating the downstream ORFs, although the biological role of the ORFs is unknown. Third, the pseudoknot structure has a moderate complexity that is typical of riboswitches. Finally, the observation of regulation of a downstream ORF by nitrogen available also suggests a cis-regulatory role of the element. The subsequent determination that both Downstream-peptide RNAs and glnA RNAs selectively bind glutamine supports these hypotheses.".
- Downstream-peptide_motif thumbnail Downstream-peptide-RNA.svg?width=300.
- Downstream-peptide_motif wikiPageID "26609919".
- Downstream-peptide_motif wikiPageLength "4507".
- Downstream-peptide_motif wikiPageOutDegree "27".
- Downstream-peptide_motif wikiPageRevisionID "661009281".
- Downstream-peptide_motif wikiPageWikiLink Amino_acid.
- Downstream-peptide_motif wikiPageWikiLink Bacteria.
- Downstream-peptide_motif wikiPageWikiLink Bacteriophage.
- Downstream-peptide_motif wikiPageWikiLink Bioinformatics.
- Downstream-peptide_motif wikiPageWikiLink Category:Cis-regulatory_RNA_elements.
- Downstream-peptide_motif wikiPageWikiLink Category:Riboswitch.
- Downstream-peptide_motif wikiPageWikiLink Cis-Regulatory_element.
- Downstream-peptide_motif wikiPageWikiLink Cyanobacteria.
- Downstream-peptide_motif wikiPageWikiLink DNA.
- Downstream-peptide_motif wikiPageWikiLink Five_prime_untranslated_region.
- Downstream-peptide_motif wikiPageWikiLink Genus.
- Downstream-peptide_motif wikiPageWikiLink GlnA_RNA_motif.
- Downstream-peptide_motif wikiPageWikiLink Glutamine.
- Downstream-peptide_motif wikiPageWikiLink Marine_(ocean).
- Downstream-peptide_motif wikiPageWikiLink Nitrogen.
- Downstream-peptide_motif wikiPageWikiLink Nitrogen_cycle.
- Downstream-peptide_motif wikiPageWikiLink Non-coding_RNA.
- Downstream-peptide_motif wikiPageWikiLink Nucleotide.
- Downstream-peptide_motif wikiPageWikiLink Open_reading_frame.
- Downstream-peptide_motif wikiPageWikiLink Peptide.
- Downstream-peptide_motif wikiPageWikiLink Prochlorococcus.
- Downstream-peptide_motif wikiPageWikiLink RNA.
- Downstream-peptide_motif wikiPageWikiLink Riboswitch.
- Downstream-peptide_motif wikiPageWikiLink Synechococcus.
- Downstream-peptide_motif wikiPageWikiLinkText "Downstream-peptide motif".
- Downstream-peptide_motif caption "Consensus secondary structure of Downstream-peptide RNAs".
- Downstream-peptide_motif id "RF01704".
- Downstream-peptide_motif name "Downstream peptide RNA".
- Downstream-peptide_motif name "Downstream-peptide RNA".
- Downstream-peptide_motif rfam "RF01704".
- Downstream-peptide_motif rnaType "Cis-regulatory element".
- Downstream-peptide_motif symbol "Downstream-peptide".
- Downstream-peptide_motif taxDomain "Prochlorococcus and Synechococcus".
- Downstream-peptide_motif wikiPageUsesTemplate Template:Infobox_rfam.
- Downstream-peptide_motif wikiPageUsesTemplate Template:Rfam.
- Downstream-peptide_motif subject Category:Cis-regulatory_RNA_elements.
- Downstream-peptide_motif subject Category:Riboswitch.
- Downstream-peptide_motif type Element.
- Downstream-peptide_motif comment "The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera Synechococcus and Prochlorococcus and one phage that infects such bacteria. It was also detected in marine samples of DNA from uncultivated bacteria, which are presumably other species of cyanobacteria.Downstream-peptide RNAs are found upstream of short open reading frames (ORFs) that are predicted to encode short peptides (usually between 17 and 100 amino acids).".
- Downstream-peptide_motif label "Downstream-peptide motif".
- Downstream-peptide_motif sameAs Q5303296.
- Downstream-peptide_motif sameAs m.0bh74tz.
- Downstream-peptide_motif sameAs Q5303296.
- Downstream-peptide_motif wasDerivedFrom Downstream-peptide_motif?oldid=661009281.
- Downstream-peptide_motif depiction Downstream-peptide-RNA.svg.
- Downstream-peptide_motif isPrimaryTopicOf Downstream-peptide_motif.