Difference between revisions of "RNA processing"

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Work from April 9th session:
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== Work from April 9th session ==
  
 
proposed ontology structure:
 
proposed ontology structure:
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......non-templated
 
......non-templated
 
....dimethylation during SSU biogenesis *H
 
....dimethylation during SSU biogenesis *H
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 +
 +
*H = Harold to work on
 +
*C = Ceri to work on
 +
*K = Karen to work on
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</pre>
 
</pre>
  
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rRNA modification_The covalent alteration of one or more nucleotides within an rRNA molecule,.
 
rRNA modification_The covalent alteration of one or more nucleotides within an rRNA molecule,.
  
i--rRNA editing_The insertion, deletion or substitution of nucleotide residues within nascent    rRNA transcripts to produce rRNA molecules with sequences that differ from those coded genetically. (how to distinguish this from methylation, pseudoU?)
+
i--rRNA editing - The insertion, deletion or substitution of nucleotide residues within nascent    rRNA transcripts to produce rRNA molecules with sequences that differ from those coded genetically. (how to distinguish this from methylation, pseudoU?)
  
i--rRNA methylation_The posttranscriptional addition of methyl groups to specific nucleotide residues in an rRNA molecule.
+
i--rRNA methylation - The posttranscriptional addition of methyl groups to specific nucleotide residues in an rRNA molecule.
  
i---rRNA 2’-O-methylation _The posttranscriptional addition of a methyl group to the 2'-O atom of a nucleotide residue in an rRNA molecule (check F def for 2’-O-methylation)
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i---rRNA 2’-O-methylation - The posttranscriptional addition of a methyl group to the 2'-O atom of a nucleotide residue in an rRNA molecule (check F def for 2’-O-methylation)
  
i----snoRNA guided rRNA 2’-O-methylation _The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule using a snoRNA guide. (synonym: templated…???)
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i----snoRNA guided rRNA 2’-O-methylation - The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule using a snoRNA guide. (synonym: templated…???)
  
i----non-guided rRNA 2’-O-methylation _The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule without using a guide RNA. (need to rephrase this to avoid a negation of the guided methylation term)
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i----non-guided rRNA 2’-O-methylation - The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule without using a guide RNA. (need to rephrase this to avoid a negation of the guided methylation term)
  
i--rRNA pseudouridine synthesis_The intramolecular conversion of uridine to pseudouridine in an rRNA molecule.
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i--rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine in an rRNA molecule.
  
i--- snoRNA guided rRNA pseudouridine synthesis_The intramolecular conversion of uridine to pseudouridine in an rRNA molecule using a snoRNA guide.
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i--- snoRNA guided rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine in an rRNA molecule using a snoRNA guide.
  
i--- non-guided rRNA pseudouridine synthesis _The intramolecular conversion of uridine to pseudouridine with no guide RNA.  (need to rephrase this to avoid a negation of the guided pseudouridylation term)
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i--- non-guided rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine with no guide RNA.  (need to rephrase this to avoid a negation of the guided pseudouridylation term)

Revision as of 12:11, 7 May 2007

Work from April 9th session

proposed ontology structure:

rRNA processing
..endonucleolytic cleavages *K
....cleavage of  tricistronic rRNA transcript (SSU.5.8S.LSU) *K
......cleavage of  5’ETS *K
......cleavage between SSU.rRNA and 5.8S.LSU *K
......cleavage between 5.8S and LSU *K
....cleavage of  tricistronic rRNA transcript (SSU.LSU.5S) *H
......cleavage between SSU and LSU *H
......cleavage between LSU and 5S *H
....cleavage of bicistronic rRNA transcript (SSU.LSU) *K
......cleavage between SSU and LSU *K
....cleavage of  monocistronic primary LSU rRNA transcript *K
....cleavage of  monocistronic primary SSU rRNA transcript *K

..exonucleolytic trimming

.rRNA modification (existing) *C and below
..base modification
....pseudouridylation during ribosome biogenesis
......templated
......non-templated
....2’-O-methylation during ribosome biogenesis
......templated
......non-templated
....dimethylation during SSU biogenesis *H


*H = Harold to work on
*C = Ceri to work on
*K = Karen to work on

proposed defs:

rRNA modification_The covalent alteration of one or more nucleotides within an rRNA molecule,.

i--rRNA editing - The insertion, deletion or substitution of nucleotide residues within nascent rRNA transcripts to produce rRNA molecules with sequences that differ from those coded genetically. (how to distinguish this from methylation, pseudoU?)

i--rRNA methylation - The posttranscriptional addition of methyl groups to specific nucleotide residues in an rRNA molecule.

i---rRNA 2’-O-methylation - The posttranscriptional addition of a methyl group to the 2'-O atom of a nucleotide residue in an rRNA molecule (check F def for 2’-O-methylation)

i----snoRNA guided rRNA 2’-O-methylation - The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule using a snoRNA guide. (synonym: templated…???)

i----non-guided rRNA 2’-O-methylation - The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule without using a guide RNA. (need to rephrase this to avoid a negation of the guided methylation term)

i--rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine in an rRNA molecule.

i--- snoRNA guided rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine in an rRNA molecule using a snoRNA guide.

i--- non-guided rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine with no guide RNA. (need to rephrase this to avoid a negation of the guided pseudouridylation term)