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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0009451 RNA modification #24394

Closed ValWood closed 1 year ago

ValWood commented 1 year ago

Please provide as much information as you can:

GO:0009451 RNA modification and children

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Code | Name |   | Count -- | -- | -- | -- GO:0030488 | tRNA methylation | 113 GO:0031167 | rRNA methylation | 97 GO:0080009 | mRNA methylation | 89 GO:0002098 | tRNA wobble uridine modification | 71 GO:0006400 | tRNA modification | 65 GO:0016554 | cytidine to uridine editing | 46 GO:0070475 | rRNA base methylation | 42 GO:0016556 | mRNA modification | 39 GO:0002143 | tRNA wobble position uridine thiolation | 38 GO:0031119 | tRNA pseudouridine synthesis | 37 GO:0031118 | rRNA pseudouridine synthesis | 36 GO:0080156 | mitochondrial mRNA modification | 33 GO:0002949 | tRNA threonylcarbamoyladenosine modification | 32 GO:0009451 | RNA modification | 30 GO:0001510 | RNA methylation | 27 GO:0006382 | adenosine to inosine editing | 27 GO:1990481 | mRNA pseudouridine synthesis | 23 GO:0000454 | snoRNA guided rRNA pseudouridine synthesis | 19 GO:0031120 | snRNA pseudouridine synthesis | 19 GO:0034227 | tRNA thio-modification | 16 GO:1900865 | chloroplast RNA modification | 15 GO:0000455 | enzyme-directed rRNA pseudouridine synthesis | 14 GO:0035553 | oxidative single-stranded RNA demethylation | 14 GO:0036261 | 7-methylguanosine cap hypermethylation | 13 GO:0002128 | tRNA nucleoside ribose methylation | 11 GO:0002926 | tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation | 11 GO:0031591 | wybutosine biosynthetic process | 11 GO:0101030 | tRNA-guanine transglycosylation | 10 GO:0002100 | tRNA wobble adenosine to inosine editing | 9 GO:1900864 | mitochondrial RNA modification | 9 GO:0000451 | rRNA 2'-O-methylation | 8 GO:0070901 | mitochondrial tRNA methylation | 8 GO:0000154 | rRNA modification | 7 GO:0002943 | tRNA dihydrouridine synthesis | 7 GO:0000452 | snoRNA guided rRNA 2'-O-methylation | 6 GO:0002130 | wobble position ribose methylation | 6 GO:0002939 | tRNA N1-guanine methylation | 6 GO:0071951 | conversion of methionyl-tRNA to N-formyl-methionyl-tRNA | 6 GO:0016553 | base conversion or substitution editing | 5 GO:0035600 | tRNA methylthiolation | 5 GO:0040031 | snRNA modification | 5 GO:0106004 | tRNA (guanine-N7)-methylation | 5 GO:0106217 | tRNA C3-cytosine methylation | 5 GO:0120049 | snRNA (adenine-N6)-methylation | 5 GO:1900871 | chloroplast mRNA modification | 5 GO:0000453 | enzyme-directed rRNA 2'-O-methylation | 4 GO:0001522 | pseudouridine synthesis | 4 GO:0002097 | tRNA wobble base modification | 4 GO:0002101 | tRNA wobble cytosine modification | 4 GO:0002127 | tRNA wobble base cytosine methylation | 4 GO:0002938 | tRNA guanine ribose methylation | 4 GO:0002940 | tRNA N2-guanine methylation | 4 GO:0061504 | cyclic threonylcarbamoyladenosine biosynthetic process | 4 GO:0070476 | rRNA (guanine-N7)-methylation | 4 GO:0097309 | cap1 mRNA methylation | 4 GO:0106005 | RNA 5'-cap (guanine-N7)-methylation | 4 GO:0002927 | archaeosine-tRNA biosynthetic process | 3 GO:0051391 | tRNA acetylation | 3 GO:0070329 | tRNA seleno-modification | 3 GO:0070899 | mitochondrial tRNA wobble uridine modification | 3 GO:0070900 | mitochondrial tRNA modification | 3 GO:0002099 | tRNA wobble guanine modification | 2 GO:0002131 | wobble position cytosine ribose methylation | 2 GO:0002937 | tRNA 4-thiouridine biosynthesis | 2 GO:0002946 | tRNA C5-cytosine methylation | 2 GO:0019988 | charged-tRNA amino acid modification | 2 GO:0035513 | oxidative RNA demethylation | 2 GO:0070705 | RNA nucleotide insertion | 2 GO:0070706 | RNA nucleotide deletion | 2 GO:0070903 | mitochondrial tRNA thio-modification | 2 GO:0080178 | 5-carbamoylmethyl uridine residue modification | 2 GO:1904812 | rRNA acetylation involved in maturation of SSU-rRNA | 2 GO:1990438 | U6 2'-O-snRNA methylation | 2 GO:1990882 | rRNA acetylation | 2 GO:1990983 | tRNA demethylation | 2 GO:0002129 | wobble position guanine ribose methylation | 1 GO:0002132 | wobble position uridine ribose methylation | 1 GO:0002136 | tRNA wobble base lysidine biosynthesis | 1 GO:0070902 | mitochondrial tRNA pseudouridine synthesis | 1 GO:0072670 | mitochondrial tRNA threonylcarbamoyladenosine modification | 1 GO:0097310 | cap2 mRNA methylation | 1 GO:0106349 | snRNA methylation | 1 GO:1990799 | mitochondrial tRNA wobble position uridine thiolation | 1

Describes a molecular function

pfey03 commented 1 year ago

Just checked we have 25 dictybase annotations, some ISS, I will take care of them after Thanksgiving

ValWood commented 1 year ago

For these cases where the entire branch will be obsoleted it would be nicer if there could be some automation. @cmungall @pgaudet can we discuss. For these we think we will be able to do replaced_by in which case won't the tools deal with it?

pgaudet commented 1 year ago

Are you sure all these are 'single steps'?

ValWood commented 1 year ago

No, actually some of them aren't. Definitely tRNA wobble position uridine thiolation and GO:0001522 | pseudouridine synthesis

The methylation/demethylation/acetylation are...so it isn't the entire branch.

pfey03 commented 1 year ago

@ValWood, @pgaudet Will the non single single step then retained or also obsoleted? I did annotate the functions but have not yet deleted BP GO:0002098: tRNA wobble uridine modification

Thanks

ValWood commented 1 year ago

I don't think the multi-step processes will be obsoleted, but they will move from under the modification term I think. @pgaudet is that correct?

pgaudet commented 1 year ago

Yes this is correct.

I'll close this for now because it's misleading, this is more terms than we want to obsolete

pfey03 commented 1 year ago

Dicty is done