Pathway Human Homo sapiens

rRNA modification in the nucleus and cytosol

R-HSA-6790901 in Reactome release 97: under rRNA processing in the nucleus and cytosol, with 63 genes placed in it by the mapping files and 0 child pathways in the hierarchy.

The same number in the other species

Reactome writes the mouse and rat events it infers from a human pathway under the human number with the species token. A door opens only where that species' own list in this release holds the id; neither of the other two lists holds it. Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

Scripts are off

This page reads the pathway's record from its source while you read the rest; with scripts off the card stays at its loading line. Reload with scripts on to see it, or open the source's own page from the link in the card.

01The record

Reactome's own record of this pathway

What this tells you

The pathway list, the hierarchy and the genes on this page are read from the files Reactome publishes for Reactome release 97, built into this site on 2026-09-09: the pathway list, the hierarchy relationship file and the two gene mapping files. The record card is the one live read, Reactome's own record of this pathway.

Reactome's download page describes the mapping files: Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. [R13] The gene list here is the all-levels mapping of NCBI Gene ids, filled from the all-levels mapping of Ensembl ids where the NCBI file has no row for a gene; each row names which file it came from by the shape of its source id. Each row carries the evidence codes the file writes for it, as written and unranked, and both where the file writes both; no page of Reactome's documentation the survey read defines the codes, so this page does not expand them. A gene id the identity files do not name is kept as the source's own id with no door rather than turned into a symbol.

On citing what a search finds, Reactome says: It should be remembered that while we strive to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available. [R12] The record card prints the literature Reactome attaches to a curated pathway for that reason. The data are public domain: All data in the Reactome database and files derived from that data are licensed under the Creative Commons Public Domain Dedication (CC0). User may copy, modify, and distribute these data, even for commercial purposes, without asking for permission. Attribution is encouraged but not required. [R10] The pathway illustrations are licensed apart, under CC BY 4.0, and none is shown here.

A gene on this list is one Reactome places in this pathway in this release, and that is all the row says: it does not say the gene is expressed in a tissue or associated with a disease, which are the other two explorers' questions, read from other sources. Reactome's papers of record are [R01] [R02].

[R01] Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, et al. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Research 54:D673-D681. PMID 41251150, doi 10.1093/nar/gkaf1223.
[R02] Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, et al. (2024). The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52:D672-D678. PMID 37941124, doi 10.1093/nar/gkad1025.
[R10] Reactome, reactome.org. License Agreement. https://reactome.org/license, read 2026-09-09.
[R12] Reactome, reactome.org. Citing us. https://reactome.org/cite, read 2026-09-09.
[R13] Reactome, reactome.org. Download. https://reactome.org/download-data, read 2026-09-09.

Stable id: R-HSA-6790901.6
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2016-03-23
Last updated: 2017-04-20
Events inside: 8, counted from the record

Human ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Hernandez-Verdun et al. 2010, Boschi-Muller and Motorin 2013). The modified residues occur in regions of the rRNAs that are located in functionally important parts of the ribosome, notably in the A and P peptidyl transfer sites, the polypeptide exit tunnel, and intersubunit contacts (Polikanov et al. 2015, reviewed in Decatur and Fournier 2002, Chow et al. 2007, Sharma and Lafontaine 2015). The two most common modifications are pseudouridines and 2'-O-methylribonucleotides. Formation of pseudouridine from encoded uridine is catalyzed by box H/ACA small nucleolar ribonucleoprotein (snoRNP) complexes (reviewed in Hamma and Ferre-D'Amare 2010, Watkins and Bohnsack 2011, Ge and Yu 2013, Kierzek et al. 2014, Yu and Meier 2014) and methylation of the hydroxyl group of the 2' carbon is catalyzed by box C/D snoRNPs (Kiss-Laszlo et al. 1996, Lapinaite et al. 2013, reviewed in Watkins and Bohnsack 2011). The snoRNP complexes contain common sets of protein subunits and unique snoRNAs that guide each complex to its target nucleotide of the rRNA by base-pairing between the snoRNA and the rRNA (reviewed in Henras et al. 2004, Watkins and Bohnsack 2011). Other modifications of rRNA include 5-methylcytidine (reviewed in Squires and Preiss 2010), 1-methylpseudouridine, 7-methylguanosine, 6-dimethyladenosine, and 4-acetylcytidine (reviewed in Sharma and Lafontaine 2015). In yeast most modifications are introduced co-transcriptionally (Kos and Tollervey 2010, reviewed in Turowski and Tollervey 2015), however the order of modification events and pre-rRNA cleavage events is not well characterized.

Literature Reactome attaches

RNA-guided isomerization of uridine to pseudouridine--pseudouridylationRNA Biol, 2014, vol. 11, p. 1483-94PubMed 25590339
Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modificationBiochemistry Mosc., 2013, vol. 78, p. 1392-404PubMed 24490730
RNA structure and function in C/D and H/ACA s(no)RNPsCurr. Opin. Struct. Biol., 2004, vol. 14, p. 335-43PubMed 15193314
Function and detection of 5-methylcytosine in eukaryotic RNAEpigenomics, 2010, vol. 2, p. 709-15PubMed 22122054
The nucleolus: structure/function relationship in RNA metabolismWiley Interdiscip Rev RNA, 2010, vol. 1, p. 415-31PubMed 21956940
The contribution of pseudouridine to stabilities and structure of RNAsNucleic Acids Res., 2014, vol. 42, p. 3492-501PubMed 24369424
RNA pseudouridylation: new insights into an old modificationTrends Biochem. Sci., 2013, vol. 38, p. 210-8PubMed 23391857
The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modificationJ. Biol. Chem., 2010, vol. 285, p. 805-9PubMed 19917616
Expanding the nucleotide repertoire of the ribosome with post-transcriptional modificationsACS Chem. Biol., 2007, vol. 2, p. 610-9PubMed 17894445
Yeast pre-rRNA processing and modification occur cotranscriptionallyMol. Cell, 2010, vol. 37, p. 809-20PubMed 20347423
Cotranscriptional events in eukaryotic ribosome synthesisWiley Interdiscip Rev RNA, 2015, vol. 6, p. 129-39PubMed 25176256
Locations of methyl groups in 28 S rRNA of Xenopus laevis and man. Clustering in the conserved core of moleculeJ. Mol. Biol., 1988, vol. 201, p. 289-314PubMed 3418702
Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problemChromosoma, 1997, vol. 105, p. 391-400PubMed 9211966
Methylated nucleotide sequences in HeLa-cell ribosomal ribonucleic acid. Correlation between the results from 'fingerprinting' hydrolysates obtained by digestion with T1 ribonuclease and with T1 plus pancreatic ribonucleaseBiochem. J., 1977, vol. 167, p. 211-21PubMed 412496
'View From A Bridge': A New Perspective on Eukaryotic rRNA Base ModificationTrends Biochem. Sci., 2015, vol. 40, p. 560-75PubMed 26410597
The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNAWiley Interdiscip Rev RNA, 2012, vol. 3, p. 397-414PubMed 22065625
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assemblyNat. Struct. Mol. Biol., 2015, vol. 22, p. 342-4PubMed 25775268
Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAsCell, 1996, vol. 85, p. 1077-88PubMed 8674114
The structure of the box C/D enzyme reveals regulation of RNA methylationNature, 2013, vol. 502, p. 519-23PubMed 24121435
rRNA modifications and ribosome functionTrends Biochem. Sci., 2002, vol. 27, p. 344-51PubMed 12114023

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-09-30 ET · Reactome pathway browser"rRNA modification in the nucleus and cytosol". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-6790901 with StableID: R-HSA-6790901.6 (accessed 2026-09-30 ET). Reactome version 97 (CC0).

Reading this pathway's record from Reactome (the pathway record).Still reading. A first read of a pathway can take a while; this page waits up to 35 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.

02The genes

Genes Reactome places in this human pathway

The mapping files place 63 genes in this human pathway; showing 1 to 63, in pages of 100, sorted by symbol for reading. The order carries no ranking. 2 of the rows shown carry an id the identity file does not name, kept as the source wrote it.

Genes Reactome places in this human pathway, page 1 of 1
Gene	Authority id	Mapping file id	Evidence codes
GeneBMS1	AuthorityHGNC:23505	Mapping file id9790 NCBI file	EvidenceIEA
GeneBUD23	AuthorityHGNC:16405	Mapping file id114049 NCBI file	EvidenceTAS
GeneDCAF13	AuthorityHGNC:24535	Mapping file id25879 NCBI file	EvidenceIEA
GeneDDX47	AuthorityHGNC:18682	Mapping file id51202 NCBI file	EvidenceIEA
GeneDDX49	AuthorityHGNC:18684	Mapping file id54555 NCBI file	EvidenceIEA
GeneDDX52	AuthorityHGNC:20038	Mapping file id11056 NCBI file	EvidenceIEA
GeneDHX37	AuthorityHGNC:17210	Mapping file id57647 NCBI file	EvidenceIEA
GeneDIMT1	AuthorityHGNC:30217	Mapping file id27292 NCBI file	EvidenceTAS
GeneDKC1	AuthorityHGNC:2890	Mapping file id1736 NCBI file	EvidenceTAS
GeneEMG1	AuthorityHGNC:16912	Mapping file id10436 NCBI file	EvidenceIEA
GeneFBL	AuthorityHGNC:3599	Mapping file id2091 NCBI file	EvidenceIEA
GeneFCF1	AuthorityHGNC:20220	Mapping file id51077 NCBI file	EvidenceIEA
GeneGAR1	AuthorityHGNC:14264	Mapping file id54433 NCBI file	EvidenceTAS
GeneHEATR1	AuthorityHGNC:25517	Mapping file id55127 NCBI file	EvidenceIEA
GeneIMP3	AuthorityHGNC:14497	Mapping file id55272 NCBI file	EvidenceIEA
GeneIMP4	AuthorityHGNC:30856	Mapping file id92856 NCBI file	EvidenceIEA
GeneKRR1	AuthorityHGNC:5176	Mapping file id11103 NCBI file	EvidenceIEA
GeneMPHOSPH10	AuthorityHGNC:7213	Mapping file id10199 NCBI file	EvidenceIEA
GeneNAT10	AuthorityHGNC:29830	Mapping file id55226 NCBI file	EvidenceTAS
GeneNHP2	AuthorityHGNC:14377	Mapping file id55651 NCBI file	EvidenceTAS
GeneNOC4L	AuthorityHGNC:28461	Mapping file id79050 NCBI file	EvidenceIEA
GeneNOL11	AuthorityHGNC:24557	Mapping file id25926 NCBI file	EvidenceIEA
GeneNOL6	AuthorityHGNC:19910	Mapping file id65083 NCBI file	EvidenceIEA
GeneNOP10	AuthorityHGNC:14378	Mapping file id55505 NCBI file	EvidenceTAS
GeneNOP14	AuthorityHGNC:16821	Mapping file id8602 NCBI file	EvidenceIEA
GeneNOP2	AuthorityHGNC:7867	Mapping file id4839 NCBI file	EvidenceIEA
GeneNOP56	AuthorityHGNC:15911	Mapping file id10528 NCBI file	EvidenceIEA
GeneNOP58	AuthorityHGNC:29926	Mapping file id51602 NCBI file	EvidenceIEA
GenePDCD11	AuthorityHGNC:13408	Mapping file id22984 NCBI file	EvidenceIEA
GenePNO1	AuthorityHGNC:32790	Mapping file id56902 NCBI file	EvidenceTAS
GenePWP2	AuthorityHGNC:9711	Mapping file id5822 NCBI file	EvidenceIEA
GeneRCL1	AuthorityHGNC:17687	Mapping file id10171 NCBI file	EvidenceIEA
GeneRNA45SN5	AuthorityHGNC:53530	Mapping file id100861532 NCBI file	EvidenceIEA, TAS
GeneRPS14	AuthorityHGNC:10387	Mapping file id6208 NCBI file	EvidenceIEA
GeneRPS2	AuthorityHGNC:10404	Mapping file id6187 NCBI file	EvidenceIEA
GeneRPS6	AuthorityHGNC:10429	Mapping file id6194 NCBI file	EvidenceIEA
GeneRPS7	AuthorityHGNC:10440	Mapping file id6201 NCBI file	EvidenceIEA
GeneRPS9	AuthorityHGNC:10442	Mapping file id6203 NCBI file	EvidenceIEA
GeneRRP36	AuthorityHGNC:21374	Mapping file id88745 NCBI file	EvidenceIEA
GeneRRP7A	AuthorityHGNC:24286	Mapping file id27341 NCBI file	EvidenceIEA
GeneRRP9	AuthorityHGNC:16829	Mapping file id9136 NCBI file	EvidenceIEA
GeneSNU13	AuthorityHGNC:7819	Mapping file id4809 NCBI file	EvidenceIEA
GeneTBL3	AuthorityHGNC:11587	Mapping file id10607 NCBI file	EvidenceIEA
GeneTHUMPD1	AuthorityHGNC:23807	Mapping file id55623 NCBI file	EvidenceTAS
GeneTRMT112	AuthorityHGNC:26940	Mapping file id51504 NCBI file	EvidenceTAS
GeneTSR3	AuthorityHGNC:14175	Mapping file id115939 NCBI file	EvidenceTAS
GeneUTP11	AuthorityHGNC:24329	Mapping file id51118 NCBI file	EvidenceIEA
GeneUTP14A	AuthorityHGNC:10665	Mapping file id10813 NCBI file	EvidenceIEA
GeneUTP14C	AuthorityHGNC:20321	Mapping file id9724 NCBI file	EvidenceIEA
GeneUTP15	AuthorityHGNC:25758	Mapping file id84135 NCBI file	EvidenceIEA
GeneUTP18	AuthorityHGNC:24274	Mapping file id51096 NCBI file	EvidenceIEA
GeneUTP20	AuthorityHGNC:17897	Mapping file id27340 NCBI file	EvidenceIEA
GeneUTP25	AuthorityHGNC:28440	Mapping file id27042 NCBI file	EvidenceIEA
GeneUTP3	AuthorityHGNC:24477	Mapping file id57050 NCBI file	EvidenceIEA
GeneUTP4	AuthorityHGNC:1983	Mapping file id84916 NCBI file	EvidenceIEA
GeneUTP6	AuthorityHGNC:18279	Mapping file id55813 NCBI file	EvidenceIEA
GeneWDR3	AuthorityHGNC:12755	Mapping file id10885 NCBI file	EvidenceIEA
GeneWDR36	AuthorityHGNC:30696	Mapping file id134430 NCBI file	EvidenceIEA
GeneWDR43	AuthorityHGNC:28945	Mapping file id23160 NCBI file	EvidenceIEA
GeneWDR46	AuthorityHGNC:13923	Mapping file id9277 NCBI file	EvidenceIEA
GeneWDR75	AuthorityHGNC:25725	Mapping file id84128 NCBI file	EvidenceIEA
Geneno symbol in the identity file	Authoritynone	Mapping file idNR_006880 as written	EvidenceIEA
Geneno symbol in the identity file	Authoritynone	Mapping file idNR_046235 as written	EvidenceIEA, TAS

Evidence codes on this page: IEA, TAS, as the mapping file writes them; a row carrying two was written twice by the file, once under each. The mapping file id says which file placed the gene: an NCBI Gene id from NCBI2Reactome_All_Levels.txt, an Ensembl gene id from Ensembl2Reactome_All_Levels.txt. The two files can disagree about a code, so a row's codes are the one file's view. Measured by this site's build over this release on 2026-09-09: of the 138,908 human pathway-gene pairs both files place, 207 (0.149 per cent, over 47 genes) carry TAS in the Ensembl file where the NCBI rows carry IEA alone.

Reactome mapping files, the human rows for this pathway · Reactome release 97 · read 2026-09-09 · Reactome downloads"NCBI2Reactome_All_Levels.txt" and "Ensembl2Reactome_All_Levels.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.

03The hierarchy

Parents and children in this release's hierarchy

Parents

rRNA processing in the nucleus and cytosolR-HSA-8868773196 genes

Children

None: no pathway of this release's list names this one as a parent.

Reactome's hierarchy is a graph rather than a tree: a pathway can sit under more than one parent, and the gene counts are each pathway's own placements at every level under it, so a parent's count is not the sum of its children's.

Reactome, the human pathway list and hierarchy relationship file · Reactome release 97 · read 2026-09-09 · Reactome downloads"ReactomePathways.txt" and "ReactomePathwaysRelation.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.