Pathway Human Homo sapiens

Nuclear RNA decay

R-HSA-9930044 in Reactome release 97: under Metabolism of RNA, with 35 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: R-MMU-9930044 (mouse), R-RNO-9930044 (rat). Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

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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-9930044.3
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2025-03-26
Events inside: 15, counted from the record

In addition to protein coding mRNAs and stable RNAs such as rRNAs, tRNAs, snoRNAs, and snRNAs, the human genome is pervasively transcribed (Clark et al. 2011) to yield other non-coding RNAs such as enhancer transcripts, promoter upstream transcripts (PROMPTs, Preker et al. 2008), long non-coding RNAs (lncRNAs), and apparently non-functional transcripts (reviewed in Ogami and Suzuki 2021). In addition, processing intermediates and abortive transcripts are produced during transcription of mRNAs and stable RNAs. In the nucleus, pervasive unstable transcripts are degraded by nucleases such as the RNA exosome complex (a 3'-5' exonuclease), XRN2 (a 5'-3' exonuclease), and DXO (a 5'-3' exonuclease and a decapping enzyme) (reviewed in Wolin and Maquat 2019, Rambout and Maquat 2024). RNA substrates are directed to the RNA exosome by the nuclear exosome targeting (NEXT) complex, the poly(A) tail exosome targeting (PAXT) connection, and the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex. This sorting is crucial to the removal of malformed transcripts and misassembled RNA-protein complexes (reviewed in Wolin and Maquat 2019, Garland and Jensen 2024). Through ZC3H18 or ZC3H4, the NEXT complex (RBM7:ZCCHC8:MTREX) binds capped nonpolyadenylated RNAs (Wu et al. 2020), such as abortive transcripts from RNA polymerase II, recruits the RNA exosome, then the MTREX (MTR4, SKIV2L2) subunit of NEXT unwinds the RNA for introduction into the barrel-shaped RNA exosome (Lubas et al. 2011, Andersen et al. 2013). The PAXT connection (ZFC3H1:MTREX) targets more mature, capped and polyadenylated transcripts (Meola et al. 2016, Wu et al. 2020), and the nucleolar TRAMP complex (MTREX:TENT4A,B:ZCCHC7) targets processing products of rRNA maturation (Sudo et al. 2016). The 5'-3' exonuclease XRN2 is active on RNAs that possess a 5' monophosphate group (inferred from the yeast homolog in Stevens and Poole 1995), but is blocked by a 5' triphosphate or cap structure (reviewed in Miki and Großhans 2013, Nagarajan et al. 2013). Substrates of XRN2 include decapped RNAs and the 3' cleavage products of RNA polymerase II transcripts (reviewed in Miki and Großhans 2013, Nagarajan et al. 2013). The decapping 5'-3 exonuclease DXO can both remove 5' triphosphate or caps (especially unmethylated caps) and exonucleolytically hydrolyze RNAs (Jiao et al. 2013, Doamekpor et al. 2020). DXO is also active on nicotinamide adenine dinucleotide (NAD) cap on RNAs (Jiao et al. 2017) and other "metabolic caps" (several activities and references can be added here, see below). The exonuclease activity of DXO is distributive, while that for XRN2 is processive. The human TRAMP complex is found in a complex with the RNA exosome in the nucleolus where it directs the 5' external transcribed sequence that is cleaved from the 47S pre-rRNA during production of the 45S pre-rRNA (Lubas et al. 2011, Sudo et al. 2016).

Literature Reactome attaches

Nuclear mRNA decay: regulatory networks that control gene expressionNat Rev Genet, 2024, vol. 25, p. 679-697PubMed 38637632
Nuclear sorting of short RNA polymerase II transcriptsMol Cell, 2024, vol. 84, p. 3644-3655PubMed 39366352
Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome FunctionInt J Mol Sci, 2021, vol. 22PubMed 34948199
RNA exosome depletion reveals transcription upstream of active human promotersScience, 2008, vol. 322, p. 1851-4PubMed 19056938
The reality of pervasive transcriptionPLoS Biol, 2011, vol. 9, p. e1000625; discussion e1001102PubMed 21765801
Interaction profiling identifies the human nuclear exosome targeting complexMol. Cell, 2011, vol. 43, p. 624-37PubMed 21855801
The human cap-binding complex is functionally connected to the nuclear RNA exosomeNat Struct Mol Biol, 2013, vol. 20, p. 1367-76PubMed 24270879

Reactome's record lists 12 orthologous events, R-MMU-9930044 (Mus musculus), R-RNO-9930044 (Rattus norvegicus) among the species this site serves, and 10 in species this site opens no page for.

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-10-01 ET · Reactome pathway browser"Nuclear RNA decay". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-9930044 with StableID: R-HSA-9930044.3 (accessed 2026-10-01 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 35 genes in this human pathway; showing 1 to 35, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 1 of 1
Gene	Authority id	Mapping file id	Evidence codes
GeneC1D	AuthorityHGNC:29911	Mapping file id10438 NCBI file	EvidenceTAS
GeneDIS3	AuthorityHGNC:20604	Mapping file id22894 NCBI file	EvidenceTAS
GeneDXO	AuthorityHGNC:2992	Mapping file id1797 NCBI file	EvidenceIEA
GeneEXOSC1	AuthorityHGNC:17286	Mapping file id51013 NCBI file	EvidenceTAS
GeneEXOSC10	AuthorityHGNC:9138	Mapping file id5394 NCBI file	EvidenceTAS
GeneEXOSC2	AuthorityHGNC:17097	Mapping file id23404 NCBI file	EvidenceTAS
GeneEXOSC3	AuthorityHGNC:17944	Mapping file id51010 NCBI file	EvidenceTAS
GeneEXOSC4	AuthorityHGNC:18189	Mapping file id54512 NCBI file	EvidenceTAS
GeneEXOSC5	AuthorityHGNC:24662	Mapping file id56915 NCBI file	EvidenceTAS
GeneEXOSC6	AuthorityHGNC:19055	Mapping file id118460 NCBI file	EvidenceTAS
GeneEXOSC7	AuthorityHGNC:28112	Mapping file id23016 NCBI file	EvidenceTAS
GeneEXOSC8	AuthorityHGNC:17035	Mapping file id11340 NCBI file	EvidenceTAS
GeneEXOSC9	AuthorityHGNC:9137	Mapping file id5393 NCBI file	EvidenceTAS
GeneMPHOSPH6	AuthorityHGNC:7214	Mapping file id10200 NCBI file	EvidenceTAS
GeneMTREX	AuthorityHGNC:18734	Mapping file id23517 NCBI file	EvidenceTAS
GeneNCBP1	AuthorityHGNC:7658	Mapping file id4686 NCBI file	EvidenceTAS
GeneNCBP2	AuthorityHGNC:7659	Mapping file id22916 NCBI file	EvidenceTAS
GenePABPN1	AuthorityHGNC:8565	Mapping file id8106 NCBI file	EvidenceTAS
GenePAPOLG	AuthorityHGNC:14982	Mapping file id64895 NCBI file	EvidenceTAS
GeneRBM26	AuthorityHGNC:20327	Mapping file id64062 NCBI file	EvidenceTAS
GeneRBM27	AuthorityHGNC:29243	Mapping file id54439 NCBI file	EvidenceTAS
GeneRBM7	AuthorityHGNC:9904	Mapping file id10179 NCBI file	EvidenceTAS
GeneSRRT	AuthorityHGNC:24101	Mapping file id51593 NCBI file	EvidenceTAS
GeneTENT4A	AuthorityHGNC:16705	Mapping file id11044 NCBI file	EvidenceTAS
GeneTENT4B	AuthorityHGNC:30758	Mapping file id64282 NCBI file	EvidenceTAS
GeneWDR82	AuthorityHGNC:28826	Mapping file id80335 NCBI file	EvidenceTAS
GeneXRN2	AuthorityHGNC:12836	Mapping file id22803 NCBI file	EvidenceIEA
GeneYTHDC1	AuthorityHGNC:30626	Mapping file id91746 NCBI file	EvidenceTAS
GeneYTHDC2	AuthorityHGNC:24721	Mapping file id64848 NCBI file	EvidenceTAS
GeneZC3H18	AuthorityHGNC:25091	Mapping file id124245 NCBI file	EvidenceTAS
GeneZC3H3	AuthorityHGNC:28972	Mapping file id23144 NCBI file	EvidenceTAS
GeneZC3H4	AuthorityHGNC:17808	Mapping file id23211 NCBI file	EvidenceTAS
GeneZCCHC7	AuthorityHGNC:26209	Mapping file id84186 NCBI file	EvidenceTAS
GeneZCCHC8	AuthorityHGNC:25265	Mapping file id55596 NCBI file	EvidenceTAS
GeneZFC3H1	AuthorityHGNC:28328	Mapping file id196441 NCBI file	EvidenceTAS

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

Metabolism of RNAR-HSA-8953854751 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.