Pathway Human Homo sapiens

RNA polymerase II transcribes snRNA genes

R-HSA-6807505 in Reactome release 97: under RNA Polymerase II Transcription, with 81 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-6807505 (mouse), R-RNO-6807505 (rat). 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-6807505.4
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2016-03-23
Last updated: 2023-03-29
Events inside: 11, counted from the record

Small nuclear RNAs (snRNAs) play key roles in splicing and some of them, specifically the U1 and U2 snRNAs, are encoded by multicopy snRNA gene clusters containing tandem arrays of genes, about 30 in the RNU1 cluster (Bernstein et al. 1985) and about 10-20 in the RNU2 cluster (Van Ardsell and Weiner 1984). Whereas U6 snRNA genes are transcribed by RNA polymerase III, U1,U2, U4, U4atac, U5, U11, and U12 genes are transcribed by RNA polymerase II. Transcription of the U1 and U2 genes has been most extensively studied and the other snRNA genes as well as other genes with similar promoter structures, for example the SNORD13 gene, are inferred to be transcribed by similar reactions. The snRNA genes transcribed by RNA polymerase II are distinguished from mRNA-encoding genes by the presence of a proximal sequence element (PSE) rather than a TATA box and the presence of the Integrator complex rather than the Mediator complex (reviewed in Egloff et al. 2008, Jawdeker and Henry 2008).

The snRNA genes are among the most rapidly transcribed genes in the genome. The 5' transcribed region of the U2 snRNA gene is largely single-stranded during interphase and metaphase (Pavelitz et al. 2008) and chromatin within the transcribed region is cleared of nucleosomes (O'Reilly et al. 2014). Transcriptional activation of the RNA polymerase II transcribed snRNA genes begins with binding of transcription factors to the distal sequence element (DSE) of the promoter (reviewed in Hernandez 2001, Egloff et al. 2008, Jawdeker and Henry 2008). The factors, which include POU2F1 (Oct-1), POU2F2 (Oct-2), ZNF143 (Staf) and Sp1, promote binding of the SNAPc complex (also known as PTF and PBP) to the PSE. SNAPc helps clear the gene of nucleosomes (O'Reilly et al. 2014) and recruits initiation factors (TFIIA, TFIIB, TFIIE, TFIIF, and snTAFc:TBP) which recruit RNA polymerase II. Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (reviewed in Egloff and Murphy 2008) by CDK7 recruits RPAP2 and the Integrator complex, which is required for later processing of the 3' end of the pre-snRNA transcript (reviewed in Chen and Wagner 2010, Baillat and Wagner 2015). The Little Elongation Complex (LEC) also appears to bind around the time of transcription initiation (Hu et al. 2013). As transcription proceeds, RPAP2 dephosphorylates serine-5 and P-TEFb phosphorylates serine-2 of the CTD. As transcription reaches the end of the snRNA gene serine-7 of the CTD is phosphorylated. These marks serve to bind protein complexes and are required for 3' processing of the pre-snRNA (reviewed in Egloff and Murphy 2008). After transcription proceeds through the conserved 3' processing sequence of the pre-snRNA the Integrator complex cleaves the pre-snRNA. Transcription then terminates downstream in a less well characterized reaction that requires elements of the polyadenylation system.

Literature Reactome attaches

Expression of human snRNA genes from beginning to endBiochem. Soc. Trans., 2008, vol. 36, p. 590-4PubMed 18631122
Role of the C-terminal domain of RNA polymerase II in expression of small nuclear RNA genesBiochem. Soc. Trans., 2008, vol. 36, p. 537-9PubMed 18482001
Updating the RNA polymerase CTD code: adding gene-specific layersTrends Genet., 2012, vol. 28, p. 333-41PubMed 22622228
Transcriptional regulation of human small nuclear RNA genesBiochim. Biophys. Acta, 2008, vol. 1779, p. 295-305PubMed 18442490
Small nuclear RNA genes: a model system to study fundamental mechanisms of transcriptionJ. Biol. Chem., 2001, vol. 276, p. 26733-6PubMed 11390411
Human U2 snRNA genes exhibit a persistently open transcriptional state and promoter disassembly at metaphaseMol. Cell. Biol., 2008, vol. 28, p. 3573-88PubMed 18378697
Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transpositionMol. Cell. Biol., 1985, vol. 5, p. 2159-71

Reactome's record lists 13 orthologous events, R-MMU-6807505 (Mus musculus), R-RNO-6807505 (Rattus norvegicus) among the species this site serves, and 11 in species this site opens no page for.

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-10-02 ET · Reactome pathway browser"RNA polymerase II transcribes snRNA genes". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-6807505 with StableID: R-HSA-6807505.4 (accessed 2026-10-02 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 81 genes in this human pathway; showing 1 to 81, 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
GeneCCNK	AuthorityHGNC:1596	Mapping file id8812 NCBI file	EvidenceIEA, TAS
GeneCCNT1	AuthorityHGNC:1599	Mapping file id904 NCBI file	EvidenceIEA, TAS
GeneCCNT2	AuthorityHGNC:1600	Mapping file id905 NCBI file	EvidenceIEA, TAS
GeneCDK7	AuthorityHGNC:1778	Mapping file id1022 NCBI file	EvidenceIEA, TAS
GeneCDK9	AuthorityHGNC:1780	Mapping file id1025 NCBI file	EvidenceIEA, TAS
GeneELL	AuthorityHGNC:23114	Mapping file id8178 NCBI file	EvidenceIEA, TAS
GeneELL2	AuthorityHGNC:17064	Mapping file id22936 NCBI file	EvidenceIEA, TAS
GeneELL3	AuthorityHGNC:23113	Mapping file id80237 NCBI file	EvidenceIEA, TAS
GeneGTF2A1	AuthorityHGNC:4646	Mapping file id2957 NCBI file	EvidenceIEA, TAS
GeneGTF2A2	AuthorityHGNC:4647	Mapping file id2958 NCBI file	EvidenceIEA, TAS
GeneGTF2B	AuthorityHGNC:4648	Mapping file id2959 NCBI file	EvidenceIEA, TAS
GeneGTF2E1	AuthorityHGNC:4650	Mapping file id2960 NCBI file	EvidenceIEA, TAS
GeneGTF2E2	AuthorityHGNC:4651	Mapping file id2961 NCBI file	EvidenceIEA, TAS
GeneGTF2F1	AuthorityHGNC:4652	Mapping file id2962 NCBI file	EvidenceIEA, TAS
GeneGTF2F2	AuthorityHGNC:4653	Mapping file id2963 NCBI file	EvidenceIEA, TAS
GeneICE1	AuthorityHGNC:29154	Mapping file id23379 NCBI file	EvidenceIEA, TAS
GeneICE2	AuthorityHGNC:29885	Mapping file id79664 NCBI file	EvidenceIEA, TAS
GeneINTS1	AuthorityHGNC:24555	Mapping file id26173 NCBI file	EvidenceIEA, TAS
GeneINTS10	AuthorityHGNC:25548	Mapping file id55174 NCBI file	EvidenceIEA, TAS
GeneINTS11	AuthorityHGNC:26052	Mapping file id54973 NCBI file	EvidenceIEA, TAS
GeneINTS12	AuthorityHGNC:25067	Mapping file id57117 NCBI file	EvidenceIEA, TAS
GeneINTS13	AuthorityHGNC:20174	Mapping file id55726 NCBI file	EvidenceIEA, TAS
GeneINTS14	AuthorityHGNC:25372	Mapping file id81556 NCBI file	EvidenceIEA, TAS
GeneINTS2	AuthorityHGNC:29241	Mapping file id57508 NCBI file	EvidenceIEA, TAS
GeneINTS3	AuthorityHGNC:26153	Mapping file id65123 NCBI file	EvidenceIEA, TAS
GeneINTS4	AuthorityHGNC:25048	Mapping file id92105 NCBI file	EvidenceIEA, TAS
GeneINTS5	AuthorityHGNC:29352	Mapping file id80789 NCBI file	EvidenceIEA, TAS
GeneINTS6	AuthorityHGNC:14879	Mapping file id26512 NCBI file	EvidenceIEA, TAS
GeneINTS7	AuthorityHGNC:24484	Mapping file id25896 NCBI file	EvidenceIEA, TAS
GeneINTS8	AuthorityHGNC:26048	Mapping file id55656 NCBI file	EvidenceIEA, TAS
GeneINTS9	AuthorityHGNC:25592	Mapping file id55756 NCBI file	EvidenceIEA, TAS
GeneNABP1	AuthorityHGNC:26232	Mapping file id64859 NCBI file	EvidenceIEA, TAS
GeneNABP2	AuthorityHGNC:28412	Mapping file id79035 NCBI file	EvidenceIEA, TAS
GeneNCBP1	AuthorityHGNC:7658	Mapping file id4686 NCBI file	EvidenceTAS
GeneNCBP2	AuthorityHGNC:7659	Mapping file id22916 NCBI file	EvidenceTAS
GenePCF11	AuthorityHGNC:30097	Mapping file id51585 NCBI file	EvidenceTAS
GenePHAX	AuthorityHGNC:10241	Mapping file id51808 NCBI file	EvidenceTAS
GenePOLR2A	AuthorityHGNC:9187	Mapping file id5430 NCBI file	EvidenceIEA, TAS
GenePOLR2B	AuthorityHGNC:9188	Mapping file id5431 NCBI file	EvidenceIEA, TAS
GenePOLR2C	AuthorityHGNC:9189	Mapping file id5432 NCBI file	EvidenceIEA, TAS
GenePOLR2D	AuthorityHGNC:9191	Mapping file id5433 NCBI file	EvidenceIEA, TAS
GenePOLR2E	AuthorityHGNC:9192	Mapping file id5434 NCBI file	EvidenceIEA, TAS
GenePOLR2F	AuthorityHGNC:9193	Mapping file id5435 NCBI file	EvidenceIEA, TAS
GenePOLR2G	AuthorityHGNC:9194	Mapping file id5436 NCBI file	EvidenceIEA, TAS
GenePOLR2H	AuthorityHGNC:9195	Mapping file id5437 NCBI file	EvidenceIEA, TAS
GenePOLR2I	AuthorityHGNC:9196	Mapping file id5438 NCBI file	EvidenceIEA, TAS
GenePOLR2J	AuthorityHGNC:9197	Mapping file id5439 NCBI file	EvidenceIEA, TAS
GenePOLR2K	AuthorityHGNC:9198	Mapping file id5440 NCBI file	EvidenceIEA, TAS
GenePOLR2L	AuthorityHGNC:9199	Mapping file id5441 NCBI file	EvidenceIEA, TAS
GenePOU2F1	AuthorityHGNC:9212	Mapping file id5451 NCBI file	EvidenceIEA, TAS
GenePOU2F2	AuthorityHGNC:9213	Mapping file id5452 NCBI file	EvidenceIEA, TAS
GeneRNU1-1	AuthorityHGNC:10120	Mapping file idENSG00000206652 Ensembl file	EvidenceIEA, TAS
GeneRNU11	AuthorityHGNC:10108	Mapping file idENSG00000274978 Ensembl file	EvidenceIEA, TAS
GeneRNU12	AuthorityHGNC:19380	Mapping file idENSG00000276027 Ensembl file	EvidenceIEA, TAS
GeneRNU2-1	AuthorityHGNC:10142	Mapping file idENSG00000274585 Ensembl file	EvidenceIEA, TAS
GeneRNU4-1	AuthorityHGNC:10192	Mapping file idENSG00000200795 Ensembl file	EvidenceIEA, TAS
GeneRNU4ATAC	AuthorityHGNC:34016	Mapping file idENSG00000264229 Ensembl file	EvidenceIEA, TAS
GeneRNU5A-1	AuthorityHGNC:10211	Mapping file idENSG00000199568 Ensembl file	EvidenceIEA, TAS
GeneRPAP2	AuthorityHGNC:25791	Mapping file id79871 NCBI file	EvidenceIEA, TAS
GeneRPRD1A	AuthorityHGNC:25560	Mapping file id55197 NCBI file	EvidenceIEA, TAS
GeneRPRD1B	AuthorityHGNC:16209	Mapping file id58490 NCBI file	EvidenceIEA, TAS
GeneRPRD2	AuthorityHGNC:29039	Mapping file id23248 NCBI file	EvidenceIEA, TAS
GeneSNAPC1	AuthorityHGNC:11134	Mapping file id6617 NCBI file	EvidenceIEA, TAS
GeneSNAPC2	AuthorityHGNC:11135	Mapping file id6618 NCBI file	EvidenceIEA, TAS
GeneSNAPC3	AuthorityHGNC:11136	Mapping file id6619 NCBI file	EvidenceIEA, TAS
GeneSNAPC4	AuthorityHGNC:11137	Mapping file id6621 NCBI file	EvidenceIEA, TAS
GeneSNAPC5	AuthorityHGNC:15484	Mapping file id10302 NCBI file	EvidenceIEA, TAS
GeneSP1	AuthorityHGNC:11205	Mapping file id6667 NCBI file	EvidenceIEA, TAS
GeneSRRT	AuthorityHGNC:24101	Mapping file id51593 NCBI file	EvidenceTAS
GeneSSU72	AuthorityHGNC:25016	Mapping file id29101 NCBI file	EvidenceTAS
GeneSUPT4H1	AuthorityHGNC:11467	Mapping file id6827 NCBI file	EvidenceTAS
GeneSUPT5H	AuthorityHGNC:11469	Mapping file id6829 NCBI file	EvidenceTAS
GeneTAF11	AuthorityHGNC:11544	Mapping file id6882 NCBI file	EvidenceIEA, TAS
GeneTAF13	AuthorityHGNC:11546	Mapping file id6884 NCBI file	EvidenceIEA, TAS
GeneTAF5	AuthorityHGNC:11539	Mapping file id6877 NCBI file	EvidenceIEA, TAS
GeneTAF6	AuthorityHGNC:11540	Mapping file id6878 NCBI file	EvidenceIEA, TAS
GeneTAF8	AuthorityHGNC:17300	Mapping file id129685 NCBI file	EvidenceIEA, TAS
GeneTAF9	AuthorityHGNC:11542	Mapping file id6880 NCBI file	EvidenceIEA, TAS
GeneTBP	AuthorityHGNC:11588	Mapping file id6908 NCBI file	EvidenceIEA, TAS
GeneZC3H8	AuthorityHGNC:30941	Mapping file id84524 NCBI file	EvidenceIEA, TAS
GeneZNF143	AuthorityHGNC:12928	Mapping file id7702 NCBI file	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

RNA Polymerase II TranscriptionR-HSA-738571,343 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.