RPO21 DNA-directed RNA polymerase II core subunit RPO21 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: RPO21
Official Full Name: DNA-directed RNA polymerase II core subunit RPO21
Primary source: SGD:S000002299
Locus tag: YDL140C
See related: AllianceGenome:SGD:S000002299; FungiDB:YDL140C; VEuPathDB:YDL140C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: RPB1; RPB220; SIT1; SUA8
Summary: Enables DNA binding activity. Contributes to RNA polymerase II activity and RNA-dependent RNA polymerase activity. Involved in transcription by RNA polymerase II and translesion synthesis. Located in cytoplasmic stress granule; mitochondrion; and nucleus. Part of RNA polymerase II, core complex. Used to study Cockayne syndrome. Orthologous to human POLR2A (RNA polymerase II subunit A). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See RPO21 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (205360..210561, complement)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs.
Title: Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs.
Contractions of the C-Terminal Domain of Saccharomyces cerevisiae Rpb1p Are Mediated by Rad5p.
Title: Contractions of the C-Terminal Domain of Saccharomyces cerevisiae Rpb1p Are Mediated by Rad5p.
A SUMO-dependent pathway controls elongating RNA Polymerase II upon UV-induced damage.
Title: A SUMO-dependent pathway controls elongating RNA Polymerase II upon UV-induced damage.
Data show that a mutation in the universally conserved hinge region of the trigger loop, E1103G, induces a gain of function in the RNA Polymerase II (Pol II) elongation rate, whereas the corresponding mutation in RNA Polymerase I (Pol I), E1224G, results in a loss of function.
Title: A Novel Assay for RNA Polymerase I Transcription Elongation Sheds Light on the Evolutionary Divergence of Eukaryotic RNA Polymerases.
Results provide evidence that Bur1 phosphorylates residues in the Rpb1 linker region.
Title: Selective Kinase Inhibition Shows That Bur1 (Cdk9) Phosphorylates the Rpb1 Linker In Vivo.
The absence of the catalytic domains of Saccharomyces cerevisiae DNA polymerase epsilon strongly reduces DNA replication fidelity.
Title: The absence of the catalytic domains of Saccharomyces cerevisiae DNA polymerase ϵ strongly reduces DNA replication fidelity.
findings demonstrate that Ccr4-Not controls the ubiquitylation and turnover of Rpb1, the largest subunit of RNAPII, during transcription arrest
Title: Ccr4-Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII.
Here, the authors identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex.
Title: RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit.
The authors determined that the tandem SH2 domain of Saccharomyces cerevisiae Spt6 binds the linker region of the RNA polymerase II subunit Rpb1 rather than the expected sites in its heptad repeat domain. The 4 nM binding affinity requires phosphorylation at Rpb1 S1493 and either T1471 or Y1473.
Title: A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription.
Data suggest the binding motif in the RPB1 (RPO21) switch 1 of RNA polymerase II (pol II) can sense the structural changes of the DNA minor groove (minor groove sensor) before duplex unwinding.
Title: RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif.

Submit: New GeneRIF Correction See all GeneRIFs (31)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables 5'-3' RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-directed 5'-3' RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase I activity	IEA Inferred from Electronic Annotation more info
contributes_to RNA polymerase II activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to RNA polymerase II activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase III activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase IV activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase V activity	IEA Inferred from Electronic Annotation more info
contributes_to RNA-dependent RNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables mitochondrial single subunit type RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables plastid single subunit type RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial transcription	IEA Inferred from Electronic Annotation more info
involved_in plastid transcription	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase I	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase III	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase IV	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase V	IEA Inferred from Electronic Annotation more info
involved_in translesion synthesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of DNA-directed RNA polymerase complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II, core complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase II, core complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic stress granule	HDA more info	PubMed
located_in mitochondrion	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA-directed RNA polymerase II core subunit RPO21

NP_010141.1

EC 2.7.7.6

RNA polymerase II largest subunit B220; part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001136.10 Reference assembly

Range

205360..210561 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180200.1 → NP_010141.1 TPA: DNA-directed RNA polymerase II core subunit RPO21 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010141.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VRK8, P04050, Q12364, Q92315

UniProtKB/TrEMBL

A6ZXI7, C7GKZ2, G2WC21, N1PAM7

Conserved Domains (4) summary

cd02584
Location:1035 → 1446

RNAP_II_Rpb1_C; Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

cd02733
Location:15 → 853

RNAP_II_RPB1_N; Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain

pfam04992
Location:873 → 1056

RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6

pfam05001
Location:1698 → 1709

RNA_pol_Rpb1_R; RNA polymerase Rpb1 C-terminal repeat