POLR2A RNA polymerase II subunit A [Homo sapiens (human)] - Gene

Summary

Official Symbol: POLR2Aprovided by HGNC
Official Full Name: RNA polymerase II subunit Aprovided by HGNC
Primary source: HGNC:HGNC:9187
See related: Ensembl:ENSG00000181222 MIM:180660; AllianceGenome:HGNC:9187
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RPB1; RPO2; POLR2; POLRA; RPBh1; RPOL2; NEDHIB; RpIILS; hsRPB1; hRPB220
Summary: This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains a carboxy terminal domain composed of heptapeptide repeats that are essential for polymerase activity. These repeats contain serine and threonine residues that are phosphorylated in actively transcribing RNA polymerase. In addition, this subunit, in combination with several other polymerase subunits, forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. [provided by RefSeq, Jul 2008]
Annotation information: Annotation category: suggests misassembly
Expression: Ubiquitous expression in testis (RPKM 59.5), skin (RPKM 31.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.1

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (7484366..7514616)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (7388413..7418678)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (7387685..7417933)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

POLR2A Mutation is a Poor Prognostic Marker of Cerebellopontine Angle Meningioma.
Title: POLR2A Mutation is a Poor Prognostic Marker of Cerebellopontine Angle Meningioma.
HIV-1 Transcriptional Activator Tat Inhibits IL2 Expression by Preventing the Presence of Pol II on the IL2 Promoter.
Title: HIV-1 Transcriptional Activator Tat Inhibits IL2 Expression by Preventing the Presence of Pol II on the IL2 Promoter.
ERK-mediated NELF-A phosphorylation promotes transcription elongation of immediate-early genes by releasing promoter-proximal pausing of RNA polymerase II.
Title: ERK-mediated NELF-A phosphorylation promotes transcription elongation of immediate-early genes by releasing promoter-proximal pausing of RNA polymerase II.
DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression.
Title: DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression.
CircPOLR2A Promotes Proliferation and Impedes Apoptosis of Glioblastoma Multiforme Cells by Up-regulating POU3F2 to Facilitate SOX9 Transcription.
Title: CircPOLR2A Promotes Proliferation and Impedes Apoptosis of Glioblastoma Multiforme Cells by Up-regulating POU3F2 to Facilitate SOX9 Transcription.
ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia.
Title: ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia.
Micro-RNA378a-3p Induces Apoptosis in Sarcomatoid Renal Cell Carcinoma and Regulates POLR2A and RUNX2 Expression.
Title: Micro-RNA378a-3p Induces Apoptosis in Sarcomatoid Renal Cell Carcinoma and Regulates POLR2A and RUNX2 Expression.
ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control.
Title: ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control.
SPT5 stabilization of promoter-proximal RNA polymerase II.
Title: SPT5 stabilization of promoter-proximal RNA polymerase II.
Telomerase RNA recruits RNA polymerase II to target gene promoters to enhance myelopoiesis.
Title: Telomerase RNA recruits RNA polymerase II to target gene promoters to enhance myelopoiesis.

Submit: New GeneRIF Correction See all GeneRIFs (111)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities MedGen: C5231423 OMIM: 618603 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs). EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of polymerase (RNA) II (DNA directed) polypeptide A (POLR2A, 220kDa) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	The transcription factors and kinases c-Jun, JNK, MEK, p38 MAPK, STAT-3, JAK-1, TFII D, TFII F, eIF-4E, and RNA polymerase II are induced by HIV-1 gp120	PubMed
Tat	tat	The interaction of Tip110 with HIV-1 Tat leads to a higher efficiency of elongation for RNAPII complexes formed on the LTR promoter	PubMed
	tat	Expression of both Tip110 and Tat enhances phosphorylation of RNAPII at both serine 2 and serine 5, which account for Tip110 function in transcription activation	PubMed
	tat	The interaction of Tip110 with HIV-1 Tat and the RNAPII C-terminal domain leads to the recruitment of increased CDK9/CycT1 to the transcription complex	PubMed
	tat	HIV-1 Tat complexes with RNA polymerase II and cellular transcription factors as part of the HIV-1 transcription preinitiation and elongation complexes and stimulates RNA polymerase II processivity by inducing the phosphorylation of its C-terminal Domain	PubMed
	tat	A small molecule compound C3 inhibits HIV-1 replication by suppressing HIV-1 Tat-mediated HIV-1 LTR-driven gene expression and phosphorylation of RNAPII through inhibition of Tat binding to CycT1	PubMed
	tat	JQ1, a small molecule inhibitor of Brd4, directly dissociates Brd4 from HIV-1 promoter and promotes subsequently HIV-1 Tat binding to HIV-1 promoter, resulting in increased phosphorylation of RNA polymerase II and viral transcription	PubMed
	tat	HIV-1 I39Q Tat mutant shows reduced phosphorylation of the RNAP II C-terminal domain compared to the WT Tat. The Q35L mutation dramatically rescues this function	PubMed
	tat	HIV-1 Tat 41/44 peptide TAALS from the core domain of Tat inhibits Tat-mediated HIV-1 gene expression and replication by binding the Cdk2/Cyclin E complex and inhibiting the phosphorylation of serine 5 of RNAPII	PubMed
	tat	HIV-1 Tat, through its basic domain (amino acids 52-57) specifically interacts with the largest subunit of RNA polymerase II (amino acids 1325-1630)	PubMed
Vif	vif	HIV-1 Vif interacts with POL2A; predicted interaction to be relevant to gene regulation	PubMed
Vpr	vpr	HIV-1 Vpr interacts with basal transcription complexes such as P-TEFb, TFIIH, TFIID (TBP) and TFIIB which activate RNA polymerase II gene transcription	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80168 (e-PCR)
- UniSTS:91921

WI-1288 (e-PCR)
- UniSTS:39990

WI-16243 (e-PCR)
- UniSTS:7743

G43606 (e-PCR)
- UniSTS:95041

NoName (e-PCR)
- UniSTS:225108

RH104382 (e-PCR)
- UniSTS:98707

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	NAS Non-traceable Author Statement more info	PubMed
enables DNA-directed 5'-3' RNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-directed 5'-3' RNA polymerase activity	NAS Non-traceable Author Statement more info	PubMed
enables RNA binding	HDA more info	PubMed
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
enables RNA polymerase II activity	TAS Traceable Author Statement more info	PubMed
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
enables RNA-dependent RNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables microfibril binding	EXP Inferred from Experiment more info	PubMed
enables microfibril binding	IDA Inferred from Direct Assay more info	PubMed
enables mitochondrial single subunit type RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables plastid single subunit type RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription termination	IMP Inferred from Mutant Phenotype more info	PubMed
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 positive regulation of RNA splicing	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in transcription by RNA polymerase I	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement 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

Component	Evidence Code	Pubs
part_of Prp19 complex	IDA Inferred from Direct Assay more info	PubMed
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 chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
NOT located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
is_active_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: DNA-directed RNA polymerase II subunit RPB1

Names: 3'-5' exoribonuclease; DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit; DNA-directed RNA polymerase II subunit A; DNA-directed RNA polymerase III largest subunit; RNA polymerase II subunit B1; RNA-directed RNA polymerase II subunit RPB1; polymerase (RNA) II (DNA directed) polypeptide A, 220kDa; polymerase (RNA) II subunit A

NP_000928.1

EC 2.7.7.48

EC 2.7.7.6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_027747.2 RefSeqGene

Range

4988..35236

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000937.5 → NP_000928.1 DNA-directed RNA polymerase II subunit RPB1

See identical proteins and their annotated locations for NP_000928.1

Status: REVIEWED

Source sequence(s)

AC113189, AW589665, BC137231, BQ353795, BU730469, X63564

UniProtKB/Swiss-Prot

A6NN93, B9EH88, P24928, Q6NX41

UniProtKB/TrEMBL

A0A6Q8PGB0, A0AAG2TJB2

Related

ENST00000617998.6

Conserved Domains (5) summary

cd02584
Location:1058 → 1476

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

smart01104
Location:1491 → 1610

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

cd02733
Location:19 → 876

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

pfam05109
Location:1854 → 1959

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

pfam04992
Location:896 → 1079

RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6