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

Gene ID: 5430, updated on 14-Apr-2024

Summary

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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
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Genomic context

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Location:
17p13.1
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7484366..7514616)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7388413..7418678)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7387685..7417933)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8121 Neighboring gene cholinergic receptor nicotinic beta 1 subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7359010-7359511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7368787-7369309 Neighboring gene zinc finger and BTB domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11623 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7386897-7387891 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7387892-7388885 Neighboring gene solute carrier family 35 member G6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:7405086-7406285 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:7414586-7415785 Neighboring gene TNFSF12-TNFSF13 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7458208-7458708 Neighboring gene TNF superfamily member 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7460817-7461610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11628 Neighboring gene TNF superfamily member 13

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression. Muñoz JC, et al. Genes (Basel), 2022 Oct 26. PMID 36360188, Free PMC Article
  2. Associations of pathological diagnosis and genetic abnormalities in meningiomas with the embryological origins of the meninges. Okano A, et al. Sci Rep, 2021 Mar 26. PMID 33772057, Free PMC Article
  3. RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells. Imada T, et al. Genes Cells, 2021 May. PMID 33608942, Free PMC Article
  4. The CTD Is Not Essential for the Post-Initiation Control of RNA Polymerase II Activity. Gerber A, et al. J Mol Biol, 2020 Sep 4. PMID 32707132, Free PMC Article
  5. Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses. Hosmillo M, et al. mBio, 2020 Mar 17. PMID 32184238, Free PMC Article

See all (604) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression.
    Title: DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. SPT5 stabilization of promoter-proximal RNA polymerase II.
    Title: SPT5 stabilization of promoter-proximal RNA polymerase II.
  9. 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.
  10. Associations of pathological diagnosis and genetic abnormalities in meningiomas with the embryological origins of the meninges.
    Title: Associations of pathological diagnosis and genetic abnormalities in meningiomas with the embryological origins of the meninges.
Submit: New GeneRIF Correction See all GeneRIFs (110)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

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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Markers

Homology

Clone Names

  • MGC75453

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 PubMed 
contributes_to RNA polymerase II activity IBA
Inferred from Biological aspect of Ancestor
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 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 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 II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
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 

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

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

  1. NG_027747.2 RefSeqGene

    Range
    4988..35236
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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
    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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    7484366..7514616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107299.1 Reference GRCh38.p14 PATCHES

    Range
    104823..135071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    7388413..7418678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P24928.2 GenPept UniProtKB/Swiss-Prot:P24928

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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