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

    Gene ID: 5430, updated on 3-Nov-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
    mouse all
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    Genomic context

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    See POLR2A in Genome Data Viewer
    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_000017.11Genomic 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 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. RNA polymerase II stalled on a DNA template during transcription elongation is ubiquitinated and the ubiquitination facilitates displacement of the elongation complex. Yang LY, et al. Int J Oncol, 2003 Mar. PMID 12579324
    2. RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. Wang G, et al. PLoS One, 2010 Nov 2. PMID 21072189, Free PMC Article
    3. 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
    4. Kaposi's Sarcoma-Associated Herpesvirus Hijacks RNA Polymerase II To Create a Viral Transcriptional Factory. Chen CP, et al. J Virol, 2017 Jun 1. PMID 28331082, Free PMC Article
    5. 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

    See all (631) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. POLR2A Mutation is a Poor Prognostic Marker of Cerebellopontine Angle Meningioma.
      Title: POLR2A Mutation is a Poor Prognostic Marker of Cerebellopontine Angle Meningioma.
    2. 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.
    3. 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.
    4. DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression.
      Title: DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. SPT5 stabilization of promoter-proximal RNA polymerase II.
      Title: SPT5 stabilization of promoter-proximal RNA polymerase II.
    10. 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

    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 polymerase II activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 
    involved_in transcription by RNA polymerase II TAS
    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 
    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

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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, 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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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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