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

Gene ID: 5430, updated on 5-Jul-2020

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
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]
Expression
Ubiquitous expression in testis (RPKM 59.5), skin (RPKM 31.0) and 25 other tissues See more
Orthologs

Genomic context

See POLR2A in Genome Data Viewer
Location:
17p13.1
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (7484366..7514616)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7387698..7417935)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene cholinergic receptor nicotinic beta 1 subunit Neighboring gene zinc finger and BTB domain containing 4 Neighboring gene solute carrier family 35 member G6 Neighboring gene TNFSF12-TNFSF13 readthrough Neighboring gene TNF superfamily member 12 Neighboring gene TNF superfamily member 13

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND VARIABLE INTELLECTUAL AND BEHAVIORAL ABNORMALITIES
MedGen: C5231423 OMIM: 618603 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs).
NHGRI GWA Catalog

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC75453

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
contributes_to DNA-directed 5'-3' RNA polymerase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-directed 5'-3' RNA polymerase activity NAS
Non-traceable Author Statement
more info
PubMed 
RNA binding HDA PubMed 
contributes_to RNA polymerase II activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA-directed 5'-3' RNA polymerase activity IEA
Inferred from Electronic Annotation
more info
 
kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
promoter-specific chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
7-methylguanosine mRNA capping TAS
Traceable Author Statement
more info
 
DNA-templated transcription, termination IMP
Inferred from Mutant Phenotype
more info
PubMed 
RNA metabolic process TAS
Traceable Author Statement
more info
 
fibroblast growth factor receptor signaling pathway TAS
Traceable Author Statement
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
positive regulation of RNA splicing IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of viral transcription TAS
Traceable Author Statement
more info
 
regulation of gene silencing by miRNA TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
snRNA transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
somatic stem cell population maintenance TAS
Traceable Author Statement
more info
 
transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription elongation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
transcription, DNA-templated TAS
Traceable Author Statement
more info
 
transcription, RNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with Prp19 complex IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II, core complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II, core complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
DNA-directed RNA polymerase II subunit RPB1
Names
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)

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_000937.5NP_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
    P24928
    Related
    ENST00000617998.6
    Conserved Domains (5) summary
    cd02584
    Location:10581476
    RNAP_II_Rpb1_C; Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain
    smart01104
    Location:14911610
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    cd02733
    Location:19876
    RNAP_II_RPB1_N; Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain
    pfam05109
    Location:18541959
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam04992
    Location:8961079
    RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_016107299.1 Reference GRCh38.p13 PATCHES

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