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POLR2B RNA polymerase II subunit B [ Homo sapiens (human) ]

Gene ID: 5431, updated on 14-Apr-2024

Summary

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Official Symbol
POLR2Bprovided by HGNC
Official Full Name
RNA polymerase II subunit Bprovided by HGNC
Primary source
HGNC:HGNC:9188
See related
Ensembl:ENSG00000047315 MIM:180661; AllianceGenome:HGNC:9188
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
RPB2; POL2RB; hRPB140
Summary
This gene encodes the second largest subunit of RNA polymerase II (Pol II), a DNA-dependent RNA polymerase that catalyzes the transcription of DNA into precursors of mRNA, snRNA and microRNA. This subunit and the largest subunit form opposite sides of the center cleft of Pol II. Deletion of the flap loop region of this subunit results in a decrease in the rate of transcriptional elongation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in lymph node (RPKM 28.6), testis (RPKM 28.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q12
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (56978896..57031158)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (60470344..60522595)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (57845062..57897324)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:57773523-57774452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:57775383-57776312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:57780934-57781434 Neighboring gene RE1 silencing transcription factor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:57802865-57804064 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:57831417-57831519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21588 Neighboring gene nitric oxide associated 1 Neighboring gene uncharacterized LOC124900913 Neighboring gene RNA, U6 small nuclear 998, pseudogene Neighboring gene Sharpr-MPRA regulatory region 7637 Neighboring gene insulin like growth factor binding protein 7 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 3 Neighboring gene small nucleolar RNA U13

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. The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation. Palangat M, et al. Mol Cell Biol, 2011 Aug. PMID 21670157, Free PMC Article
  2. Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Nechaev S, et al. Biochim Biophys Acta, 2011 Jan. PMID 21081187, Free PMC Article
  3. The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II. Langelier MF, et al. Nucleic Acids Res, 2005. PMID 15886393, Free PMC Article
  4. Primary structure of the second largest subunit of human RNA polymerase II (or B). Acker J, et al. J Mol Biol, 1992 Aug 20. PMID 1518060
  5. ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control. Lykke-Andersen S, et al. Biochem Soc Trans, 2021 Jun 30. PMID 34060620

See all (260) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The RNA polymerase II subunit B (RPB2) functions as a growth regulator in human glioblastoma.
    Title: The RNA polymerase II subunit B (RPB2) functions as a growth regulator in human glioblastoma.
  2. 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.
  3. Studies indicate transcription of many genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region.
    Title: Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator)
    Title: Genetic polymorphisms in 85 DNA repair genes and bladder cancer risk.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Polymorphism discovery in 62 DNA repair genes and haplotype associations with risks for lung and head and neck cancers.
  7. Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation
    Title: Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation.
  8. The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of magnesium and is required for both for the polymerization and cleavage reactions.
    Title: The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II.
  9. the human Maf1 protein negatively regulates transcription by all three nuclear Pols, Pol I, Pol II and Pol III
    Title: Mammalian Maf1 is a negative regulator of transcription by all three nuclear RNA polymerases.
  10. By reducing transcriptional fidelity in terms of not only discrimination of incoming nucleotides but also recognition of templates, HDAg may facilitate the unusual RNA-dependent RNA synthesis by Pol II.
    Title: Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study identifies two susceptibility loci for exudative age-related macular degeneration in the Japanese population.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
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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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 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 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
Vif vif HIV-1 Vif interacts with POLR2B; predicted interaction to be relevant to gene regulation 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

  • FLJ14133, FLJ40952

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-directed 5'-3' RNA polymerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
contributes_to RNA polymerase II activity IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to RNA polymerase II activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA-dependent RNA polymerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribonucleoside binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
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 
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA-directed RNA polymerase II subunit RPB2
Names
3'-5' exoribonuclease
DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-directed RNA polymerase II subunit B
RNA polymerase II second largest subunit
RNA polymerase II subunit 2
RNA polymerase II subunit B2
RNA-directed RNA polymerase II subunit RPB2
polymerase (RNA) II (DNA directed) polypeptide B, 140kDa
polymerase (RNA) II subunit B
NP_000929.1
NP_001290197.1
NP_001290198.1

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.

mRNA and Protein(s)

  1. NM_000938.3 → NP_000929.1  DNA-directed RNA polymerase II subunit RPB2 isoform 1

    See identical proteins and their annotated locations for NP_000929.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK294901, BC023503
    Consensus CDS
    CCDS3511.1
    UniProtKB/Swiss-Prot
    A8K1A8, P30876, Q8IZ61
    UniProtKB/TrEMBL
    B4DHJ3
    Related
    ENSP00000312735.5, ENST00000314595.6
    Conserved Domains (1) summary
    PRK08565
    Location:27 → 1172
    PRK08565; DNA-directed RNA polymerase subunit B; Provisional

  2. NM_001303268.2 → NP_001290197.1  DNA-directed RNA polymerase II subunit RPB2 isoform 2

    See identical proteins and their annotated locations for NP_001290197.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks an alternate exon in the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. This results in isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK294901, BC023503
    UniProtKB/TrEMBL
    B4DH29
    Related
    ENSP00000391096.3, ENST00000431623.6
    Conserved Domains (1) summary
    PRK08565
    Location:7 → 1097
    PRK08565; DNA-directed RNA polymerase subunit B; Provisional

  3. NM_001303269.2 → NP_001290198.1  DNA-directed RNA polymerase II subunit RPB2 isoform 3

    See identical proteins and their annotated locations for NP_001290198.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in its 5' UTR and initiates translation at an in-frame downstream start codon, compared to variant 1. This results in isoform 3, which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AK294901, AK295132, BC023503
    Consensus CDS
    CCDS77915.1
    UniProtKB/TrEMBL
    B4DHJ3, C9J2Y9
    Related
    ENSP00000391452.2, ENST00000441246.6
    Conserved Domains (1) summary
    PRK08565
    Location:20 → 1165
    PRK08565; DNA-directed RNA polymerase subunit B; Provisional

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    56978896..57031158
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    60470344..60522595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P30876.1 GenPept UniProtKB/Swiss-Prot:P30876

Gene LinkOut

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

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