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

    Gene ID: 5431, updated on 14-Nov-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
    mouse all
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    Genomic context

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    See POLR2B in Genome Data Viewer
    Location:
    4q12
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (56978896..57031158)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (60470344..60522595)
    RS_2024_09 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 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. M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops. Lin H, et al. Cell Death Dis, 2024 Aug 1. PMID 39090090, Free PMC Article
    2. 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
    3. 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
    4. 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
    5. 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

    See all (288) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops.
      Title: M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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 Variation Viewer (GRCh37.p13)

    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 
    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
    		  
    contributes_to RNA polymerase II activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 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 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 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 mitochondrial transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in plastid transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 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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    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.

    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_2024_08

    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous