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

Gene ID: 5431, updated on 13-Mar-2020

Summary

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
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

Genomic context

See POLR2B in Genome Data Viewer
Location:
4q12
Exon count:
26
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (56978640..57031162)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (57844944..57897334)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RE1 silencing transcription factor Neighboring gene nitric oxide associated 1 Neighboring gene RNA, U6 small nuclear 998, pseudogene Neighboring gene insulin like growth factor binding protein 7 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 3 Neighboring gene IGFBP7 antisense RNA 1 Neighboring gene uncharacterized LOC107986283

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

NHGRI GWAS Catalog

Description
Genome-wide association study identifies two susceptibility loci for exudative age-related macular degeneration in the Japanese population.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

HIV-1 interactions

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 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
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

  • FLJ14133, FLJ40952

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to DNA-directed 5'-3' RNA polymerase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding HDA PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ribonucleoside binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
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 
membrane HDA PubMed 
colocalizes_with nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA-directed RNA polymerase II subunit RPB2
Names
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
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)

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_000938.3NP_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
    P30876
    UniProtKB/TrEMBL
    B4DH29
    Related
    ENSP00000312735.5, ENST00000314595.6
    Conserved Domains (1) summary
    PRK08565
    Location:271172
    PRK08565; DNA-directed RNA polymerase subunit B; Provisional
  2. NM_001303268.1NP_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, BU619780, DC323029
    Consensus CDS
    CCDS77916.1
    UniProtKB/Swiss-Prot
    P30876
    UniProtKB/TrEMBL
    A0A1W2PPT5, B4DH29
    Related
    ENSP00000491706.1, ENST00000639658.1
    Conserved Domains (1) summary
    cl27131
    Location:71097
    RNA_pol_Rpb2_7; RNA polymerase Rpb2, domain 7
  3. NM_001303269.1NP_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, BU619780, DC323029
    Consensus CDS
    CCDS77915.1
    UniProtKB/Swiss-Prot
    P30876
    UniProtKB/TrEMBL
    B4DH29, B4DHJ3, C9J2Y9
    Related
    ENSP00000391452.2, ENST00000441246.6
    Conserved Domains (1) summary
    cl27131
    Location:201165
    RNA_pol_Rpb2_7; RNA polymerase Rpb2, domain 7

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_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    56978640..57031162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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