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POLR2D RNA polymerase II subunit D [ Homo sapiens (human) ]

Gene ID: 5433, updated on 27-Nov-2024

Summary

Official Symbol
POLR2Dprovided by HGNC
Official Full Name
RNA polymerase II subunit Dprovided by HGNC
Primary source
HGNC:HGNC:9191
See related
Ensembl:ENSG00000144231 MIM:606017; AllianceGenome:HGNC:9191
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
RBP4; RPB4; RPB16; HSRBP4; HSRPB4
Summary
This gene encodes the fourth largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. In yeast, this polymerase subunit is associated with the polymerase under suboptimal growth conditions and may have a stress protective role. A sequence for a ribosomal pseudogene is contained within the 3' untranslated region of the transcript from this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in testis (RPKM 27.2), lymph node (RPKM 9.2) and 25 other tissues See more
Orthologs
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Genomic context

See POLR2D in Genome Data Viewer
Location:
2q14.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (127843553..127858155, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (128278790..128293413, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (128601127..128615729, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16505 Neighboring gene MPRA-validated peak3858 silencer Neighboring gene ZFP91 pseudogene 1 Neighboring gene RNA, U6 small nuclear 395, pseudogene Neighboring gene ribosomal protein S26 pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11937 Neighboring gene uncharacterized LOC107985803 Neighboring gene AMMECR1 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:128643401-128643996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11941 Neighboring gene uncharacterized LOC107985944

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

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
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables translation initiation factor binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in transcription initiation at RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
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 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
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

Preferred Names
DNA-directed RNA polymerase II subunit RPB4
Names
DNA-directed RNA polymerase II 16 kDa polypeptide
DNA-directed RNA polymerase II subunit D
RNA polymerase II 16 kDa subunit
RNA polymerase II subunit B4
RNA polymerase II subunit hsRBP4
RNA polymerase II subunit hsRPB4
polymerase (RNA) II (DNA directed) polypeptide D
polymerase (RNA) II subunit D
NP_004796.1

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_004805.4NP_004796.1  DNA-directed RNA polymerase II subunit RPB4

    See identical proteins and their annotated locations for NP_004796.1

    Status: REVIEWED

    Source sequence(s)
    AA775787, AC006011, BC093795
    Consensus CDS
    CCDS2151.1
    UniProtKB/Swiss-Prot
    O15514, Q52LT4
    Related
    ENSP00000272645.3, ENST00000272645.9
    Conserved Domains (1) summary
    smart00657
    Location:24141
    RPOL4c; DNA-directed RNA-polymerase II subunit

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    127843553..127858155 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    128278790..128293413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)