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 transc... See more...

Aliases for POLR2D Gene

Aliases for POLR2D Gene

  • RNA Polymerase II Subunit D 2 3 5
  • Polymerase (RNA) II (DNA Directed) Polypeptide D 2 3
  • DNA-Directed RNA Polymerase II Subunit RPB4 3 4
  • DNA-Directed RNA Polymerase II Subunit D 3 4
  • RNA Polymerase II Subunit HsRPB4 2 3
  • RNA Polymerase II 16 KDa Subunit 3 4
  • RNA Polymerase II Subunit B4 3 4
  • RPB16 3 4
  • RPB4 2 3
  • DNA-Directed RNA Polymerase II 16 KDa Polypeptide 3
  • RNA Polymerase II Subunit HsRBP4 3
  • Polymerase (RNA) II Subunit D 3
  • HSRBP4 3
  • HSRPB4 3
  • POLR2D 5
  • RBP4 3

External Ids for POLR2D Gene

Previous GeneCards Identifiers for POLR2D Gene

  • GC02M125901
  • GC02M126528
  • GC02M128509
  • GC02M128697
  • GC02M128320
  • GC02M128606
  • GC02M120910
  • GC02M128608
  • GC02M128620
  • GC02M128637
  • GC02M128649
  • GC02M128663
  • GC02M127847
  • GC02M127855
  • GC02M127930
  • GC02M127936
  • GC02M127939
  • GC02M127963
  • GC02M127864
  • GC02M127872
  • GC02M127882
  • GC02M127890
  • GC02M127897
  • GC02M127905
  • GC02M127912
  • GC02M127920

Summaries for POLR2D Gene

Entrez Gene Summary for POLR2D Gene

  • 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]

GeneCards Summary for POLR2D Gene

POLR2D (RNA Polymerase II Subunit D) is a Protein Coding gene. Diseases associated with POLR2D include Nemaline Myopathy 7 and Leukodystrophy, Hypomyelinating, 10. Among its related pathways are Transcription-Coupled Nucleotide Excision Repair (TC-NER) and Signaling by FGFR2 in disease. Gene Ontology (GO) annotations related to this gene include nucleotide binding and single-stranded RNA binding.

UniProtKB/Swiss-Prot Summary for POLR2D Gene

  • DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity).

Gene Wiki entry for POLR2D Gene

Additional gene information for POLR2D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for POLR2D Gene

Genomics for POLR2D Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for POLR2D Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around POLR2D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for POLR2D

Top Transcription factor binding sites by QIAGEN in the POLR2D gene promoter:
  • CUTL1
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • POU2F1
  • POU2F1a
  • SRF
  • ZIC2

Genomic Locations for POLR2D Gene

Genomic Locations for POLR2D Gene
chr2:127,843,553-127,858,155
(GRCh38/hg38)
Size:
14,603 bases
Orientation:
Minus strand
chr2:128,603,840-128,615,731
(GRCh37/hg19)
Size:
11,892 bases
Orientation:
Minus strand

Genomic View for POLR2D Gene

Genes around POLR2D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POLR2D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POLR2D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POLR2D Gene

Proteins for POLR2D Gene

  • Protein details for POLR2D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15514-RPB4_HUMAN
    Recommended name:
    DNA-directed RNA polymerase II subunit RPB4
    Protein Accession:
    O15514
    Secondary Accessions:
    • Q52LT4

    Protein attributes for POLR2D Gene

    Size:
    142 amino acids
    Molecular mass:
    16311 Da
    Quaternary structure:
    • Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex.

    Three dimensional structures from OCA and Proteopedia for POLR2D Gene

neXtProt entry for POLR2D Gene

Post-translational modifications for POLR2D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for POLR2D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for POLR2D Gene

Domains & Families for POLR2D Gene

Gene Families for POLR2D Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for POLR2D Gene

InterPro:
Blocks:
  • RNA polymerase Rpb4
ProtoNet:

Suggested Antigen Peptide Sequences for POLR2D Gene

GenScript: Design optimal peptide antigens:
  • RNA polymerase II 16 kDa subunit (RPB4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15514

UniProtKB/Swiss-Prot:

RPB4_HUMAN :
  • Belongs to the eukaryotic RPB4 RNA polymerase subunit family.
Family:
  • Belongs to the eukaryotic RPB4 RNA polymerase subunit family.
genes like me logo Genes that share domains with POLR2D: view

Function for POLR2D Gene

Molecular function for POLR2D Gene

UniProtKB/Swiss-Prot Function:
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity).
GENATLAS Biochemistry:
polymerase II,RNA DNA directed,polypeptide D likely associating with POLR2G (RPB7)

Phenotypes From GWAS Catalog for POLR2D Gene

Gene Ontology (GO) - Molecular Function for POLR2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003824 catalytic activity IEA --
GO:0003899 contributes_to DNA-directed 5'-3' RNA polymerase activity IBA,IMP 9528765
GO:0031369 translation initiation factor binding IBA 21873635
genes like me logo Genes that share ontologies with POLR2D: view
genes like me logo Genes that share phenotypes with POLR2D: view

Animal Model Products

CRISPR Products

miRNA for POLR2D Gene

miRTarBase miRNAs that target POLR2D

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POLR2D

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for POLR2D Gene

Localization for POLR2D Gene

Subcellular locations from UniProtKB/Swiss-Prot for POLR2D Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for POLR2D gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for POLR2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA 21873635
GO:0005634 nucleus IEA,IDA 9852112
GO:0005654 nucleoplasm IDA,TAS --
GO:0005665 RNA polymerase II, core complex IDA 9528765
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with POLR2D: view

Pathways & Interactions for POLR2D Gene

PathCards logo

SuperPathways for POLR2D Gene

SuperPathway Contained pathways
1 HIV Transcription Elongation
2 RNA Polymerase II Transcription Initiation And Promoter Clearance
.91
.91
.33
3 HIV Life Cycle
.45
4 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
5 Signaling by FGFR2 in disease
genes like me logo Genes that share pathways with POLR2D: view

Pathways by source for POLR2D Gene

3 GeneGo (Thomson Reuters) pathways for POLR2D Gene
  • ATP/ITP metabolism
  • DNA damage_Role of Brca1 and Brca2 in DNA repair
  • Transcription Ligand-Dependent Transcription of Retinoid-Target genes
2 Qiagen pathways for POLR2D Gene
  • Assembly of RNA Polymerase-II Initiation Complex
  • Transcription of mRNA

Gene Ontology (GO) - Biological Process for POLR2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IBA 21873635
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006351 transcription, DNA-templated TAS --
GO:0006352 DNA-templated transcription, initiation IEA --
genes like me logo Genes that share ontologies with POLR2D: view

No data available for SIGNOR curated interactions for POLR2D Gene

Drugs & Compounds for POLR2D Gene

(4) Drugs for POLR2D Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cytidine triphosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
Uridine triphosphate Experimental, Investigational Pharma 0
ATP Investigational Nutra Agonist, Activator, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

(1) Additional Compounds for POLR2D Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
14000-31-8
genes like me logo Genes that share compounds with POLR2D: view

Transcripts for POLR2D Gene

mRNA/cDNA for POLR2D Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POLR2D

Alternative Splicing Database (ASD) splice patterns (SP) for POLR2D Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e
SP1: - -
SP2: -
SP3: - - -
SP4: - - -
SP5: -
SP6: - - - -

Relevant External Links for POLR2D Gene

GeneLoc Exon Structure for
POLR2D

Expression for POLR2D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for POLR2D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for POLR2D Gene

This gene is overexpressed in Testis (x4.4).

Protein differential expression in normal tissues from HIPED for POLR2D Gene

This gene is overexpressed in Peripheral blood mononuclear cells (37.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for POLR2D Gene



Protein tissue co-expression partners for POLR2D Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for POLR2D

SOURCE GeneReport for Unigene cluster for POLR2D Gene:

Hs.715348

Evidence on tissue expression from TISSUES for POLR2D Gene

  • Skin(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with POLR2D: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for POLR2D Gene

Orthologs for POLR2D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for POLR2D Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia POLR2D 30 31
  • 99.53 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia POLR2D 31
  • 99 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 99 (a)
OneToMany
-- 31
  • 86 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
-- 31
  • 80 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia POLR2D 30 31
  • 92.25 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia POLR2D 30 31
  • 91.55 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Polr2d 30
  • 87.79 (n)
Mouse
(Mus musculus)
Mammalia Polr2d 30 17 31
  • 87.56 (n)
OneToOne
Chicken
(Gallus gallus)
Aves POLR2D 30 31
  • 83.1 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia POLR2D 31
  • 96 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia polr2d 30
  • 77.93 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8056 30
Zebrafish
(Danio rerio)
Actinopterygii polr2d 30 31
  • 77.78 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2260 30
Fruit Fly
(Drosophila melanogaster)
Insecta Rpb4 30 31
  • 68.46 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001228 30
  • 64.49 (n)
Worm
(Caenorhabditis elegans)
Secernentea rpb-4 30 31
  • 58.39 (n)
OneToOne
F43E2.2 32
  • 57 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPB4 31 33
  • 19 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons NRPB4 30
  • 51.52 (n)
Rice
(Oryza sativa)
Liliopsida Os02g0116900 30
  • 49.75 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3457 31
  • 77 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4840 30
Species where no ortholog for POLR2D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for POLR2D Gene

ENSEMBL:
Gene Tree for POLR2D (if available)
TreeFam:
Gene Tree for POLR2D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for POLR2D: view image

Paralogs for POLR2D Gene

Pseudogenes.org Pseudogenes for POLR2D Gene

genes like me logo Genes that share paralogs with POLR2D: view

No data available for Paralogs for POLR2D Gene

Variants for POLR2D Gene

Additional dbSNP identifiers (rs#s) for POLR2D Gene

Structural Variations from Database of Genomic Variants (DGV) for POLR2D Gene

Variant ID Type Subtype PubMed ID
esv3402278 CNV insertion 20981092

Variation tolerance for POLR2D Gene

Residual Variation Intolerance Score: 57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.06; 1.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for POLR2D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
POLR2D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for POLR2D Gene

Disorders for POLR2D Gene

MalaCards: The human disease database

(3) MalaCards diseases for POLR2D Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for POLR2D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with POLR2D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for POLR2D Gene

Publications for POLR2D Gene

  1. Analysis of the interaction of the novel RNA polymerase II (pol II) subunit hsRPB4 with its partner hsRPB7 and with pol II. (PMID: 9528765) Khazak V … Golemis EA (Molecular and cellular biology 1998) 2 3 4
  2. Genetic polymorphisms in 85 DNA repair genes and bladder cancer risk. (PMID: 19237606) Michiels S … Benhamou S (Carcinogenesis 2009) 3 41
  3. Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. (PMID: 16282592) Meka H … Brick P (Nucleic acids research 2005) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Immunoaffinity purification and functional characterization of human transcription factor IIH and RNA polymerase II from clonal cell lines that conditionally express epitope-tagged subunits of the multiprotein complexes. (PMID: 9852112) Kershnar E … Chiang CM (The Journal of biological chemistry 1998) 3 4

Products for POLR2D Gene

Sources for POLR2D Gene