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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 D 3 4
  • RNA Polymerase II Subunit HsRBP4 2 3
  • RNA Polymerase II 16 KDa Subunit 3 4
  • RNA Polymerase II Subunit B4 3 4
  • RPB16 3 4
  • DNA-Directed RNA Polymerase II 16 KDa Polypeptide 3
  • DNA-Directed RNA Polymerase II Subunit RPB4 3
  • Polymerase (RNA) II Subunit D 3
  • HSRBP4 3
  • HSRPB4 3
  • 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
  • GC02M127864
  • GC02M127872
  • GC02M127882

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 Myasthenic Syndrome, Congenital, 5 and Congenital Myasthenic Syndrome. Among its related pathways are HIV Life Cycle and Formation of HIV elongation complex in the absence of HIV Tat. GO annotations related to this gene include nucleotide binding and single-stranded RNA binding.

UniProtKB/Swiss-Prot 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for POLR2D Gene

Genomics for POLR2D Gene

Regulatory Elements for POLR2D Gene

Enhancers for POLR2D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G127857 1.6 FANTOM5 Ensembl ENCODE 28.9 -0.7 -668 3.6 HDGF PKNOX1 FOXA2 MLX CREB3L1 ZFP64 ARID4B SIN3A DMAP1 YY1 POLR2D PIR62035
GH02G127829 1.5 FANTOM5 Ensembl ENCODE 8.1 +27.8 27816 2.3 HDGF TBP PKNOX1 TBL1XR1 WRNIP1 BMI1 YBX1 ZBTB40 CBX5 ZNF143 ENSG00000260634 LIMS2 POLR2D MAP3K2 WDR33 ENSG00000200390 GC02M127830 LOC100131832
GH02G127695 1.3 FANTOM5 Ensembl ENCODE 7.9 +162.2 162162 1.2 CTCF MAX RAD21 JUND POLR2A HDAC2 CTBP2 SMC3 KDM1A SFT2D3 GPR17 POLR2D AMMECR1L MAP3K2 IWS1 LIMS2
GH02G127700 1.1 ENCODE 8.2 +156.3 156283 3.4 HDGF PKNOX1 MLX CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 AMMECR1L WDR33 POLR2D PIR38126 PIR55015
GH02G127658 1.2 Ensembl ENCODE dbSUPER 6 +197.5 197485 3.7 CTCF CEBPG ZIC2 ZFHX2 ZNF316 POLR2A NFYB EGR2 HLF CEBPB POLR2D PIR45039 PIR41862 GC02P127669
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around POLR2D on UCSC Golden Path with GeneCards custom track

Promoters for POLR2D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000122925 157 1601 PKNOX1 FOXA2 MLX CREB3L1 ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF143

Genomic Location for POLR2D Gene

Chromosome:
2
Start:
127,843,551 bp from pter
End:
127,858,157 bp from pter
Size:
14,607 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

Protein Domains for POLR2D Gene

Suggested Antigen Peptide Sequences for POLR2D Gene

GenScript: Design optimal peptide antigens:

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

GENATLAS Biochemistry:
polymerase II,RNA DNA directed,polypeptide D likely associating with POLR2G (RPB7)
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).

Gene Ontology (GO) - Molecular Function for POLR2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003697 contributes_to single-stranded DNA binding IBA --
GO:0003727 contributes_to single-stranded RNA binding IBA --
GO:0003824 catalytic activity IEA --
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

Clone Products

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

Gene Ontology (GO) - Cellular Components for POLR2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA --
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA,IDA 9852112
GO:0005654 nucleoplasm IDA,TAS --
GO:0005665 DNA-directed RNA polymerase II, core complex IDA 9528765
genes like me logo Genes that share ontologies with POLR2D: view

Pathways & Interactions for POLR2D Gene

SuperPathways for POLR2D Gene

SuperPathway Contained pathways
1 Formation of HIV elongation complex in the absence of HIV Tat
2 RNA Polymerase II Transcription Initiation And Promoter Clearance
3 mRNA Capping
4 HIV Life Cycle
.45
5 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
genes like me logo Genes that share pathways with POLR2D: view

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 --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006351 transcription, DNA-templated TAS,IEA --
GO:0006366 transcription from RNA polymerase II promoter TAS --
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
Adenosine triphosphate Approved Nutra 0
Cytidine triphosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
Uridine triphosphate Experimental Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with POLR2D: view

Transcripts for POLR2D Gene

Unigene Clusters for POLR2D Gene

Polymerase (RNA) II (DNA directed) polypeptide D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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
ECgene alternative splicing isoforms for
POLR2D

Expression for POLR2D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for POLR2D Gene



Protein tissue co-expression partners for POLR2D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of POLR2D Gene:

POLR2D

SOURCE GeneReport for Unigene cluster for POLR2D Gene:

Hs.715348

Evidence on tissue expression from TISSUES for POLR2D Gene

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

Primer Products

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 34 35
  • 99.53 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 99 (a)
OneToMany
-- 35
  • 86 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
-- 35
  • 80 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia POLR2D 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia POLR2D 34 35
  • 92.25 (n)
cow
(Bos Taurus)
Mammalia POLR2D 34 35
  • 91.55 (n)
rat
(Rattus norvegicus)
Mammalia Polr2d 34
  • 87.79 (n)
mouse
(Mus musculus)
Mammalia Polr2d 34 16 35
  • 87.56 (n)
chicken
(Gallus gallus)
Aves POLR2D 34 35
  • 83.1 (n)
lizard
(Anolis carolinensis)
Reptilia POLR2D 35
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia polr2d 34
  • 77.93 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8056 34
zebrafish
(Danio rerio)
Actinopterygii polr2d 34 35
  • 77.78 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2260 34
fruit fly
(Drosophila melanogaster)
Insecta Rpb4 34 35
  • 68.46 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001228 34
  • 64.49 (n)
worm
(Caenorhabditis elegans)
Secernentea rpb-4 34 35
  • 58.39 (n)
F43E2.2 36
  • 57 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPB4 35 37
  • 19 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons NRPB4 34
  • 51.52 (n)
rice
(Oryza sativa)
Liliopsida Os02g0116900 34
  • 49.75 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3457 35
  • 77 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4840 34
Species where no ortholog for POLR2D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

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

Sequence variations from dbSNP and Humsavar for POLR2D Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000311521 -- 127,856,292(+) TCTCA(A/G)AAAAA intron-variant
rs1000320983 -- 127,856,475(+) GTCCC(A/C)GCTAC intron-variant, upstream-variant-2KB
rs1000587245 -- 127,850,355(+) GAATC(A/G)CTTGA intron-variant
rs1001195528 -- 127,856,583(+) CCCTA(A/T)CTCAA intron-variant, upstream-variant-2KB
rs1001205437 -- 127,856,926(+) AGCTA(C/G)TCGGG intron-variant, upstream-variant-2KB

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)

Relevant External Links for POLR2D Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for POLR2D Gene

Disorders for POLR2D Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
myasthenic syndrome, congenital, 5
  • congenital myasthenic syndrome 5
congenital myasthenic syndrome
  • familial limb-girdle myasthenia
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for POLR2D

Genetic Association Database (GAD)
POLR2D
Human Genome Epidemiology (HuGE) Navigator
POLR2D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
POLR2D
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 E.A. (Mol. Cell. Biol. 1998) 2 3 4 64
  2. Genetic polymorphisms in 85 DNA repair genes and bladder cancer risk. (PMID: 19237606) Michiels S. … Benhamou S. (Carcinogenesis 2009) 3 46 64
  3. Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. (PMID: 16282592) Meka H. … Brick P. (Nucleic Acids Res. 2005) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  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 C.-M. (J. Biol. Chem. 1998) 3 4 64

Products for POLR2D Gene

Sources for POLR2D Gene

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