Tdark POLR2D DNA-directed RNA polymerase II subunit RPB4

Protein Summary

Description

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). 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]

Uniprot Accession IDs

• O15514
• Q52LT4
• RNA polymerase II subunit B4

Gene Name

• POLR2D

Ensembl ID

• ENST00000272645
• ENSP00000272645
• ENSG00000144231

Symbol

• RBP4
• RPB16
• HSRBP4
• HSRPB4

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological process	0.95
disease perturbation	0.9
kinase perturbation	0.88
transcription factor perturbation	0.84
histone modification site profile	0.81

Protein Classes

PANTHER Classes

Protein / Transcription Factor / Dna-directed Rna Polymerase Ii Subunit Rpb4

DTO Classes

Protein / Transcription Factor / Dna-directed Rna Polymerase Ii Subunit Rpb4

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 4.46   (req: < 5)

Gene RIFs: 3   (req: <= 3)

Antibodies: 174   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 4.46   (req: >= 5)

Gene RIFs: 3   (req: > 3)

Antibodies: 174   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 17

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

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No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (573)

Explore Interacting Targets

1 – 10 of 573

• See Interactions on String-DB

Q6EEV4

Tbio

Family:  Enzyme

Novelty:  0.11413088

p_int:  1

Score:  0.858

Data Source:  BioPlex,STRINGDB

RPRD1B

Tbio

Novelty:  0.0444394

p_int:  0.999999987

p_ni:  1.3e-8

Score:  0.98

Data Source:  BioPlex,STRINGDB

POLR2G

Tbio

Family:  Enzyme

Novelty:  0.01235379

p_int:  0.999999802

p_ni:  1.98e-7

Score:  0.999

Data Source:  BioPlex,STRINGDB

RECQL5

Tbio

Family:  Enzyme

Novelty:  0.01558497

p_int:  0.999922341

p_ni:  0.000077658

Score:  0.827

Data Source:  BioPlex,STRINGDB

RPAP2

Tbio

Family:  Enzyme

Novelty:  0.03383659

p_int:  0.999765861

p_ni:  0.000234139

Score:  0.991

Data Source:  BioPlex,STRINGDB

PIH1D1

Tbio

Novelty:  0.10737369

p_int:  0.999298249

p_ni:  0.000700874

p_wrong:  8.77e-7

Score:  0.725

Data Source:  BioPlex,STRINGDB

GPN3

Tbio

Family:  Enzyme

Novelty:  0.13817794

p_int:  0.999249167

p_ni:  0.000750833

Score:  0.804

Data Source:  BioPlex,STRINGDB

RPRD1A

Tbio

Novelty:  0.13521196

p_int:  0.999026448

p_ni:  0.000973542

p_wrong:  1e-8

Score:  0.98

Data Source:  BioPlex,STRINGDB

LMO2

Tbio

Novelty:  0.0038279

p_int:  0.997517528

p_ni:  0.002482468

p_wrong:  4e-9

Score:  0.555

Data Source:  BioPlex,STRINGDB

SYDE1

Tbio

Family:  Enzyme

Novelty:  0.04683299

p_int:  0.995407075

p_ni:  0.004592925

Score:  0.821

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (73)

Reactome (70)

KEGG (2)

WikiPathways (1)

Abortive elongation of HIV-1 transcript in the absence of Tat (R-HSA-167242)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Abortive elongation of HIV-1 transcript in the absence of Tat	23 targets	R-HSA-167242
Reactome	Activation of HOX genes during differentiation	90 targets	R-HSA-5619507
Reactome	Activation of anterior HOX genes in hindbrain development during early embryogenesis	90 targets	R-HSA-5617472
Reactome	DNA Repair	306 targets	R-HSA-73894
Reactome	Developmental Biology	1055 targets	R-HSA-1266738

Name	Explore in Pharos	Explore in Source
Abortive elongation of HIV-1 transcript in the absence of Tat	23 targets	R-HSA-167242
Activation of HOX genes during differentiation	90 targets	R-HSA-5619507
Activation of anterior HOX genes in hindbrain development during early embryogenesis	90 targets	R-HSA-5617472
DNA Repair	306 targets	R-HSA-73894
Developmental Biology	1055 targets	R-HSA-1266738

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (23)

Functions (3)

Components (6)

Processes (14)

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Items per page:

10

1 – 3 of 3

GO Term	Evidence	Assigned by
DNA-directed 5'-3' RNA polymerase activity	Inferred from Mutant Phenotype (IMP)	UniProtKB
translation initiation factor binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
nucleotide binding	Inferred from Electronic Annotation (IEA)	InterPro

Disease Associations (null)

No disease associations found

GWAS Traits (3)

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1 – 3 of 3

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
leukocyte count	EFO_0004308	1	1	1		33.1
high density lipoprotein cholesterol measurement	EFO_0004612	1	1	1		11.8
apolipoprotein A 1 measurement	EFO_0004614	1	1	1		10

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 3 of 3

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
leukocyte count	EFO_0004308	1		33.1
high density lipoprotein cholesterol measurement	EFO_0004612	1		11.8
apolipoprotein A 1 measurement	EFO_0004614	1		10

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Complete proteome
DNA-directed RNA polymerase
Nucleus
Reference proteome
Transcription

GWAS Trait Find Similar Targets

No Header	No Header
apolipoprotein A 1 measurement
high density lipoprotein cholesterol measurement
leukocyte count

IDG Resources

No IDG generated resources found

Orthologs (13)

1 – 5 of 13

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	RNA polymerase II subunit D	VGNC:8361	100612569
Macaque	RNA polymerase II subunit D		699945
Mouse	polymerase (RNA) II (DNA directed) polypeptide D	MGI:1916491	69241
Rat	RNA polymerase II subunit D	RGD:1308565	364834
Dog	RNA polymerase II subunit D	VGNC:44795	483863

Species	Name	OMA	EggNOG	Inparanoid
Chimp	RNA polymerase II subunit D
Macaque	RNA polymerase II subunit D
Mouse	polymerase (RNA) II (DNA directed) polypeptide D
Rat	RNA polymerase II subunit D
Dog	RNA polymerase II subunit D

Publication Statistics

PubMed Score 4.46

PubMed score by year

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PubTator Score 1.81

PubTator score by year

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Related Publications

Text Mined References (74)

GeneRif Annotations (3)

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10

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PMID	Year	Title