RPAP3 Gene (Protein Coding)

RNA Polymerase II Associated Protein 3

GC12M047661
GIFtS:
33
This gene encodes an RNA polymerase II-associated protein. The encoded protein may function in transcriptional regulation and may also regulate apoptosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009] See more...

Aliases for RPAP3 Gene

Aliases for RPAP3 Gene

  • RNA Polymerase II Associated Protein 3 2 3 5
  • RNA Polymerase II-Associated Protein 3 3 4
  • HSpagh 2 3
  • Tah1 2 3
  • FLJ21908 2
  • RPAP3 5
  • Spag 2

External Ids for RPAP3 Gene

Previous GeneCards Identifiers for RPAP3 Gene

  • GC12M046344
  • GC12M048057
  • GC12M045086

Summaries for RPAP3 Gene

Entrez Gene Summary for RPAP3 Gene

  • This gene encodes an RNA polymerase II-associated protein. The encoded protein may function in transcriptional regulation and may also regulate apoptosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

GeneCards Summary for RPAP3 Gene

RPAP3 (RNA Polymerase II Associated Protein 3) is a Protein Coding gene. Diseases associated with RPAP3 include Primary Ciliary Dyskinesia. An important paralog of this gene is SPAG1.

UniProtKB/Swiss-Prot Summary for RPAP3 Gene

  • Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation.

Additional gene information for RPAP3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPAP3 Gene

Genomics for RPAP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RPAP3 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 RPAP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPAP3

Top Transcription factor binding sites by QIAGEN in the RPAP3 gene promoter:
  • AML1a
  • AP-1
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • PPAR-alpha

Genomic Locations for RPAP3 Gene

Genomic Locations for RPAP3 Gene
chr12:47,661,249-47,706,061
(GRCh38/hg38)
Size:
44,813 bases
Orientation:
Minus strand
chr12:48,055,715-48,099,844
(GRCh37/hg19)
Size:
44,130 bases
Orientation:
Minus strand

Genomic View for RPAP3 Gene

Genes around RPAP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPAP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPAP3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RPAP3 Gene

Proteins for RPAP3 Gene

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  2. Protein
  3. Assay

  • Protein details for RPAP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H6T3-RPAP3_HUMAN
    Recommended name:
    RNA polymerase II-associated protein 3
    Protein Accession:
    Q9H6T3
    Secondary Accessions:
    • B4DRW9
    • Q6PHR5

    Protein attributes for RPAP3 Gene

    Size:
    665 amino acids
    Molecular mass:
    75719 Da
    Quaternary structure:
    • Tightly associated with the RNA polymerase II complex (PubMed:17643375). Component of the R2TP complex composed at least of PIHD1, RUVBL1, RUVBL2 and RPAP3 (PubMed:20864032). Interacts with PIH1D1 (PubMed:21078300). Interacts with TSC1 and TSC2 (PubMed:28561026). Interacts with PRPF8 and EFTUD2 in a ZNHIT2-dependent manner (PubMed:28561026).

    Three dimensional structures from OCA and Proteopedia for RPAP3 Gene

    Alternative splice isoforms for RPAP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPAP3 Gene

Protein Expression for RPAP3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RPAP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RPAP3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RPAP3 Gene

Domains & Families for RPAP3 Gene

Gene Families for RPAP3 Gene

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

Protein Domains for RPAP3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RPAP3 Gene

GenScript: Design optimal peptide antigens:
  • RNA polymerase II-associated protein 3 (RPAP3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H6T3

UniProtKB/Swiss-Prot:

RPAP3_HUMAN :
  • Belongs to the RPAP3 family.
Family:
  • Belongs to the RPAP3 family.
genes like me logo Genes that share domains with RPAP3: view

Function for RPAP3 Gene

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  2. CRISPR
  3. miRNA
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Molecular function for RPAP3 Gene

UniProtKB/Swiss-Prot Function:
Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation.

Phenotypes From GWAS Catalog for RPAP3 Gene

Gene Ontology (GO) - Molecular Function for RPAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18538670
genes like me logo Genes that share ontologies with RPAP3: view
genes like me logo Genes that share phenotypes with RPAP3: view

Animal Model Products

CRISPR Products

miRNA for RPAP3 Gene

miRTarBase miRNAs that target RPAP3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPAP3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPAP3 Gene

Localization for RPAP3 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 RPAP3 gene
Compartment Confidence
cytosol 5
nucleus 3
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IDA --
GO:0036157 outer dynein arm IEA --
GO:0097255 R2TP complex IDA 26711270
genes like me logo Genes that share ontologies with RPAP3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RPAP3 Gene

Pathways & Interactions for RPAP3 Gene

PathCards logo

SuperPathways for RPAP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070286 axonemal dynein complex assembly IEA --
genes like me logo Genes that share ontologies with RPAP3: view

No data available for Pathways by source and SIGNOR curated interactions for RPAP3 Gene

Drugs & Compounds for RPAP3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RPAP3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RPAP3 Gene

3 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
7 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 RPAP3

Alternative Splicing Database (ASD) splice patterns (SP) for RPAP3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17
SP1: - -
SP2: - - -
SP3:
SP4:

Relevant External Links for RPAP3 Gene

GeneLoc Exon Structure for
RPAP3

Expression for RPAP3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPAP3 Gene

mRNA expression in normal human tissues for RPAP3 Gene
mRNA expression by GTEx for RPAP3 GenemRNA expression by BioGPS for RPAP3 Gene

Protein differential expression in normal tissues from HIPED for RPAP3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.6), Lymph node (13.3), and Breast (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RPAP3 Gene



Protein tissue co-expression partners for RPAP3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPAP3

SOURCE GeneReport for Unigene cluster for RPAP3 Gene:

Hs.437855

Evidence on tissue expression from TISSUES for RPAP3 Gene

  • Blood(4.4)
  • Liver(4.3)
  • Nervous system(3.1)
  • Skin(2.3)
  • Kidney(2.1)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with RPAP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPAP3 Gene

Orthologs for RPAP3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RPAP3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RPAP3 30 31
  • 99.35 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RPAP3 30 31
  • 91.7 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RPAP3 30 31
  • 90.51 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rpap3 30
  • 80.75 (n)
Mouse
(Mus musculus)
 Mammalia Rpap3 30 17 31
  • 80.29 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 78 (a)
 OneToMany
-- 31
  • 51 (a)
 OneToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia RPAP3 31
  • 55 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves RPAP3 30 31
  • 71.98 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RPAP3 31
  • 58 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rpap3 30
  • 63.07 (n)
Str.10319 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.4828 30
Zebrafish
(Danio rerio)
 Actinopterygii rpap3 30 31
  • 55.14 (n)
 OneToMany
RPAP3 (2 of 2) 31
  • 44 (a)
 OneToMany
zgc56178 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.9134 30
Fruit Fly
(Drosophila melanogaster)
 Insecta spag 30 31
  • 43.68 (n)
 ManyToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP005014 30
  • 42.28 (n)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes SGT2 31
  • 20 (a)
 OneToMany
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT1G56440 30
  • 46.65 (n)
Rice
(Oryza sativa)
 Liliopsida Os05g0129900 30
  • 48.58 (n)
Species where no ortholog for RPAP3 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for RPAP3 Gene

ENSEMBL:
Gene Tree for RPAP3 (if available)
TreeFam:
Gene Tree for RPAP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPAP3: view image

Paralogs for RPAP3 Gene

Paralogs for RPAP3 Gene

genes like me logo Genes that share paralogs with RPAP3: view

Variants for RPAP3 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPAP3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs11168196 - p.Asp564Tyr

Additional dbSNP identifiers (rs#s) for RPAP3 Gene

Structural Variations from Database of Genomic Variants (DGV) for RPAP3 Gene

Variant ID Type Subtype PubMed ID
esv2751101 CNV gain 17911159
nsv1050043 CNV gain 25217958
nsv517899 CNV gain 19592680
nsv518487 CNV loss 19592680
nsv695 CNV deletion 18451855

Variation tolerance for RPAP3 Gene

Residual Variation Intolerance Score: 22.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.59; 30.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPAP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPAP3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPAP3 Gene

Disorders for RPAP3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPAP3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
primary ciliary dyskinesia
  • pcd
- elite association - COSMIC cancer census association via MalaCards
Search RPAP3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RPAP3

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RPAP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPAP3 Gene

Publications for RPAP3 Gene

  1. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. (PMID: 17643375) Jeronimo C … Coulombe B (Molecular cell 2007) 2 3 4
  2. R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein. (PMID: 28561026) Cloutier P … Coulombe B (Nature communications 2017) 3 4
  3. CK2 phospho-dependent binding of R2TP complex to TEL2 is essential for mTOR and SMG1 stability. (PMID: 20864032) Horejsí Z … Boulton SJ (Molecular cell 2010) 3 4
  4. PIH1D1, a subunit of R2TP complex, inhibits doxorubicin-induced apoptosis. (PMID: 21078300) Inoue M … Kamisaki Y (Biochemical and biophysical research communications 2010) 3 4
  5. Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome. (PMID: 31738558) Cloutier P … Coulombe B (Journal of proteome research 2020) 3

ExternalLinks

View latest publications for RPAP3 gene in Mastermind

Products for RPAP3 Gene

  • Signalway Proteins for RPAP3

Sources for RPAP3 Gene