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Aliases for RPAP3 Gene

Aliases for RPAP3 Gene

  • RNA Polymerase II Associated Protein 3 2 3 5
  • RNA Polymerase II-Associated Protein 3 3
  • HSpagh 3

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. An important paralog of this gene is TTC12.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for RPAP3 Gene

Genomics for RPAP3 Gene

GeneHancer (GH) Regulatory Elements for RPAP3 Gene

Promoters and enhancers for RPAP3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I047704 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 550.8 -0.3 -279 2.8 HDGF SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF207 ENSG00000257433 LOC105369748 RPAP3 OR5BK1P VDR SLC48A1 RAPGEF3 H1FNT HDAC7 SENP1
GH12I048681 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 36.5 -976.0 -976039 2.2 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B KANSL2 SENP1 CCNT1 DDX23 KMT2D RPAP3 LMBR1L ENSG00000257964 PRPF40B LOC390314
GH12I048104 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.3 -400.2 -400229 4.1 ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 SENP1 PFKM DDX23 KMT2D CCNT1 LOC390314 KANSL2 RPL37P19 OR5BK1P HDAC7
GH12I047772 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 11.9 -69.4 -69434 5.5 HDGF PKNOX1 SMAD1 ARNT ZFP64 SIN3A ZNF2 ZNF766 ZNF143 FOS SLC48A1 RPAP3 ENDOU KANSL2 SENP1 ENSG00000205537 ENSG00000268069 RAPGEF3 GC12M047752
GH12I047768 Enhancer 1.1 ENCODE dbSUPER 23 -62.6 -62647 0.9 PKNOX1 FOXA2 ARID4B FEZF1 ZNF121 ZNF213 KLF7 ZNF548 SP3 TSHZ1 ENSG00000277173 CCNT1 KANSL2 HDAC7 ENSG00000268069 RPAP3 SENP1 CCDC184 RAPGEF3 GC12M047752
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RPAP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPAP3 gene promoter:

Genomic Locations for RPAP3 Gene

Genomic Locations for RPAP3 Gene
44,813 bases
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 StructureGene Density

RefSeq DNA sequence for RPAP3 Gene

Proteins for RPAP3 Gene

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

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

    Protein attributes for RPAP3 Gene

    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).

    Three dimensional structures from OCA and Proteopedia for RPAP3 Gene

    Alternative splice isoforms for RPAP3 Gene


neXtProt entry for RPAP3 Gene

Post-translational modifications for RPAP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RPAP3 Gene

No data available for DME Specific Peptides for RPAP3 Gene

Domains & Families for RPAP3 Gene

Gene Families for RPAP3 Gene

Protein Domains for RPAP3 Gene

Suggested Antigen Peptide Sequences for RPAP3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



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

Function for RPAP3 Gene

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

miRNA for RPAP3 Gene

miRTarBase miRNAs that target RPAP3

Clone Products

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

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 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RPAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IDA --
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

SuperPathways for RPAP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPAP3 Gene


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

Drugs & Compounds for RPAP3 Gene

No Compound Related Data Available

Transcripts for RPAP3 Gene

Unigene Clusters for RPAP3 Gene

RNA polymerase II associated protein 3:
Representative Sequences:

Clone Products

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: - - -

Relevant External Links for RPAP3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RPAP3 Gene

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

Protein tissue co-expression partners for RPAP3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPAP3 Gene:


SOURCE GeneReport for Unigene cluster for RPAP3 Gene:


Evidence on tissue expression from TISSUES for RPAP3 Gene

  • Blood(4.3)
  • Liver(4.2)
  • Nervous system(2.6)
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
(Pan troglodytes)
Mammalia RPAP3 33 34
  • 99.35 (n)
(Canis familiaris)
Mammalia RPAP3 33 34
  • 91.7 (n)
(Bos Taurus)
Mammalia RPAP3 33 34
  • 90.51 (n)
(Rattus norvegicus)
Mammalia Rpap3 33
  • 80.75 (n)
(Mus musculus)
Mammalia Rpap3 33 16 34
  • 80.29 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 78 (a)
-- 34
  • 51 (a)
(Ornithorhynchus anatinus)
Mammalia RPAP3 34
  • 55 (a)
(Gallus gallus)
Aves RPAP3 33 34
  • 71.98 (n)
(Anolis carolinensis)
Reptilia RPAP3 34
  • 58 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rpap3 33
  • 63.07 (n)
Str.10319 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.4828 33
(Danio rerio)
Actinopterygii rpap3 33 34
  • 55.14 (n)
RPAP3 (2 of 2) 34
  • 44 (a)
zgc56178 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9134 33
fruit fly
(Drosophila melanogaster)
Insecta spag 33 34
  • 43.68 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005014 33
  • 42.28 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SGT2 34
  • 20 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G56440 33
  • 46.65 (n)
(Oryza sativa)
Liliopsida Os05g0129900 33
  • 48.58 (n)
Species where no ortholog for RPAP3 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 squirt (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

Gene Tree for RPAP3 (if available)
Gene Tree for RPAP3 (if available)

Paralogs for RPAP3 Gene

Paralogs for RPAP3 Gene

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

Variants for RPAP3 Gene

Sequence variations from dbSNP and Humsavar for RPAP3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000047953 -- 47,700,335(-) G/A intron_variant
rs1000186126 -- 47,669,606(-) A/G intron_variant
rs1000190090 -- 47,688,044(-) A/G intron_variant
rs1000262604 -- 47,676,268(-) C/A intron_variant
rs1000284848 -- 47,687,698(-) G/C intron_variant

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RPAP3 Gene

Additional Disease Information for RPAP3

No disorders were found for RPAP3 Gene.

No data available for MalaCards , 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 58
  2. 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 58
  3. PIH1D1, a subunit of R2TP complex, inhibits doxorubicin-induced apoptosis. (PMID: 21078300) Inoue M … Kamisaki Y (Biochemical and biophysical research communications 2010) 3 4 58
  4. Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. (PMID: 28330616) Yadav L … Varjosalo M (Cell systems 2017) 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for RPAP3 Gene

Sources for RPAP3 Gene

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