This protein forms part of the RNA polymerase II (RNAPII) enzyme complex and may recruit RNAPII to chromatin through its interaction with acetylated histones. [provided by RefSeq, Jul 2012] See more...

Aliases for RPAP1 Gene

Aliases for RPAP1 Gene

  • RNA Polymerase II Associated Protein 1 2 3 5
  • RNA Polymerase II-Associated Protein 1 3 4
  • KIAA1403 2 4
  • DKFZP727M111 2
  • FLJ12732 2
  • MGC858 2
  • RPAP1 5

External Ids for RPAP1 Gene

Previous GeneCards Identifiers for RPAP1 Gene

  • GC15M039526
  • GC15M039596
  • GC15M041809
  • GC15M018657

Summaries for RPAP1 Gene

Entrez Gene Summary for RPAP1 Gene

  • This protein forms part of the RNA polymerase II (RNAPII) enzyme complex and may recruit RNAPII to chromatin through its interaction with acetylated histones. [provided by RefSeq, Jul 2012]

GeneCards Summary for RPAP1 Gene

RPAP1 (RNA Polymerase II Associated Protein 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include binding and DNA-directed 5'-3' RNA polymerase activity.

UniProtKB/Swiss-Prot Summary for RPAP1 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. Required for interaction of the RNA polymerase II complex with acetylated histone H3.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPAP1 Gene

Genomics for RPAP1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RPAP1 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 RPAP1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPAP1

Top Transcription factor binding sites by QIAGEN in the RPAP1 gene promoter:
  • AML1a

Genomic Locations for RPAP1 Gene

Latest Assembly
chr15:41,517,176-41,544,269
(GRCh38/hg38)
Size:
27,094 bases
Orientation:
Minus strand

Previous Assembly
chr15:41,809,374-41,836,455
(GRCh37/hg19 by Entrez Gene)
Size:
27,082 bases
Orientation:
Minus strand

chr15:41,809,374-41,836,467
(GRCh37/hg19 by Ensembl)
Size:
27,094 bases
Orientation:
Minus strand

Genomic View for RPAP1 Gene

Genes around RPAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPAP1 Gene

Proteins for RPAP1 Gene

  • Protein details for RPAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BWH6-RPAP1_HUMAN
    Recommended name:
    RNA polymerase II-associated protein 1
    Protein Accession:
    Q9BWH6
    Secondary Accessions:
    • Q9H9I2
    • Q9NSQ5
    • Q9P2E4
    • Q9UFS7

    Protein attributes for RPAP1 Gene

    Size:
    1393 amino acids
    Molecular mass:
    152755 Da
    Quaternary structure:
    • Part of an RNA polymerase II complex that contains POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, RPAP1, FCP1 plus the general transcription factors TFIIB and TFIIF.
    SequenceCaution:
    • Sequence=BAA92641.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for RPAP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPAP1 Gene

Post-translational modifications for RPAP1 Gene

  • Ubiquitination at Lys537 and Lys1337
  • Modification sites at PhosphoSitePlus

Other Protein References for RPAP1 Gene

No data available for DME Specific Peptides for RPAP1 Gene

Domains & Families for RPAP1 Gene

Gene Families for RPAP1 Gene

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

Protein Domains for RPAP1 Gene

Suggested Antigen Peptide Sequences for RPAP1 Gene

GenScript: Design optimal peptide antigens:
  • RNA polymerase II-associated protein 1 (RPAP1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BWH6

UniProtKB/Swiss-Prot:

RPAP1_HUMAN :
  • Belongs to the RPAP1 family.
Family:
  • Belongs to the RPAP1 family.
genes like me logo Genes that share domains with RPAP1: view

Function for RPAP1 Gene

Molecular function for RPAP1 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. Required for interaction of the RNA polymerase II complex with acetylated histone H3.

Phenotypes From GWAS Catalog for RPAP1 Gene

Gene Ontology (GO) - Molecular Function for RPAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003899 DNA-directed 5'-3' RNA polymerase activity IEA --
GO:0005515 protein binding IPI 21044950
GO:0016740 transferase activity IEA --
GO:0016779 nucleotidyltransferase activity IEA --
genes like me logo Genes that share ontologies with RPAP1: view
genes like me logo Genes that share phenotypes with RPAP1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPAP1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPAP1 Gene

Localization for RPAP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPAP1 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 RPAP1 gene
Compartment Confidence
nucleus 4
plasma membrane 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with RPAP1: view

Pathways & Interactions for RPAP1 Gene

PathCards logo

SuperPathways for RPAP1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription by RNA polymerase II IEA,IBA 21873635
genes like me logo Genes that share ontologies with RPAP1: view

No data available for Pathways by source and SIGNOR curated interactions for RPAP1 Gene

Drugs & Compounds for RPAP1 Gene

No Compound Related Data Available

Transcripts for RPAP1 Gene

mRNA/cDNA for RPAP1 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPAP1

Alternative Splicing Database (ASD) splice patterns (SP) for RPAP1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17a ·
SP1: - - - - - -
SP2:
SP3:
SP4: -
SP5: - - -
SP6: - - -
SP7:
SP8: -
SP9:
SP10:
SP11: - -

ExUns: 17b · 17c ^ 18 ^ 19a · 19b · 19c ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25a · 25b ^ 26 ^ 27a · 27b
SP1: - -
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for RPAP1 Gene

GeneLoc Exon Structure for
RPAP1

Expression for RPAP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPAP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RPAP1 Gene

This gene is overexpressed in CD8 Tcells (11.9), Blymphocyte (9.4), Lymph node (9.0), and Testis (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RPAP1 Gene



Protein tissue co-expression partners for RPAP1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPAP1

SOURCE GeneReport for Unigene cluster for RPAP1 Gene:

Hs.371045

Evidence on tissue expression from TISSUES for RPAP1 Gene

  • Nervous system(4.8)
  • Eye(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with RPAP1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPAP1 Gene

Orthologs for RPAP1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RPAP1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RPAP1 29 30
  • 99.62 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RPAP1 29 30
  • 86.21 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RPAP1 29 30
  • 85.88 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rpap1 29 16 30
  • 82.66 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rpap1 29
  • 82.48 (n)
Oppossum
(Monodelphis domestica)
Mammalia RPAP1 30
  • 67 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RPAP1 30
  • 63 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RPAP1 29 30
  • 60.29 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RPAP1 30
  • 52 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rpap1 29
  • 58.21 (n)
Zebrafish
(Danio rerio)
Actinopterygii rpap1 29 30
  • 53.29 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10870 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG32104 30
  • 26 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RBA50 30 32
  • 21 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 35 (a)
OneToOne
Species where no ortholog for RPAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RPAP1 Gene

ENSEMBL:
Gene Tree for RPAP1 (if available)
TreeFam:
Gene Tree for RPAP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPAP1: view image
Alliance of Genome Resources:
Additional Orthologs for RPAP1

Paralogs for RPAP1 Gene

No data available for Paralogs for RPAP1 Gene

Variants for RPAP1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPAP1 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs372712659 A colorectal cancer sample p.Arg525Gln
rs61731588 Benign: not provided 41,537,118(-) G/A
NM_015540.4(RPAP1):c.8C>T (p.Ser3Leu)
MISSENSE
rs7170898 Likely Benign: not provided 41,520,864(-) G/Cp.Arg1108Gly
NM_015540.4(RPAP1):c.3322C>G (p.Arg1108Gly)
MISSENSE
rs11630901 -- p.Arg582Gly
rs1200345 -- p.Glu506Lys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RPAP1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RPAP1 Gene

Variant ID Type Subtype PubMed ID
nsv471241 CNV loss 18288195
nsv524476 CNV loss 19592680
nsv569234 CNV loss 21841781

Variation tolerance for RPAP1 Gene

Residual Variation Intolerance Score: 99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.71; 83.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPAP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPAP1
Leiden Open Variation Database (LOVD)
RPAP1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPAP1 Gene

Disorders for RPAP1 Gene

Additional Disease Information for RPAP1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for RPAP1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RPAP1 Gene

Publications for RPAP1 Gene

  1. RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. (PMID: 15282305) Jeronimo C … Coulombe B (Molecular and cellular biology 2004) 3 4 22
  2. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  4. 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) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for RPAP1 Gene

Sources for RPAP1 Gene