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Aliases for RPAP1 Gene

Aliases for RPAP1 Gene

  • RNA Polymerase II Associated Protein 1 2 3 5
  • KIAA1403 4

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. GO annotations related to this gene include binding and DNA-directed RNA polymerase activity.

UniProtKB/Swiss-Prot 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 Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPAP1 Gene

Genomics for RPAP1 Gene

Regulatory Elements for RPAP1 Gene

Enhancers for RPAP1 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
GH15F040959 0.7 Ensembl ENCODE 39.4 +583.7 583675 1.8 TBP ZFP64 MAX ZNF140 ZNF266 ZNF514 ZIC2 ZNF101 ZNF664 ZFHX2 ENSG00000259211 RAD51-AS1 BAHD1 ENSG00000260814 DNAJC17 RPAP1 OIP5-AS1 SRP14 NDUFAF1 EHD4-AS1
GH15F040955 1 Ensembl ENCODE 29.5 +587.0 587009 3.4 ZNF493 ZFP64 ZEB1 ZNF121 ZNF354C ZNF202 ZNF680 ZNF362 SP3 ZNF654 ENSG00000259211 RAD51-AS1 DNAJC17 ENSG00000260814 BAHD1 RPAP1 NDUFAF1 CHST14 SRP14 CHAC1
GH15F041566 0.9 Ensembl ENCODE 27.5 -24.0 -24040 3.9 PKNOX1 MLX ZFP64 ARID4B DMAP1 ETS1 SP5 ZHX2 MIER2 REST RPAP1 LTK SPTBN5 PLA2G4B GC15M041574 TYRO3
GH15F041583 0.5 ENCODE 25.5 -39.8 -39761 0.2 TFAP4 SAP130 CEBPA ARID4B CEBPB CEBPG RPAP1 TYRO3 GC15P041578 PIR47510
GH15F040823 1.3 Ensembl ENCODE 23.9 +719.1 719098 3.9 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZFYVE19 RPAP1 RAD51-AS1 EIF2AK4 BAHD1 ENSG00000260814 CHP1 PIR57888 PPP1R14D
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RPAP1 on UCSC Golden Path with GeneCards custom track

Promoters for RPAP1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000406825 177 1801 ATF1 CREB3L1 ARID4B SIN3A DMAP1 ZNF48 ETS1 YY1 ZNF143 ZNF263

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

Genomic Location for RPAP1 Gene

Chromosome:
15
Start:
41,517,176 bp from pter
End:
41,544,277 bp from pter
Size:
27,102 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=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for RPAP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPAP1 Gene

Post-translational modifications for RPAP1 Gene

  • Ubiquitination at Lys 537 and Lys 1337
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RPAP1 Gene

Domains & Families for RPAP1 Gene

Protein Domains for RPAP1 Gene

Suggested Antigen Peptide Sequences for RPAP1 Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for RPAP1 Gene

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.

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 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

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

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
Jensen Localization Image for RPAP1 Gene COMPARTMENTS Subcellular localization image for RPAP1 gene
Compartment Confidence
nucleus 4
plasma membrane 3
cytosol 2

Gene Ontology (GO) - Cellular Components for RPAP1 Gene

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

Pathways & Interactions for RPAP1 Gene

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 from RNA polymerase II promoter IBA --
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

Transcripts for RPAP1 Gene

Unigene Clusters for RPAP1 Gene

RNA polymerase II associated protein 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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
ECgene alternative splicing isoforms for
RPAP1

Expression for RPAP1 Gene

mRNA expression in normal human tissues for RPAP1 Gene

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, PaxDb, MaxQB, and MOPED for RPAP1 Gene



Protein tissue co-expression partners for RPAP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPAP1 Gene:

RPAP1

SOURCE GeneReport for Unigene cluster for RPAP1 Gene:

Hs.371045
genes like me logo Genes that share expression patterns with RPAP1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.62 (n)
dog
(Canis familiaris)
Mammalia RPAP1 34 35
  • 86.21 (n)
cow
(Bos Taurus)
Mammalia RPAP1 34 35
  • 85.88 (n)
mouse
(Mus musculus)
Mammalia Rpap1 34 16 35
  • 82.66 (n)
rat
(Rattus norvegicus)
Mammalia Rpap1 34
  • 82.48 (n)
oppossum
(Monodelphis domestica)
Mammalia RPAP1 35
  • 67 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RPAP1 35
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPAP1 34 35
  • 60.29 (n)
lizard
(Anolis carolinensis)
Reptilia RPAP1 35
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpap1 34
  • 58.21 (n)
zebrafish
(Danio rerio)
Actinopterygii rpap1 34 35
  • 53.29 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10870 34
fruit fly
(Drosophila melanogaster)
Insecta CG32104 35
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RBA50 35 37
  • 21 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 35 (a)
OneToOne
Species where no ortholog for RPAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for RPAP1 Gene

No data available for Paralogs for RPAP1 Gene

Variants for RPAP1 Gene

Sequence variations from dbSNP and Humsavar for RPAP1 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs372712659 A colorectal cancer sample 41,527,460(+) GAGGC(C/T)GGCTT reference, missense
rs10152274 -- 41,541,031(+) gtcac(C/G)tcaga intron-variant
rs10851405 -- 41,516,888(+) CCGAC(A/C)GACAG downstream-variant-500B
rs11070332 -- 41,517,007(+) CCACT(A/G)TGCCT downstream-variant-500B
rs11070333 -- 41,517,332(+) CCCAG(C/T)ACAGA utr-variant-3-prime

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)

Relevant External Links for RPAP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPAP1

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

Disorders for RPAP1 Gene

Relevant External Links for RPAP1

Genetic Association Database (GAD)
RPAP1
Human Genome Epidemiology (HuGE) Navigator
RPAP1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RPAP1

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. (Mol. Cell. Biol. 2004) 3 4 22 64
  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 Res. 2000) 2 3 4 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  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. (Mol. Cell 2007) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for RPAP1 Gene

Sources for RPAP1 Gene

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