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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RPAP1 Gene

protein-coding   GIFtS: 49
GCID: GC15M041809

RNA Polymerase II Associated Protein 1

  Search for RPAP1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
RNA Polymerase II Associated Protein 11 2
KIAA14033 5
RNA Polymerase II-Associated Protein 12

External Ids:    HGNC: 245671   Entrez Gene: 260152   Ensembl: ENSG000001039327   OMIM: 6114755   UniProtKB: Q9BWH63   

Export aliases for RPAP1 gene to outside databases

Previous GC identifers: GC15M039526 GC15M039596 GC15M018657


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 DNA-directed RNA polymerase activity and DNA binding.

UniProtKB/Swiss-Prot: RPAP1_HUMAN, Q9BWH6
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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000015.9  NT_010194.17  NC_018926.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RPAP1 gene promoter:
         AML1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPAP1 promoter sequence
   Search SABiosciences Chromatin IP Primers for RPAP1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPAP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 15q15.1   Ensembl cytogenetic band:  15q15.1   HGNC cytogenetic band: 15q14

RPAP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPAP1 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M041809:  view genomic region     (about GC identifiers)

Start:
41,809,374 bp from pter      End:
41,836,467 bp from pter
Size:
27,094 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RPAP1_HUMAN, Q9BWH6 (See protein sequence)
Recommended Name: RNA polymerase II-associated protein 1  
Size: 1393 amino acids; 152755 Da
Subunit: Part of a 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
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=BAA92641.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: Q9H9I2 Q9NSQ5 Q9P2E4 Q9UFS7
Alternative splicing: 3 isoforms:  Q9BWH6-1   Q9BWH6-2   Q9BWH6-3   (No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for RPAP1: NX_Q9BWH6

Explore proteomics data for RPAP1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BWH6

  • RPAP1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RPAP1 Protein Expression
    REFSEQ proteins: NP_056355.2  
    ENSEMBL proteins: 
     ENSP00000456207   ENSP00000306123   ENSP00000455363   ENSP00000457203   ENSP00000455381  
     ENSP00000455527  

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    Cloud-Clone Corp. Proteins for RPAP1 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    RPAP1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR013929 RNA_pol_II_AP1_C
     IPR013930 RNA_pol_II_AP1_N

    Graphical View of Domain Structure for InterPro Entry Q9BWH6

    ProtoNet protein and cluster: Q9BWH6

    UniProtKB/Swiss-Prot: RPAP1_HUMAN, Q9BWH6
    Similarity: Belongs to the RPAP1 family


    RPAP1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RPAP1_HUMAN, Q9BWH6
    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): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003899DNA-directed RNA polymerase activity IEA--
    GO:0005488binding ----
         
    RPAP1 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for RPAP1 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RPAP1 
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    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate RPAP1:
    hsa-miR-371-5p
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    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RPAP1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/57 Interacting proteins for RPAP1 (Q9BWH63 ENSP000003061234) via UniProtKB, MINT, STRING, and/or I2D (see all 57)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000224774P678703, ENSP000004156154I2D: score=1 STRING: ENSP00000415615
    BAG6P463793, ENSP000003651314I2D: score=1 STRING: ENSP00000365131
    CSNK2BP678703I2D: score=1 
    ENSG00000096155P463793I2D: score=1 
    ENSG00000206406P678703I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RPAP1

    Search CenterWatch for drugs/clinical trials and news about RPAP1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RPAP1 gene: 
    NM_015540.3  

    Unigene Cluster for RPAP1:

    RNA polymerase II associated protein 1
    Hs.371045  [show with all ESTs]
    Unigene Representative Sequence: NM_015540
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000565167 ENST00000561603 ENST00000304330(uc001zod.3) ENST00000562303
    ENST00000564934 ENST00000565035 ENST00000561631 ENST00000568413 ENST00000563293
    ENST00000567866 ENST00000566863 ENST00000569829
    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate RPAP1:
    hsa-miR-371-5p
    SwitchGear 3'UTR luciferase reporter plasmidRPAP1 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: RPAP1 (NM_002337)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for RPAP1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RPAP1
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RPAP1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RPAP1

    Additional mRNA sequence: 

    AK022794.1 AK290224.1 AK308884.1 AL117479.1 AL157487.1 BC000246.1 HQ013232.1 

    14 DOTS entries:

    DT.85105418  DT.100788253  DT.100788259  DT.95173618  DT.95173623  DT.91848742  DT.95173619  DT.101961228 
    DT.100655018  DT.100704964  DT.121026877  DT.121026879  DT.121026889  DT.99937602 

    24/183 AceView cDNA sequences (see all 183):

    AL157487 AA380621 AL117479 CR610510 CR609844 AU130626 NM_015540 Z43993 
    BM463433 BQ054694 AI459998 BQ936890 BI333236 BX283361 BG397163 CR592322 
    BQ063149 BE731829 BX328242 AI052166 BG473377 AL572388 AL580227 BM823969 

    GeneLoc Exon Structure

    5/11 Alternative Splicing Database (ASD) splice patterns (SP) for RPAP1 (see all 11)    About this scheme

    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:              -                 -           -                                                                                                               

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


    ECgene alternative splicing isoforms for RPAP1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RPAP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTGCTGGCA
    RPAP1 Expression
    About this image


    See RPAP1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RPAP1

    SOURCE GeneReport for Unigene cluster: Hs.371045
        SABiosciences Custom PCR Arrays for RPAP1
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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

    Orthologs for RPAP1 gene from 7/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rpap11 , 5 RNA polymerase II associated protein 11, 5 82.66(n)1
    80.24(a)1
      2 (59.97 cM)5
    689251  NM_001163701.11  NP_001157173.11 
     1197633045 
    chicken
    (Gallus gallus)
    Aves RPAP11 RNA polymerase II associated protein 1 60.04(n)
    56.02(a)
      423217  XM_421141.3  XP_421141.3 
    lizard
    (Anolis carolinensis)
    Reptilia RPAP16
    RNA polymerase II associated protein 1
    52(a)
    1 ↔ 1
    1(41278327-41338560)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ099668.12   -- 75.16(n)    BJ099668.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BG303798.12   -- 74.92(n)    BG303798.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG321041 CG32104 42.55(n)
    32(a)
      39413  NM_140316.2  NP_648573.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RBA50(YDR527W)4 Protein involved in transcription; interacts with RNA more   --   4(1491094-1492413) 852139  NP_010816.1 


    ENSEMBL Gene Tree for RPAP1 (if available)
    TreeFam Gene Tree for RPAP1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/866 SNPs in RPAP1 are shown (see all 866)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0364694
    A colorectal cancer sample4--see VAR_0364692 R Q mis40--------
    rs1866007841,2
    --41808889(+) CGTGGG/TGGCAC 1 -- ds50010--------
    rs1911504671,2
    --41808911(+) CCCAGC/TCACTC 1 -- ds50010--------
    rs2017400711,2
    C--41809028(+) CAGAA-/ATA   
       GATAG
    ATAGA
    1 -- ds50010--------
    rs3767431111,2
    C--41809028(+) CAGAA-/ATAG  
            
    ATAGA
    1 -- ds50010--------
    rs1477935161,2
    --41809053(+) ATAGAC/TAGATA 1 -- ds50010--------
    rs1412711561,2
    --41809057(+) ATAGAC/TAGATA 1 -- ds50010--------
    rs746102711,2
    C--41809073(+) ATAGAC/TAGACC 1 -- ds50010--------
    rs350325291,2
    C,F--41809074(+) TAGACC/AGACCG 1 -- ds50013Minor allele frequency- A:0.50NA 6
    rs795962491,2
    C--41809078(+) CAGACA/CGACCG 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for RPAP1 (41809374 - 41836467 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for RPAP1:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv2362n71CNV Loss21882294
    nsv524476CNV Loss19592680
    nsv471241CNV Loss18288195
    nsv904112CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing RPAP1
    DNA2.0 Custom Variant and Variant Library Synthesis for RPAP1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    RPAP1 for disorders           About MalaCards
    OMIM gene information: 611475    OMIM disorders: --


    RPAP1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): RPAP1
    Human Genome Epidemiology (HuGE) Navigator: RPAP1 (1 document)

    Export disorders for RPAP1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RPAP1 gene, integrated from 9 sources (see all 24):
    (articles sorted by number of sources associating them with RPAP1)
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    1. 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. (PubMed id 10718198)1, 2, 3 Nagase T.... Ohara O. (2000)
    2. RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. (PubMed id 15282305)1, 2, 9 Jeronimo C.... Coulombe B. (2004)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    4. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. (PubMed id 17643375)1, 2 Jeronimo C.... Coulombe B. (2007)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    8. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. Genome-wide YFP fluorescence complementation screen id entifies new regulators for telomere signaling in human cells. (PubMed id 21044950)1 Lee O.H....Songyang Z. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 26015 HGNC: 24567 AceView: RPAP1 Ensembl:ENSG00000103932 euGenes: HUgn26015
    ECgene: RPAP1 H-InvDB: RPAP1

    (According to HUGE)
    About This Section
    HUGE: KIAA1403

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RPAP1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RPAP1 gene:
    Search GeneIP for patents involving RPAP1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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