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

RPAP2 Gene

protein-coding   GIFtS: 48
GCID: GC01P092764

RNA polymerase II associated protein 2

(Previous name: chromosome 1 open reading frame 82 )
(Previous symbol: C1orf82)
 Explore 2 diseases affiliated with
RPAP2 via our new
 Human Malady Compendium 
Biological research products
for RPAP2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
RNA Polymerase II Associated Protein 21 2     Chromosome 1 Open Reading Frame 821
C1orf821 2 3 5     Putative RNA Polymerase II Subunit B1 CTD Phosphatase RPAP22
RNA Polymerase II-Associated Protein 22 3     EC 3.1.3.163
FLJ131501     

External Ids:    HGNC: 257911   Entrez Gene: 798712   Ensembl: ENSG000001224847   OMIM: 6114765   UniProtKB: Q8IXW53   

Export aliases for RPAP2 gene to outside databases

Previous GC identifers: GC01P092537 GC01P090884


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

UniProtKB/Swiss-Prot: RPAP2_HUMAN, Q8IXW5
Function: Protein phosphatase that displays CTD phosphatase activity and regulates transcription of snRNA genes.
Recognizes and binds phosphorylated 'Ser-7' of the C-terminal heptapeptide repeat domain (CTD) of the largest RNA
polymerase II subunit POLR2A, and mediates dephosphorylation of 'Ser-5' of the CTD, thereby promoting transcription of
snRNA genes

Gene Wiki entry for RPAP2


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RPAP2 gene promoter:
         AhR   Nkx3-1   Nkx3-1 v4   AML1a   Pax-2   Pax-2a   Nkx3-1 v1   Arnt   Nkx3-1 v2   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPAP2 promoter sequence
   Search SABiosciences Chromatin IP Primers for RPAP2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPAP2


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

Entrez Gene cytogenetic band: 1p22.1   Ensembl cytogenetic band:  1p22.1   HGNC cytogenetic band: 1p22.1

RPAP2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPAP2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P092764:  view genomic region     (about GC identifiers)

Start:
92,764,522 bp from pter      End:
92,853,732 bp from pter
Size:
89,211 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RPAP2_HUMAN, Q8IXW5 (See protein sequence)
Recommended Name: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2  
Size: 612 amino acids; 69509 Da
Subunit: Associates with the RNA polymerase II complex. Interacts with transcribing RNA polymerase II phosphorylated on
'Ser-7' on CTD
Subcellular location: Cytoplasm. Nucleus. Note=Shuttles between the cytoplasm and the nucleus in a CRM1-dependent
manner
Secondary accessions: C9JKB5 Q49AS7 Q9H8Y2
Alternative splicing: 2 isoforms:  Q8IXW5-1   Q8IXW5-2   (Ref.3 (AAH31070) sequence is in conflict in position: 584:S->N)

Explore the universe of human proteins at neXtProt for RPAP2: NX_Q8IXW5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IXW5

  • RPAP2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_079089.2  
    ENSEMBL proteins: 
     ENSP00000359368  

    Human Recombinant Protein Products: 
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    Uscn Proteins for RPAP2

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA--
    GO:0016591DNA-directed RNA polymerase II, holoenzyme IDA--


    RPAP2 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    RPAP2 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007308 DUF408

    Graphical View of Domain Structure for InterPro Entry Q8IXW5

    ProtoNet protein and cluster: Q8IXW5

    UniProtKB/Swiss-Prot: RPAP2_HUMAN, Q8IXW5
    Domain: The RTR1-type zinc finger mediates interactions with RNA polymerase II complex subunits (PubMed:22137580)
    Similarity: Belongs to the RPAP2 family
    Similarity: Contains 1 RTR1-type zinc finger


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: RPAP2_HUMAN, Q8IXW5
    Function: Protein phosphatase that displays CTD phosphatase activity and regulates transcription of snRNA genes.
    Recognizes and binds phosphorylated 'Ser-7' of the C-terminal heptapeptide repeat domain (CTD) of the largest RNA
    polymerase II subunit POLR2A, and mediates dephosphorylation of 'Ser-5' of the CTD, thereby promoting transcription of
    snRNA genes
    Catalytic activity: A phosphoprotein + H(2)O = a protein + phosphate

    Enzyme Number (IUBMB): EC 3.1.3.161

    miRNA
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    hsa-miR-579 hsa-miR-361-5p hsa-miR-101* hsa-miR-452* hsa-miR-192 hsa-miR-432 hsa-miR-374a* hsa-miR-4279
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008420CTD phosphatase activity IMP--
    GO:0046872metal ion binding IEA--


    RPAP2 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for RPAP2:
     Increased S DNA content  Lamellipodia cells 

    Animal Models:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Rpap2):
     mortality/aging 

    RPAP2 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RPAP2

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

    5/56 Interacting proteins for RPAP2 (Q8IXW53 ENSP000003593684) via UniProtKB, MINT, STRING, and/or I2D (see all 56)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000206268P186153I2D: score=1 
    ENSG00000206357P186153I2D: score=1 
    ENSG00000229363P186153I2D: score=1 
    ENSG00000231044P186153I2D: score=1 
    ENSG00000233801P186153I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009301snRNA transcription IMP--
    GO:0070940dephosphorylation of RNA polymerase II C-terminal domain IMP--


    RPAP2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 RPAP2
    Search CenterWatch for drugs/clinical trials and news about RPAP2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RPAP2 gene: 
    NM_024813.2  

    Unigene Cluster for RPAP2:

    RNA polymerase II associated protein 2
    Hs.444421  [show with all ESTs]
    Unigene Representative Sequence: NM_024813
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370343(uc001dot.2 uc009wdh.2) ENST00000484158 ENST00000477322


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    hsa-miR-579 hsa-miR-361-5p hsa-miR-101* hsa-miR-452* hsa-miR-192 hsa-miR-432 hsa-miR-374a* hsa-miR-4279
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    Additional cDNA sequence: 

    AK023212.1 AK225054.1 BC031070.1 BC039014.1 

    6 DOTS entries:

    DT.113395  DT.100816781  DT.100816778  DT.92421623  DT.97832147  DT.100020492 

    24/73 AceView cDNA sequences (see all 73):

    AA227530 BU633786 AI198962 BM559559 BM546733 BC031070 CR613797 AA770422 
    CN479576 BP369593 BM672068 AK023212 BC039014 AI580293 NM_024813 BX112953 
    CB243643 AA227857 BF510344 BF797831 AL712035 BX448624 BX359787 BE869363 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for RPAP2    About this scheme

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


    ECgene alternative splicing isoforms for RPAP2

    (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

    RPAP2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATGGTCTGGT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See RPAP2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RPAP2

    SOURCE GeneReport for Unigene cluster: Hs.444421
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPAP2

    (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 eukaryotes.

    Orthologs for RPAP2 gene from 8/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rpap21 , 5 RNA polymerase II associated protein 21, 5 78.03(n)1
    71(a)1
      5 (52.23 cM)5
    2315711  NM_144911.21  NP_659160.21 
     1075973735 
    chicken
    (Gallus gallus)
    Aves RPAP21 RNA polymerase II associated protein 2 65.25(n)
    58.31(a)
      424501  XM_422341.3  XP_422341.3 
    lizard
    (Anolis carolinensis)
    Reptilia RPAP26
    --
    47(a)
    1 ↔ 1
    4(93805263-93834736)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.160312 Transcribed sequence with weak similarity to protein more 74.17(n)    AL970899.2 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.257012 Transcribed sequence with weak similarity to protein more 73.44(n)    BQ258464.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG341836
    --
    48(a)
    1 ↔ 1
    2L(9890061-9890772)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G267606
    uncharacterized protein
    14(a)
    1 ↔ 1
    5(9403598-9407301)
    rice
    (Oryza sativa)
    Liliopsida --
    expressed protein
    13(a)
    1 ↔ 1
    5(1998188-2002852)


    ENSEMBL Gene Tree for RPAP2 (if available)
    TreeFam Gene Tree for RPAP2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RPAP2 gene

    RPAP2 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for RPAP2
    PGOHUM00000238571


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/1186 NCBI SNPs in RPAP2 are shown (see all 1186    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1874005871,2
    --92766750(+) GAAAAC/TAGAAA 1 -- int10--------
    rs66954751,2
    C,F,A,H,--92766781(+) TATGCC/TGGTGA 1 -- int19Minor allele frequency- T:0.12NS EA NA WA CSA 539
    rs66040881,2
    C,F,A,--92766848(+) CCAGTC/TTGAGC 1 -- int112Minor allele frequency- T:0.21NA WA CSA EA 377
    rs1488128461,2
    F--92767099(+) ATTGTT/CGAACA 2 /V syn11Minor allele frequency- C:0.00NA 4476
    rs1433949001,2
    C,F--92767132(+) GAAGAG/CTTCCT 2 /D /E mis11Minor allele frequency- C:0.00NA 4408
    rs66040891,2
    C,F,H,--92767292(+) CATTTT/AAAAAT 1 -- int117Minor allele frequency- A:0.07NS EA NA WA CSA 769
    rs120863541,2
    C,F,H,--92767358(+) AAGTAC/TGTAAC 1 -- int113Minor allele frequency- T:0.10NS EA NA WA CSA 1314
    rs1163342571,2
    --92767507(+) CATCAC/TATACT 1 -- int11Minor allele frequency- T:0.01WA 118
    rs1911693601,2
    --92767550(+) TTAAAA/CAGCAA 1 -- int10--------
    rs1833004771,2
    --92767685(+) ATACAA/GAATTA 1 -- int10--------

    HapMap Linkage Disequilibrium report for RPAP2 (92764522 - 92853732 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for RPAP2
         1 CNV: 4234

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

    RPAP2 for disorders           About GeneDecksing

    OMIM gene information: 611476    OMIM disorders: --

    2 diseases for RPAP2:    About MalaCards
    acute pancreatitis    pancreatitis

    1 disease from the University of Copenhagen DISEASES database for RPAP2:
    Acute pancreatitis

    Export disorders for RPAP2 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)
    About This Section

    PubMed articles for RPAP2 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with RPAP2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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, 3 Jeronimo C.... Coulombe B. (2007)
    2. Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. (PubMed id 22137580)1, 2 Egloff S.... Murphy S. (2012)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)
    7. Control of the RNA polymerase II phosphorylation stat e in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. (PubMed id 22231121)2 Ni Z....Greenblatt J.F. (2011)
    8. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    9. Defining the human deubiquitinating enzyme interactio n landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (2009)
    10. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)

    (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)
    About This Section
    Entrez Gene: 79871 HGNC: 25791 AceView: FLJ13150 Ensembl:ENSG00000122484 euGenes: HUgn79871
    ECgene: RPAP2 H-InvDB: RPAP2

    (According to HUGE)
    About This Section
      --

    (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 RPAP2 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 RPAP2 gene:
    Search GeneIP for patents involving RPAP2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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