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RNF169 Gene

protein-coding   GIFtS: 40
GCID: GC11P074459

Ring Finger Protein 169

  Search for RNF169
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ring Finger Protein 1691 2 3
E3 Ubiquitin-Protein Ligase RNF1692
EC 6.3.2.-3
KIAA19913
EC 3.1.4.168
EC 3.4.24.578

External Ids:    HGNC: 269611   Entrez Gene: 2542252   Ensembl: ENSG000001664397   UniProtKB: Q8NCN43   

Export aliases for RNF169 gene to outside databases

Previous GC identifers: GC11P074138 GC11P070756


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RNF169 Gene:
RNF169 (ring finger protein 169) is a protein-coding gene. GO annotations related to this gene include nucleosome binding and ligase activity.

UniProtKB/Swiss-Prot: RN169_HUMAN, Q8NCN4
Function: Probable E3 ubiquitin-protein ligase that acts as a negative regulator of double-strand breaks (DSBs)
repair following DNA damage. Recruited to DSB repair sites by recognizing and binding ubiquitin catalyzed by
RNF168 and competes with TP53BP1 and BRCA1 for association with RNF168-modified chromatin, thereby acting as a
negative regulator of DSBs repair. E3 ubiquitin-protein ligase activity is not required for regulation of DSBs
repair




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the RNF169 gene promoter:
         c-Fos   Egr-3   AhR   AP-1   FosB   FOXO3   Roaz   FOXO3b   FOXO3a   c-Jun   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RNF169

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNF169


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

Entrez Gene cytogenetic band: 11q13.4   Ensembl cytogenetic band:  11q13.4   HGNC cytogenetic band: 11q13.4

RNF169 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNF169 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P074459:  view genomic region     (about GC identifiers)

Start:
74,459,913 bp from pter      End:
74,553,458 bp from pter
Size:
93,546 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: RN169_HUMAN, Q8NCN4 (See protein sequence)
Recommended Name: E3 ubiquitin-protein ligase RNF169  
Size: 708 amino acids; 77194 Da
Sequence caution: Sequence=BAC02700.1; Type=Erroneous initiation;
Secondary accessions: Q6N015

Explore the universe of human proteins at neXtProt for RNF169: NX_Q8NCN4

Explore proteomics data for RNF169 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys691
  • Modification sites at PhosphoSitePlus
  • 2 DME Specific Peptides for RNF169 (Q8NCN4)
     KLQQEEE  CDETAAA 


    See RNF169 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001092108.1  
    ENSEMBL proteins: 
     ENSP00000299563   ENSP00000436339  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RNF: RING-type (C3HC4) zinc fingers

    3 InterPro protein domains:
     IPR017907 Znf_RING_CS
     IPR001841 Znf_RING
     IPR013083 Znf_RING/FYVE/PHD

    Graphical View of Domain Structure for InterPro Entry Q8NCN4

    ProtoNet protein and cluster: Q8NCN4

    1 Blocks protein domain: IPB001841 Zn-finger

    UniProtKB/Swiss-Prot: RN169_HUMAN, Q8NCN4
    Domain: The MIU motif (motif interacting with ubiquitin) mediates the interaction with both 'Lys-48'- and
    'Lys-63'-linked ubiquitin chains (PubMed:22733822 and PubMed:22492721). The UMI motif also mediates interaction
    with ubiquitin. The specificity for different types of ubiquitin is mediated by juxtaposition of
    ubiquitin-binding motifs (MIU and UMI motifs) with LR motifs (LRMs) (PubMed:22742833)
    Similarity: Belongs to the RNF169 family
    Similarity: Contains 1 RING-type zinc finger


    RNF169 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RN169_HUMAN, Q8NCN4
    Function: Probable E3 ubiquitin-protein ligase that acts as a negative regulator of double-strand breaks (DSBs)
    repair following DNA damage. Recruited to DSB repair sites by recognizing and binding ubiquitin catalyzed by
    RNF168 and competes with TP53BP1 and BRCA1 for association with RNF168-modified chromatin, thereby acting as a
    negative regulator of DSBs repair. E3 ubiquitin-protein ligase activity is not required for regulation of DSBs
    repair

         Enzyme Numbers (IUBMB): EC 6.3.2.-1 EC 3.4.24.572 EC 3.1.4.162

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0016874ligase activity IEA--
    GO:0031491nucleosome binding IDA--
    GO:0070530K63-linked polyubiquitin binding IDA--
         
    RNF169 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for RNF169:
     Decreased TP53 protein express  Increased S DNA content 

         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rnf169):
     homeostasis/metabolism  skeleton  vision/eye 

    RNF169 for phenotypes           About GeneDecksing

    Animal Models:
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RN169_HUMAN, Q8NCN4: Nucleus, nucleoplasm. Note=Localizes to sites of double-strand breaks (DSBs) following DNA
    damage. Recruited to DSBs via recognition of RNF168-dependent ubiquitin products
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005886plasma membrane IDA--
    GO:0035861site of double-strand break IDA--

    RNF169 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    UniProtKB/Swiss-Prot: RN169_HUMAN, Q8NCN4
    Pathway: Protein modification; protein ubiquitination

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RNF169
    Interactions:

        Search GeneGlobe Interaction Network for RNF169

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

    Selected Interacting proteins for RNF169 (Q8NCN42 ENSP000002995634) via UniProtKB, MINT, STRING, and/or I2D (see all 37)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    BEND3Q5T5X72MINT-8173832
    CHAMP1Q96JM32MINT-8173832
    CTPS1P178122MINT-8173832
    CWC22Q9HCG82MINT-8173832
    DHX15O431432MINT-8173832
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006974cellular response to DNA damage stimulus IMP--
    GO:0016567protein ubiquitination IEA--
    GO:2000780negative regulation of double-strand break repair IMP--

    RNF169 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RNF169 (RN169)



    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RNF169 gene: 
    NM_001098638.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000299563(uc001ovl.4) ENST00000527301
    miRNA
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    hsa-miR-140-5p hsa-miR-26a-2* hsa-miR-607 hsa-miR-3194-5p hsa-miR-30d hsa-miR-4267 hsa-miR-30a hsa-miR-4325
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      QuantiFast Probe-based Assays in human, mouse, rat RNF169

    Selected AceView cDNA sequences (see all 120):

    BG679092 BI862829 BU735906 AI911676 BE047843 AA748391 CB147654 AA720793 
    BU735651 BX102462 AI468437 AA437401 AW026154 AI061064 BF439964 AI589084 
    AI082193 BU158897 BE858336 Z41883 BX648162 CK906107 AI369062 BM706434 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RNF169 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RNF169 Expression
    About this image

    RNF169 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RNF169 Protein Expression
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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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for RNF169 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rnf1691 , 5 ring finger protein 1691, 5 82.42(n)1
    79.83(a)1
      7 (54.22 cM)5
    1089371  NM_175388.31  NP_780597.21 
     999202575 
    chicken
    (Gallus gallus)
    Aves RNF1691 ring finger protein 169 67.24(n)
    65.32(a)
      419055  XM_417246.4  XP_417246.4 
    lizard
    (Anolis carolinensis)
    Reptilia RNF1696
    ring finger protein 169
    50(a)
    1 ↔ 1
    GL343489.1(504576-520039)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004935801 E3 ubiquitin-protein ligase RNF169-like 57.47(n)
    51.79(a)
      100493580  XM_002944031.2  XP_002944077.2 
    zebrafish
    (Danio rerio)
    Actinopterygii rnf1691 ring finger protein 169 56.84(n)
    51.65(a)
      795748  XM_001335976.2  XP_001336012.2 


    ENSEMBL Gene Tree for RNF169 (if available)
    TreeFam Gene Tree for RNF169 (if available)

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

    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RNF169 (see all 1773)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1427024201,2
    --74458008(+) TCTGGC/GTCTCT 1 -- us2k10--------
    rs124218991,2
    C,F,H--74458046(+) CCATTG/AGCCTT 1 -- us2k17Minor allele frequency- A:0.34NA WA EA 366
    rs1505802571,2
    --74458107(+) CATCAC/TCTTTT 1 -- us2k10--------
    rs1871781981,2
    --74458139(+) AATCAA/GTCACT 1 -- us2k10--------
    rs1395812441,2
    C--74458147(+) ACTCGG/TCACTG 1 -- us2k10--------
    rs1897348471,2
    --74458164(+) TTTACC/TGCTAG 1 -- us2k10--------
    rs1823478011,2
    --74458178(+) TGGGCA/GATCTC 1 -- us2k10--------
    rs1497136941,2
    --74458198(+) CAGGGC/TTTCTC 1 -- us2k10--------
    rs1478076231,2
    --74458226(+) ATGTTC/GATTTT 1 -- us2k10--------
    rs1877087831,2
    --74458251(+) TGTCTA/CATTCT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RNF169 (74459913 - 74553458 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for RNF169 (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2744779CNV Deletion23290073
    esv2305041CNV Deletion18987734
    esv2484083CNV Deletion19546169
    dgv5e197CNV Deletion19546169
    esv2669092CNV Deletion23128226
    nsv38718CNV Loss16902084
    nsv8839CNV Gain18304495
    dgv1223n71CNV Gain21882294
    nsv825994CNV Gain20364138
    esv34979CNV Gain17911159

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    (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.)
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      --

    (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 RNF169 gene, integrated from 10 sources (see all 23):
    (articles sorted by number of sources associating them with RNF169)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PubMed id 12056414)1, 2, 3 Ohara O.... Koseki H. (DNA Res. 2002)
    2. Tandem protein interaction modules organize the ubiquitin-dependent response to DNA double-strand breaks. (PubMed id 22742833)1, 2 Panier S.... Durocher D. (Mol. Cell 2012)
    3. Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks. (PubMed id 22492721)1, 2 Poulsen M.... Mailand N. (J. Cell Biol. 2012)
    4. Ring finger protein RNF169 antagonises the ubiquitin-dependent signaling cascade at sites of DNA Damage. (PubMed id 22733822)1, 2 Chen J.... Huen M.S. (J. Biol. Chem. 2012)
    5. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)
    6. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    7. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    8. Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (J. Biol. Chem. 2011)
    9. Comparative proteomic analysis identifies a role for SUMO in protein quality control. (PubMed id 21693764)1 Tatham M.H....Hay R.T. (Sci Signal 2011)
    10. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 254225 HGNC: 26961 AceView: KIAA1991 Ensembl:ENSG00000166439 euGenes: HUgn254225
    ECgene: RNF169 H-InvDB: RNF169

    (According to HUGE)
    About This Section

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    HUGE: KIAA1991

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RNF169 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RNF169 gene:
    Search GeneIP for patents involving RNF169

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



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