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

UBN1 Gene

protein-coding   GIFtS: 49
GCID: GC16P004897

ubinuclein 1

 Explore 6 diseases affiliated with
UBN1 via our new
 Human Malady Compendium 
Biological research products
for UBN1
    

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

Aliases
Ubinuclein 11 2     VT42
Ubiquitously Expressed Nuclear Protein2 3     Ubinuclein-11
HIRA-Binding Protein2 3     Protein VT43
VT2     

External Ids:    HGNC: 125061   Entrez Gene: 298552   Ensembl: ENSG000001189007   OMIM: 6097715   UniProtKB: Q9NPG33   

Export aliases for UBN1 gene to outside databases

Previous GC identifers: GC16P004921 GC16P004898 GC16P004838


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

UniProtKB/Swiss-Prot: UBN1_HUMAN, Q9NPG3
Function: Acts as a novel regulator of senescence. Involved in the formation of senescence-associated heterochromatin
foci (SAHF), which represses expression of proliferation-promoting genes. Binds to proliferation-promoting genes. May
be required for replication-independent chromatin assembly




(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_000016.9  NC_018927.1  NT_010393.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the UBN1 gene promoter:
         AREB6   AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUBN1 promoter sequence
   Search SABiosciences Chromatin IP Primers for UBN1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat UBN1


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

Entrez Gene cytogenetic band: 16p13.3   Ensembl cytogenetic band:  16p13.3   HGNC cytogenetic band: 16p13.3

UBN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UBN1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P004897:  view genomic region     (about GC identifiers)

Start:
4,896,666 bp from pter      End:
4,932,363 bp from pter
Size:
35,698 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: UBN1_HUMAN, Q9NPG3 (See protein sequence)
Recommended Name: Ubinuclein-1  
Size: 1134 amino acids; 121520 Da
Subunit: Component of a complex that includes at least ASF1A, CABIN1, HIRA, histone H3.3 and UBN1. Interacts with
Epstein-Barr virus BZLF1. Interacts with HIRA (via WD repeat domain); the interaction is direct. Interacts with ASF1A,
CEBPA, TJP1, TJP2 and TJP3
Subcellular location: Nucleus, nucleoplasm. Nucleus, PML body. Cell junction, tight junction. Note=Localized as a
nuclear speckled-like pattern in proliferating primary fibroblasts. Colocalizes with HIRA, PML and SP100 in PML bodies
of senescent cells. Colocalizes with TJP1 and CLDN1. Detected along the upper granular cell layer of epidermis. When
overexpressed, accumulates in the nucleus in cells showing defective cytokinesis
Secondary accessions: B7Z6D3 D3DUE8 Q13079 Q9P1P7
Alternative splicing: 2 isoforms:  Q9NPG3-1   Q9NPG3-2   

Explore the universe of human proteins at neXtProt for UBN1: NX_Q9NPG3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NPG3

  • UBN1 Protein expression data from MOPED and PaxDb:    About this image 
    UBN1 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001072982.1  NP_058632.2  

    ENSEMBL proteins: 
     ENSP00000467942   ENSP00000262376   ENSP00000468740   ENSP00000379894   ENSP00000468143  
     ENSP00000465309   ENSP00000468776   ENSP00000442379  

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    Uscn Proteins for UBN1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS10725330
    GO:0005923tight junction ISS--
    GO:0016605PML body IEA--

    UBN1 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

    UBN1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR026936 Ubinuclein-1
     IPR026947 UBN_middle_dom
     IPR026949 Ubinuclein/Yemanuclein
     IPR014840 HRD

    Graphical View of Domain Structure for InterPro Entry Q9NPG3

    ProtoNet protein and cluster: Q9NPG3

    UniProtKB/Swiss-Prot: UBN1_HUMAN, Q9NPG3
    Similarity: Belongs to the ubinuclein family


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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: UBN1_HUMAN, Q9NPG3
    Function: Acts as a novel regulator of senescence. Involved in the formation of senescence-associated heterochromatin
    foci (SAHF), which represses expression of proliferation-promoting genes. Binds to proliferation-promoting genes. May
    be required for replication-independent chromatin assembly

         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:0003700sequence-specific DNA binding transcription factor activity TAS10725330
    GO:0005515protein binding IPI18823282
         
    UBN1 for ontologies           About GeneDecksing


    Animal Models:
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UBN1


    (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 UBN1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

    5/533 Interacting proteins for UBN1 (Q9NPG32, 3 ENSP000002623764) via UniProtKB, MINT, STRING, and/or I2D (see all 533)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    TJP1Q071573, ENSP000002815374I2D: score=1 STRING: ENSP00000281537
    CDC5LQ994592, ENSP000003605324MINT-7947479 STRING: ENSP00000360532
    HIRAP541982, ENSP000002632084MINT-7947479 STRING: ENSP00000263208
    PPP1CAP621362, ENSP000003260314MINT-7947479 STRING: ENSP00000326031
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006357regulation of transcription from RNA polymerase II promoter TAS10725330
    GO:0010923negative regulation of phosphatase activity IDA19389623
    GO:0016568chromatin modification IEA--
    GO:0019048virus-host interaction IEA--
    GO:0044419interspecies interaction between organisms ----

    UBN1 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 UBN1
    Search CenterWatch for drugs/clinical trials and news about UBN1 

    (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,
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    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 UBN1 gene (2 alternative transcripts): 
    NM_001079514.1  NM_016936.3  

    Unigene Cluster for UBN1:

    Ubinuclein 1
    Hs.440219  [show with all ESTs]
    Unigene Representative Sequence: NM_016936
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000592120 ENST00000262376(uc002cyb.3) ENST00000590769 ENST00000396658(uc002cyc.3)
    ENST00000587027 ENST00000585857 ENST00000586716 ENST00000589191 ENST00000586152
    ENST00000545171(uc010uxw.2)

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    hsa-miR-520e hsa-miR-3607-3p hsa-miR-300 hsa-miR-30d hsa-miR-342-3p hsa-miR-4267 hsa-miR-30a hsa-miR-376a*
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    Additional cDNA sequence: 

    AF108460.1 AF108461.1 AK022652.1 AK056282.1 AK300131.1 BC013750.1 U19346.1 

    18 DOTS entries:

    DT.86847091  DT.314188  DT.100782121  DT.95111280  DT.100782119  DT.426270  DT.40108357  DT.120704543 
    DT.120704708  DT.91664290  DT.92439823  DT.97822528  DT.205267  DT.40109542  DT.91728209  DT.92439817 
    DT.91727203  DT.97820255 

    24/282 AceView cDNA sequences (see all 282):

    AI085355 AA143803 H97651 BE206890 AI161172 BQ674242 N92493 AI150333 
    AI341565 AI478306 CA425831 BU074174 BE674856 AI140304 AA761627 U19346 
    BM541970 CA975889 BM666068 BI438814 AI432573 BQ962619 BG677604 AU120544 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for UBN1 (see all 6)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a ·
    SP1:        -                       -                                                                                                                           
    SP2:                                -                                                                                                                           
    SP3:                                                                                                                                                            
    SP4:                                                                                                        -                                                   
    SP5:                                                                                                                                      -                     

    ExUns: 19b
    SP1:      
    SP2:      
    SP3:      
    SP4:      
    SP5:      


    ECgene alternative splicing isoforms for UBN1

    (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

    UBN1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCAAGGCAGA
    UBN1 Expression
    About this image
    See UBN1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for UBN1

    SOURCE GeneReport for Unigene cluster: Hs.440219

    UniProtKB/Swiss-Prot: UBN1_HUMAN, Q9NPG3
    Tissue specificity: Ubiquitous. Also expressed in numerous tumors and cancer cell lines

        SABiosciences Custom PCR Arrays for UBN1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UBN1

    (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.

    Orthologs for UBN1 gene from 5/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ubn11 , 5 ubinuclein 11, 5 85.76(n)1
    87.36(a)1
      16 (2.49 cM)5
    1706441  NM_026666.31  NP_080942.11 
     50500685 
    chicken
    (Gallus gallus)
    Aves UBN11 ubinuclein 1 72.13(n)
    71.59(a)
      416398  NM_001079718.1  NP_001073186.1 
    lizard
    (Anolis carolinensis)
    Reptilia UBN16
    --
    66(a)
    1 ↔ 1
    GL343263.1(1285491-1297960)
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.72952 Transcribed sequence with weak similarity to protein more 75.1(n)    CB359535.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta yemalpha6
    yemanuclein alpha
    17(a)
    1 → many
    3R(24944052-24948601)


    ENSEMBL Gene Tree for UBN1 (if available)
    TreeFam Gene Tree for UBN1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for UBN1 gene
    UBN22  
    1 SIMAP similar gene for UBN1 using alignment to 5 protein entries:     UBN1_HUMAN (see all proteins):
    UBN2

    UBN1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for UBN1
    PGOHUM00000241727


    (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

    10/75 NCBI SNPs in UBN1 are shown (see all 75    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs598828011,2
    C--4862322(+) CTAGGG/AGAAAA 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs735170311,2
    C--4862580(+) CCTAAA/GTCTCT 1 -- us2k12Minor allele frequency- G:0.13WA 120
    rs133306131,2
    C,F--4862714(+) CAGAAC/GAACAC 1 -- us2k15Minor allele frequency- G:0.07NA WA EA 362
    rs743243491,2
    F--4862731(+) CAAAAG/ATCACT 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs80505251,2
    C,F--4862928(+) CGGGCG/CGTTGT 1 -- us2k11Minor allele frequency- C:0.18WA 118
    rs560406231,2
    C,F--4863194(+) GGGACC/TGGTCG 1 -- us2k14Minor allele frequency- T:0.14NA EA 244
    rs1132810681,2
    C--4863244(+) GGGCCG/ACCAGT 1 -- us2k12Minor allele frequency- A:0.13NA 122
    rs755268581,2
    F--4863361(+) CGCCTG/AGCGCC 1 -- us2k11Minor allele frequency- A:0.06WA 118
    rs1116013081,2
    C--4863384(+) CGGCAC/GCTTCT 1 -- us2k13Minor allele frequency- G:0.13NA WA 240
    rs1121542271,2
    C--4863508(+) GACTCA/C/TCCACA 1 -- us2k11CSA 1

    HapMap Linkage Disequilibrium report for UBN1 (4896666 - 4932363 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 5 variations for UBN1
         5 CNVs: 72442 5436 72443 72444 72441

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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

    UBN1 for disorders           About GeneDecksing

    OMIM gene information: 609771    OMIM disorders: --

    6 diseases for UBN1:    About MalaCards
    hepatic vein thrombosis    laryngotracheitis    newcastle disease    histoplasmosis
    thrombosis    hepatitis


    Export disorders for UBN1 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 UBN1 gene, integrated from 9 sources (see all 23):
    (articles sorted by number of sources associating them with UBN1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Ubinuclein, a novel nuclear protein interacting with cellular and viral transcription factors. (PubMed id 10725330)1, 2, 3, 9 Aho S.... Uitto J. (2000)
    2. Characterization of the ubinuclein protein as a new member of the nuclear and adhesion complex components (NaCos). (PubMed id 18823282)1, 2, 9 Aho S.... Gruffat H. (2009)
    3. Human UBN1 is an ortholog of yeast Hpc2p and has an essential role in the HIRA/ASF1a chromatin-remodeling pathway in senescent cells. (PubMed id 19029251)1, 2 Banumathy G....Adams P.D. (2008)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. (PubMed id 14718166)1, 2 Tagami H.... Nakatani Y. (2004)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Identification of an ubinuclein 1 region required for stability and function of the human HIRA/UBN1/CABIN1/ASF1a histone H3.3 chaperon e complex. (PubMed id 22401310)1 Tang Y....Marmorstein R. (2012)
    9. Identification of new interacting partners of the shut tling protein ubinuclein (Ubn-1). (PubMed id 22245583)1 Lupo J....Boyer V. (2012)
    10. Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)

    (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: 29855 HGNC: 12506 AceView: UBN1 Ensembl:ENSG00000118900 euGenes: HUgn29855
    ECgene: UBN1 H-InvDB: UBN1

    (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 UBN1 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 UBN1 gene:
    Search GeneIP for patents involving UBN1

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



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