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

ZMYM3 Gene

protein-coding   GIFtS: 53
GCID: GC0XM070459

zinc finger, MYM-type 3

(Previous name: zinc finger protein 261 )
(Previous symbol: ZNF261)
 Explore 2 diseases affiliated with
ZMYM3 via our new
 Human Malady Compendium 
Biological research products
for ZMYM3
    

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

Aliases
Zinc Finger, MYM-Type 31 2     ZNF198L21 2
DXS6673E1 2 3 5     KIAA03851 3
ZNF2611 2 3 5     XFIM2
Zinc Finger Protein 2611 2 3     Zinc Finger MYM-Type Protein 32
MYM1 2     

External Ids:    HGNC: 130541   Entrez Gene: 92032   Ensembl: ENSG000001471307   OMIM: 3000615   UniProtKB: Q142023   

Export aliases for ZMYM3 gene to outside databases

Previous GC identifers: GC0XM070243 GC0XM070376 GC0XM064255


(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 ZMYM3:
This gene is located on the X chromosome and is subject to X inactivation. It is highly conserved in vertebrates and
most abundantly expressed in the brain. The encoded protein is a component of histone deacetylase-containing
multiprotein complexes that function through modifying chromatin structure to keep genes silent. A chromosomal
translocation (X;13) involving this gene is associated with X-linked mental retardation. Several alternatively spliced
transcript variants have been found for this gene. (provided by RefSeq, Jan 2010)

UniProtKB/Swiss-Prot: ZMYM3_HUMAN, Q14202
Function: Plays a role in the regulation of cell morphology and cytoskeletal organization

Gene Wiki entry for ZMYM3


(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_000023.10  NC_018934.1  NT_011669.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZMYM3 gene promoter:
         Max1   CREB   p53   deltaCREB   GATA-2   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): ZMYM3 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZMYM3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZMYM3


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

Entrez Gene cytogenetic band: Xq13.1   Ensembl cytogenetic band:  Xq13.1   HGNC cytogenetic band: Xq13.1

ZMYM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZMYM3 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM070459:  view genomic region     (about GC identifiers)

Start:
70,459,474 bp from pter      End:
70,475,047 bp from pter
Size:
15,574 bases      Orientation:
minus 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: ZMYM3_HUMAN, Q14202 (See protein sequence)
Recommended Name: Zinc finger MYM-type protein 3  
Size: 1370 amino acids; 152379 Da
Subunit: May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A,
RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=BAA20839.2; Type=Erroneous initiation;
Secondary accessions: D3DVV3 O15089 Q96E26
Alternative splicing: 3 isoforms:  Q14202-1   Q14202-2   Q14202-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ZMYM3: NX_Q14202

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q14202

  • ZMYM3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (4 alternative transcripts): 
    NP_001164633.1  NP_001164634.1  NP_005087.1  NP_963893.1  

    ENSEMBL proteins: 
     ENSP00000322845   ENSP00000363110   ENSP00000363096   ENSP00000363100   ENSP00000363094  
     ENSP00000363093   ENSP00000363090   ENSP00000343909  

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    Uscn Proteins for ZMYM3

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

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


    ZMYM3 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

    ZMYM3 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR021893 DUF3504
     IPR010507 Znf_MYM
     IPR011017 TRASH_dom

    Graphical View of Domain Structure for InterPro Entry Q14202

    ProtoNet protein and cluster: Q14202

    2 Blocks protein families:
    IPB010507 MYM-type zinc finger
    IPB011017 TRASH


    UniProtKB/Swiss-Prot: ZMYM3_HUMAN, Q14202
    Similarity: Contains 9 MYM-type zinc fingers


    (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: ZMYM3_HUMAN, Q14202
    Function: Plays a role in the regulation of cell morphology and cytoskeletal organization

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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:0003677DNA binding TAS10486218
    GO:0008270zinc ion binding IEA--


    ZMYM3 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ZMYM3:
     Increased circadian period len 


    (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 ZMYM3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    5/15 Interacting proteins for ZMYM3 (Q142022, 3 ENSP000003228454) via UniProtKB, MINT, STRING, and/or I2D (see all 15)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KDM1AO603413, ENSP000003490494I2D: score=1 STRING: ENSP00000349049
    HDAC2Q927693, ENSP000003813314I2D: score=1 STRING: ENSP00000381331
    ACTR3P611583I2D: score=5 
    EBF1Q9UH733I2D: score=2 
    EBF3Q9H4W63I2D: score=2 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007010cytoskeleton organization IMP--
    GO:0007275multicellular organismal development TAS10486218
    GO:0022604regulation of cell morphogenesis IMP--


    ZMYM3 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 ZMYM3
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    (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 ZMYM3 gene (4 alternative transcripts): 
    NM_001171162.1  NM_001171163.1  NM_005096.3  NM_201599.2  

    Unigene Cluster for ZMYM3:

    Zinc finger, MYM-type 3
    Hs.522684  [show with all ESTs]
    Unigene Representative Sequence: NM_001171162
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000314425(uc004dzh.2) ENST00000373998(uc004dzj.2) ENST00000489332
    ENST00000373984 ENST00000373988 ENST00000470832 ENST00000460139 ENST00000373982
    ENST00000373981(uc011mpu.2 uc004dzl.4) ENST00000373978 ENST00000353904(uc004dzi.2)


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    hsa-miR-549 hsa-miR-1321 hsa-miR-300 hsa-miR-218-1* hsa-miR-29a hsa-miR-650 hsa-miR-629* hsa-miR-3613-3p
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    Inhib. RNA
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    Additional cDNA sequence: 

    AB002383.1 AK290762.1 AY927528.1 AY927569.1 BC013009.2 BC069057.1 BT007095.1 X95808.1 

    18 DOTS entries:

    DT.97814728  DT.452810  DT.97841218  DT.100746308  DT.100740077  DT.100729208  DT.121290810  DT.100026679 
    DT.65284376  DT.95240040  DT.121290479  DT.121290775  DT.95320492  DT.95196797  DT.100740078  DT.100750223 
    DT.87016340  DT.91732055 

    24/182 AceView cDNA sequences (see all 182):

    AA630070 BE294878 AA235556 BU849599 AI299869 BT007095 CD671129 AL704548 
    AA293806 CB305871 CR614980 AI962853 BX375402 CF995670 BM904097 AL532349 
    BI254234 BM665946 CB139600 BM554778 BM711363 X95808 AA337785 AA317512 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for ZMYM3 (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20a ·
    SP1:                                                              -                                                                                   -     -   
    SP2:              -     -                                                                                                                                       
    SP3:                                                                                                                                                            
    SP4:                    -     -     -     -     -     -     -     -     -     -                                                                                 
    SP5:                                                                                                                                                            

    ExUns: 20b · 20c ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25
    SP1:  -                       -                           
    SP2:                                                      
    SP3:                                                      
    SP4:                                                      
    SP5:                          -                           


    ECgene alternative splicing isoforms for ZMYM3

    (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

    ZMYM3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCCACCCTTG

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

    About this image
    See ZMYM3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZMYM3

    SOURCE GeneReport for Unigene cluster: Hs.522684

    UniProtKB/Swiss-Prot: ZMYM3_HUMAN, Q14202
    Tissue specificity: Most abundant in brain, moderate in muscle and heart, low in other tissues except placenta

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    In Situ
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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.

    Orthologs for ZMYM3 gene from 4/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves ZMYM31 zinc finger, MYM-type 3 74.46(n)
    79.97(a)
      422209  XM_420201.3  XP_420201.3 
    lizard
    (Anolis carolinensis)
    Reptilia ZMYM36
    --
    72(a)
    1 ↔ 1
    GL343599.1(146367-175911)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.112362 Xenopus laevis transcribed sequence with moderate similarity more 76.79(n)    CA790721.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta woc6
    without children
    17(a)
    1 → many
    3R(23082315-23089758)


    ENSEMBL Gene Tree for ZMYM3 (if available)
    TreeFam Gene Tree for ZMYM3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZMYM3 gene
    ZMYM42  ZMYM12  ZMYM52  ZMYM62  ZMYM22  QRICH12  
    2 SIMAP similar genes for ZMYM3 using alignment to 7 protein entries:     ZMYM3_HUMAN (see all proteins):
    ZMYM2    ZMYM4

    ZMYM3 for paralogs           About GeneDecksing



    (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

    10/197 NCBI SNPs in ZMYM3 are shown (see all 197    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1925765201,2
    --70459158(+) GAGCCC/TGCTGG 3 -- ds50010--------
    rs2004217361,2
    C,--70459253(+) TAGCT-/AGTG  
            
    AGTGA
    3 -- ds50010--------
    rs2003410461,2
    --70459260(+) TGAGT-/GAGTATT 3 -- ds50010--------
    rs126890291,2
    C,H,--70459299(+) GTTATA/TAAAAA 3 -- ds50010--------
    rs1884696311,2
    --70459303(+) TAAAAA/CAAAAA 3 -- ds50010--------
    rs1424015991,2
    --70459383(+) AAGAAC/TGATTC 3 -- ds50010--------
    rs1479407241,2
    --70459433(+) TTATCC/TAGTGT 3 -- ds50010--------
    rs31839721,2
    C--70459597(-) TTGTTC/TTGAGG 3 -- ut31 ese32Minor allele frequency- T:0.00NA 4
    rs18030011,2
    C,F,O,H,--70459753(-) TTCTCT/CCTTCC 3 -- ut31 trp38Minor allele frequency- C:0.12MN NS EA NA CSA 605
    rs1813141861,2
    --70460565(+) ACAGAA/CGACCA 3 -- ut310--------

    HapMap Linkage Disequilibrium report for ZMYM3 (70459474 - 70475047 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for ZMYM3
         1 CNV: 7797
    Locus Specific Mutation Databases (LSDB): ZMYM3

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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

    ZMYM3 for disorders           About GeneDecksing

    OMIM gene information: 300061    OMIM disorders: --

    UniProtKB/Swiss-Prot: ZMYM3_HUMAN, Q14202
  • Note=A chromosomal aberration involving ZMYM3 may be a cause of X-linked mental retardation in Xq13.1.
  • Translocation t(X;13)(q13.1;?)

    2 diseases for ZMYM3:    About MalaCards
    x inactivation    intellectual disability


    Export disorders for ZMYM3 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 ZMYM3 gene, integrated from 9 sources (see all 31):
    (articles sorted by number of sources associating them with ZMYM3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of DXS6673E, a candidate gene for X- linked mental retardation in Xq13.1. (PubMed id 8817323)1, 2, 9 van der Maarel S.M....Ropers H.-H. (1996)
    2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    3. 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)
    4. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PubMed id 12493763)1, 2 Hakimi M.A....Shiekhattar R. (2003)
    5. Cloning and mapping of members of the MYM family. (PubMed id 10486218)1, 3 Smedley D.... Shipley J. (1999)
    6. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9205841)1, 2 Nagase T.... Ohara O. (1997)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    9. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (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)
    About This Section
    Entrez Gene: 9203 HGNC: 13054 AceView: ZNF261 Ensembl:ENSG00000147130 euGenes: HUgn9203
    ECgene: ZMYM3 H-InvDB: ZMYM3

    (According to HUGE)
    About This Section
    HUGE: KIAA0385

    (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 ZMYM3 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 ZMYM3 gene:
    Search GeneIP for patents involving ZMYM3

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



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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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