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

ZC3H12D Gene

protein-coding   GIFtS: 44
GCID: GC06M149811

Zinc Finger CCCH-Type Containing 12D

(Previous name: chromosome 6 open reading frame 95)
(Previous symbol: C6orf95)
  See related diseases
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
Zinc Finger CCCH-Type Containing 12D1 2     Zinc Finger CCCH Domain-Containing Protein 12D2 3
C6orf951 2 3 5     Chromosome 6 Open Reading Frame 951
p342 3 5     MCP Induced Protein 41
Transformed Follicular Lymphoma2 3     dJ281H8.12
MCPIP42 3     Probable Ribonuclease ZC3H12D2
TFL2 3     Tumor Suppressor TFL2
MCP-Induced Protein 42 3     EC 3.1.-.-3

External Ids:    HGNC: 211751   Entrez Gene: 3401522   Ensembl: ENSG000001781997   OMIM: 6111065   UniProtKB: A2A2883   

Export aliases for ZC3H12D gene to outside databases

Previous GC identifer: GC06M147335


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

GeneCards Summary for ZC3H12D Gene: 
ZC3H12D (zinc finger CCCH-type containing 12D) is a protein-coding gene. Diseases associated with ZC3H12D include pain agnosia, and penis carcinoma. GO annotations related to this gene include endonuclease activity and nucleic acid binding. An important paralog of this gene is NYNRIN.

UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
Function: May regulate cell growth likely by suppressing RB1 phosphorylation. May function as RNase and regulate
the levels of target RNA species (Potential). Serve as a tumor suppressor in certain leukemia cells.
Overexpression inhibits the G1 to S phase progression through suppression of RB1 phosphorylation




(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_000006.11  NC_018917.2  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZC3H12D gene promoter:
         COUP-TF1   AML1a   COUP   RelA   HNF-4alpha2   NF-kappaB   HNF-4alpha1   CP2   COUP-TF   NF-kappaB1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for ZC3H12D

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZC3H12D


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

Entrez Gene cytogenetic band: 6q25.1   Ensembl cytogenetic band:  6q25.1   HGNC cytogenetic band: 6q25.1

ZC3H12D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZC3H12D gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M149811:  view genomic region     (about GC identifiers)

Start:
149,768,766 bp from pter      End:
149,806,197 bp from pter
Size:
37,432 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: ZC12D_HUMAN, A2A288 (See protein sequence)
Recommended Name: Probable ribonuclease ZC3H12D  
Size: 527 amino acids; 58078 Da
Cofactor: Magnesium (Potential)
Subcellular location: Isoform 1: Cytoplasm. Note=Localized as discrete granules. Colocalized with mRNA-processing
body markers, AGO2 and DCP1A, but not with a stress granule maker, TIA1, in the cytoplasm
Subcellular location: Isoform 3: Cytoplasm. Nucleus
Secondary accessions: A1L178 B2RXF4 B7WNU7 B9ZZP9 B9ZZQ0 Q6ZRW2
Alternative splicing: 3 isoforms:  A2A288-1   A2A288-3   A2A288-4   (Ref.1 (BAH28269) sequence is in conflict in positions: 300:V->G, 301:L->V, 302:P->R. Ref.2 (BAC87196) sequence is in conflict in positions: 300:V->G, 301:L->V, 302:P->R)

Explore the universe of human proteins at neXtProt for ZC3H12D: NX_A2A288

Explore proteomics data for ZC3H12D at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_A2A288

  • ZC3H12D Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    ZC3H12D Protein Expression
    REFSEQ proteins: NP_997243.2  
    ENSEMBL proteins: 
     ENSP00000386616   ENSP00000395209   ENSP00000387062   ENSP00000374592   ENSP00000408686  
     ENSP00000440813  

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    Cloud-Clone Corp. Proteins for ZC3H12D 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IEA--
    GO:0043231intracellular membrane-bounded organelle IDA--

    ZC3H12D 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
    HGNC Gene Families: 
    ZC3H: Zinc fingers, CCCH-type domain containing

    2 InterPro protein domains:
     IPR000571 Znf_CCCH
     IPR021869 RNase_Zc3h12

    Graphical View of Domain Structure for InterPro Entry A2A288

    ProtoNet protein and cluster: A2A288

    UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
    Similarity: Belongs to the ZC3H12 family
    Similarity: Contains 1 C3H1-type zinc finger


    ZC3H12D 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: ZC12D_HUMAN, A2A288
    Function: May regulate cell growth likely by suppressing RB1 phosphorylation. May function as RNase and regulate
    the levels of target RNA species (Potential). Serve as a tumor suppressor in certain leukemia cells.
    Overexpression inhibits the G1 to S phase progression through suppression of RB1 phosphorylation
    Induction: By prolonged exposure to bacterial lipopolysaccharides (LPS) in acute monocytic leukemia cell line
    THP-1 cells

         Enzyme Number (IUBMB): EC 3.1.-.-1

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0004519endonuclease activity IEA--
    GO:0008270zinc ion binding ----
    GO:0046872metal ion binding IEA--
         
    ZC3H12D for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for ZC3H12D:
     Increased S DNA content 

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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 ZC3H12D

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030308negative regulation of cell growth IDA19531561
    GO:2000134negative regulation of G1/S transition of mitotic cell cycle IDA19531561

    ZC3H12D for ontologies           About GeneDecksing



    (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 ZC3H12D (ZC12D)

    Search CenterWatch for drugs/clinical trials and news about ZC3H12D / ZC12D

    (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,
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    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 ZC3H12D gene: 
    NM_207360.2  

    Unigene Cluster for ZC3H12D:

    Zinc finger CCCH-type containing 12D
    Hs.632618  [show with all ESTs]
    Unigene Representative Sequence: AK090441
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000498662 ENST00000409806 ENST00000458251 ENST00000409948 ENST00000462655
    ENST00000389942(uc010kid.3) ENST00000416573 ENST00000542614(uc003qmn.1)

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    hsa-miR-3942-5p hsa-miR-128 hsa-miR-371-5p hsa-miR-29b-1* hsa-miR-548a-3p hsa-miR-641 hsa-miR-7-1* hsa-miR-3148
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    Additional mRNA sequence: 

    AK090441.1 BC127762.1 BC157832.1 

    5 DOTS entries:

    DT.40223841  DT.95086605  DT.430132  DT.100666862  DT.100763576 

    24/154 AceView cDNA sequences (see all 154):

    AI915665 BQ185821 AI880208 BE887609 AF357880 AI720056 AA425562 BX504568 
    BC016984 BM562747 BM757769 BC064134 BQ007972 AA132257 CB160330 AA132362 
    AK092069 CA441139 CN478570 BU076634 CA418740 BQ019209 AA346646 BQ719311 

    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™, 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

    ZC3H12D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTTCAAAAAT
    ZC3H12D Expression
    About this image


    See ZC3H12D Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZC3H12D

    SOURCE GeneReport for Unigene cluster: Hs.632618

    UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
    Tissue specificity: Expressed in normal human lymphocytes but defective in some leukemia/lymphoma cell lines

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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 ZC3H12D gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zc3h12d1 , 5 zinc finger CCCH type containing 12D1, 5 73.9(n)1
    67.37(a)1
      10 (2.44 cM)5
    2372561  NM_172785.31  NP_766373.21 
     78324705 
    chicken
    (Gallus gallus)
    Aves ZC3H12D1 zinc finger CCCH-type containing 12D 67.09(n)
    68.67(a)
      421623  XM_419661.3  XP_419661.3 
    lizard
    (Anolis carolinensis)
    Reptilia ZC3H12D6
    Uncharacterized protein
    63(a)
    1 ↔ 1
    GL343259.1(168996-182261)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG108896
    --
    29(a)
    1 → many
    3R(15859603-15861777)
    worm
    (Caenorhabditis elegans)
    Secernentea C30F12.16
    Protein C30F12.1
    25(a)
    1 → many
    I(6954411-6961139)


    ENSEMBL Gene Tree for ZC3H12D (if available)
    TreeFam Gene Tree for ZC3H12D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZC3H12D gene
    NYNRIN2  ZC3H12C2  N4BP12  ZC3H12B2  KHNYN2  ZC3H12A2  
    5 SIMAP similar genes for ZC3H12D using alignment to 4 protein entries:     ZC12D_HUMAN (see all proteins):
    ZC3H12B    ZC3H12C    FLJ00361    KHNYN    ZC3H12A

    ZC3H12D for paralogs           About GeneDecksing



    (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

    10/949 SNPs in ZC3H12D are shown (see all 949)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs619972201,2,4
    C,FSome sporadic lung cancer sample4 --149783095(+) TTTCTT/CTATTT 2 /K /R mis13Minor allele frequency- C:0.07NS NA EU 789
    rs2370071,2
    C,F,A,H--149768326(-) GTGTTG/TTTCCA 1 -- ds500114Minor allele frequency- T:0.12NS EA NA 986
    rs1490107571,2
    --149768433(+) GGAGTA/GCAGAG 1 -- ds50010--------
    rs2370061,2
    C,F,A--149768451(-) TGAGAC/TTGTGC 1 -- ds50016Minor allele frequency- T:0.20NA WA EA 364
    rs1855813401,2
    --149768666(+) CCATCA/GTGCCC 1 -- ds50010--------
    rs762455151,2
    C,F--149768755(+) ATAAAG/TAATCC 1 -- ds50011Minor allele frequency- T:0.01NA 120
    rs736179191,2
    C,F--149768786(+) TATTTC/TTGAAG 1 -- ut311Minor allele frequency- T:0.50WA 2
    rs1904368361,2
    --149769106(+) AAAGCA/GTGTCT 1 -- ut310--------
    rs1424931821,2
    --149769152(+) GCCAGA/GCGCGG 1 -- ut310--------
    rs1827655111,2
    --149769174(+) TATAAA/TCCCAG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for ZC3H12D (149768766 - 149806197 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for ZC3H12D:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2670181CNV Deletion23128226
    esv2732859CNV Deletion23290073
    nsv5533CNV Loss18451855
    nsv470866CNV Gain18288195
    nsv464076CNV Gain19166990

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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.)
    About This Section
    OMIM gene information: 611106    OMIM disorders: --

    UniProtKB/Swiss-Prot: ZC12D_HUMAN, A2A288
  • Note=A chromosomal aberration involving ZC3H12D may be the cause of the transformation of follicular
    lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL). Translocation t(2;6)(p12;q25) with IGK. Resulting protein
    may not be expressed

  • 12 diseases for ZC3H12D:    About MalaCards
    pain agnosia    penis carcinoma    follicular lymphoma    patellofemoral pain syndrome
    decubitus ulcer    agnosia    paine syndrome    acute monocytic leukemia
    monocytic leukemia    diffuse large b-cell lymphoma    b-cell lymphomas    leukemia

    3 diseases from the University of Copenhagen DISEASES database for ZC3H12D:
    Pain agnosia     Patellofemoral pain syndrome     Decubitus ulcer

    ZC3H12D for disorders           About GeneDecksing


    Export disorders for ZC3H12D 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 ZC3H12D gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with ZC3H12D)
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    1. A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages. (PubMed id 18178554)1, 2, 3 Liang J....Fu M. (2008)
    2. Inhibition of G(1) to S phase progression by a novel zinc finger protein P58(TFL) at P-bodies. (PubMed id 19531561)1, 2 Minagawa K....Matsui T. (2009)
    3. Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. (PubMed id 17210687)1, 2 Wang M....You M. (2007)
    4. Deregulation of a possible tumour suppressor gene, ZC3H12D, by translocation of IGK@ in transformed follicular lymphoma with t(2;6)(p12;q25). (PubMed id 17854321)1, 2 Minagawa K.... Matsui T. (2007)
    5. 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)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    8. The putative tumor suppressor Zc3h12d modulates toll-l ike receptor signaling in macrophages. (PubMed id 22036805)1 Huang S....Fu M. (2012)
    9. Wnt signaling and Dupuytren's disease. (PubMed id 21732829)1 Dolmans G.H.... . (2011)
    10. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (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)
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    Entrez Gene: 340152 HGNC: 21175 AceView: FLJ46041 Ensembl:ENSG00000178199 euGenes: HUgn340152
    ECgene: ZC3H12D H-InvDB: ZC3H12D

    (According to HUGE)
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      --

    (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 ZC3H12D 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 ZC3H12D gene:
    Search GeneIP for patents involving ZC3H12D

    GeneCards and IP:
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