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ZC3H12D Gene

protein-coding   GIFtS: 46
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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ZC3H12D Gene:
ZC3H12D (zinc finger CCCH-type containing 12D) is a protein-coding gene. Diseases associated with ZC3H12D include follicular lymphoma, and patellofemoral pain syndrome. GO annotations related to this gene include endonuclease activity. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NC_018917.2  NT_025741.16  
Regulatory elements:
   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 Chromatin IP Primers for ZC3H12D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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: ZC12D_HUMAN, A2A288 (See protein sequence)
Recommended Name: Probable ribonuclease ZC3H12D  
Size: 527 amino acids; 58078 Da
Cofactor: Magnesium (Potential)
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: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZC3H12D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

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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:
    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,
    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: 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): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004519endonuclease activity IEA--
    GO:0046872metal ion binding IEA--
         
    ZC3H12D for ontologies           About GeneDecksing


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

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ZC3H12D
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    Selected qRT-PCR Assays for microRNAs that regulate ZC3H12D (see all 18):
    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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    (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
    ZC12D_HUMAN, A2A288: 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
    ZC12D_HUMAN, A2A288: Isoform 3: Cytoplasm. Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--
    GO:0043231intracellular membrane-bounded organelle ----

    ZC3H12D 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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ZC3H12D
    Interactions:

        Search GeneGlobe Interaction Network for ZC3H12D

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for ZC3H12D (ENSP000003745924) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RPGRIP1LENSP000003692574STRING: ENSP00000369257
    About this table

    Gene Ontology (GO): 2 biological process terms:    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, 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 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,
    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 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)

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ZC3H12D (see all 18):
    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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      QuantiFast Probe-based Assays in human, mouse, rat ZC3H12D

    Additional mRNA sequence: 

    AK090441.1 BC127762.1 BC157832.1 

    5 DOTS entries:

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

    Selected AceView cDNA sequences (see all 154):

    CB160587 AI400941 BQ185821 AI915665 BC016984 AA425562 BM562747 AA053882 
    AA346646 BC064134 BQ019209 AA132362 BM759666 BM757769 BC020986 AA132257 
    BE887609 CA441139 BQ719311 AK092069 BU076634 AI880208 AI720056 BQ019220 

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


    ZC3H12D expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Adipose (Muscoskeletal System)
             Visceral White Adipocytes Visceral White Adipose
    ZC3H12D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZC3H12D Protein Expression

    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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    (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 ZC3H12D gene from Selected species (see all 8)    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 75.05(n)1
    68.03(a)1
      10 (2.44 cM)5
    2372561  NM_172785.31  NP_766373.21 
     78324705 
    lizard
    (Anolis carolinensis)
    Reptilia ZC3H12D6
    zinc finger CCCH-type containing 12D
    63(a)
    1 ↔ 1
    GL343259.1(168996-182261)


    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)
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    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), 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 ZC3H12D (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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZC3H12D
    DNA2.0 Custom Variant and Variant Library Synthesis for ZC3H12D

    (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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    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

  • 14 diseases for ZC3H12D:    About MalaCards
    follicular lymphoma    patellofemoral pain syndrome    decubitus ulcer    pain agnosia
    agnosia    leukemia/lymphoma, t-cell    acute monocytic leukemia    paine syndrome
    monocytic leukemia    b-cell lymphomas    diffuse large b-cell lymphoma    leukemia
    multiple myeloma    myeloma

    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 10 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. (J. Biol. Chem. 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. (Mol. Cancer Res. 2009)
    3. Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. (PubMed id 17210687)1, 2 Wang M....You M. (Cancer Res. 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. (Br. J. Haematol. 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. (Genome Res. 2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    8. The putative tumor suppressor Zc3h12d modulates toll-like receptor signaling in macrophages. (PubMed id 22036805)1 Huang S....Fu M. (Cell. Signal. 2012)
    9. Wnt signaling and Dupuytren's disease. (PubMed id 21732829)1 Dolmans G.H.... . (N. Engl. J. Med. 2011)
    10. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 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, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    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:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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