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ZC3H3 Gene

protein-coding   GIFtS: 49
GCID: GC08M144519

Zinc Finger CCCH-Type Containing 3

(Previous name: zinc finger CCCH-type domain containing 3)
(Previous symbol: ZC3HDC3)
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(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 31 2
ZC3HDC31 2 3
Zinc Finger CCCH-Type Domain Containing 31 2
Zinc Finger CCCH Domain-Containing Protein 32
Zinc Finger CCCH Type Domain Containing 32
KIAA01503

External Ids:    HGNC: 289721   Entrez Gene: 231442   Ensembl: ENSG000000141647   UniProtKB: Q8IXZ23   

Export aliases for ZC3H3 gene to outside databases

Previous GC identifers: GC08M144591 GC08M139772


(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 ZC3H3 Gene:
ZC3H3 (zinc finger CCCH-type containing 3) is a protein-coding gene. An important paralog of this gene is CPSF4L.


(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 at NCBI GenBank:
NC_000008.10  NT_008046.17  NC_018919.2  NT_187571.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZC3H3 gene promoter:
         HOXA9B   HOXA9   LHX3b/Lhx3b   HTF   GATA-1   Chx10   LHX3a/Lhx3a   Cart-1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZC3H3 promoter sequence
   Search Chromatin IP Primers for ZC3H3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZC3H3


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

Entrez Gene cytogenetic band: 8q24.3   Ensembl cytogenetic band:  8q24.3   HGNC cytogenetic band: 8q24.3

ZC3H3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZC3H3 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M144519:  view genomic region     (about GC identifiers)

Start:
144,519,825 bp from pter      End:
144,623,623 bp from pter
Size:
103,799 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ZC3H3_HUMAN, Q8IXZ2 (See protein sequence)
Recommended Name: Zinc finger CCCH domain-containing protein 3  
Size: 948 amino acids; 101941 Da
Secondary accessions: Q14163 Q8N4E2 Q9BUS4
Alternative splicing: 2 isoforms:  Q8IXZ2-1   Q8IXZ2-2   

Explore the universe of human proteins at neXtProt for ZC3H3: NX_Q8IXZ2

Explore proteomics data for ZC3H3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZC3H3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055932.2  
    ENSEMBL proteins: 
     ENSP00000262577   ENSP00000436834  

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    antibodies-online peptides for ZC3H3

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    antibodies-online antibodies for ZC3H3 (16 products) 

    ZC3H3 Assay Products:

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    antibodies-online kits for ZC3H3 (4 products) 


    (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

    1 InterPro protein domain:
     IPR000571 Znf_CCCH

    Graphical View of Domain Structure for InterPro Entry Q8IXZ2

    ProtoNet protein and cluster: Q8IXZ2

    1 Blocks protein domain: IPB000571 Zn-finger

    UniProtKB/Swiss-Prot: ZC3H3_HUMAN, Q8IXZ2
    Similarity: Contains 5 C3H1-type zinc fingers


    Find genes that share domains with ZC3H3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with ZC3H3           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ZC3H3

    miRNA
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    miRTarBase miRNAs that target ZC3H3:
    hsa-mir-615-3p (MIRT039752), hsa-mir-18a-3p (MIRT040908)

    Block miRNA regulation of human, mouse, rat ZC3H3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate ZC3H3 (see all 13):
    hsa-miR-98 hsa-miR-137 hsa-let-7d hsa-miR-202 hsa-let-7c hsa-let-7i hsa-let-7g hsa-let-7e
    SwitchGear 3'UTR luciferase reporter plasmidZC3H3 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZC3H3


    (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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1
    golgi apparatus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA16115198

    Find genes that share ontologies with ZC3H3           About GenesLikeMe


    (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 ZC3H3
    Interactions:

        Search GeneGlobe Interaction Network for ZC3H3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

    Selected Interacting proteins for ZC3H3 (ENSP000002625774) via UniProtKB, MINT, STRING, and/or I2D (see all 20)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CPSF1ENSP000003393534STRING: ENSP00000339353
    RBBP6ENSP000003178724STRING: ENSP00000317872
    PAPOLAENSP000002162774STRING: ENSP00000216277
    PAPOLBENSP000003847004STRING: ENSP00000384700
    PAPOLGENSP000002387144STRING: ENSP00000238714
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006378mRNA polyadenylation IMP19364924
    GO:0010793regulation of mRNA export from nucleus IMP19364924
    GO:0016973poly(A)+ mRNA export from nucleus IMP19364924

    Find genes that share ontologies with ZC3H3           About GenesLikeMe



    (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 ZC3H3



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ZC3H3 gene: 
    NM_015117.2  

    Unigene Cluster for ZC3H3:

    Zinc finger CCCH-type containing 3
    Hs.521915  [show with all ESTs]
    Unigene Representative Sequence: NM_015117
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000262577(uc003yyd.2) ENST00000528401
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ZC3H3 (see all 13):
    hsa-miR-98 hsa-miR-137 hsa-let-7d hsa-miR-202 hsa-let-7c hsa-let-7i hsa-let-7g hsa-let-7e
    SwitchGear 3'UTR luciferase reporter plasmidZC3H3 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat ZC3H3
      QuantiFast Probe-based Assays in human, mouse, rat ZC3H3

    Additional mRNA sequence: 

    BC038670.1 D63484.1 

    7 DOTS entries:

    DT.442780  DT.75100207  DT.100009916  DT.100803446  DT.120636026  DT.97839896  DT.95273917 

    Selected AceView cDNA sequences (see all 98):

    D63484 BX341764 AW135082 BQ672330 BM148116 BI554154 AL079951 CK903970 
    BQ671910 AI917334 BX279623 BE386102 BG760659 BM053056 AW024134 BQ641558 
    BE275975 BE410183 AA806585 AW024128 BX390682 BE208462 Z46136 BG058712 

    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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    ZC3H3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACCAGCGTGT
    ZC3H3 Expression
    About this image

    ZC3H3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZC3H3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.521915
        Custom PCR Arrays for ZC3H3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZC3H3

    (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 animals and fungi.

    Orthologs for ZC3H3 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zc3h31 , 5 zinc finger CCCH type containing 31, 5 77.02(n)1
    71.37(a)1
      15 (34.84 cM)5
    2236421  NM_172121.11  NP_742119.11 
     757544475 
    chicken
    (Gallus gallus)
    Aves ZC3H31 zinc finger CCCH-type containing 3 58.06(n)
    52.04(a)
      430349  NM_001031585.2  NP_001026756.1 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.11642 Transcribed sequence with weak similarity to protein more 79.92(n)    142028447 
    zebrafish
    (Danio rerio)
    Actinopterygii zc3h31 zinc finger CCCH-type containing 3 46.73(n)
    41.11(a)
      561182  XM_684588.5  XP_689680.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta ZC3H36
    ZC3H3
    20(a)
    1 ↔ 1
    3L(8500569-8502863)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YTH16
    Essential RNA-binding component of cleavage and po...
    25(a)
    1 → many
    XVI(741438-742064) YPR107C


    ENSEMBL Gene Tree for ZC3H3 (if available)
    TreeFam Gene Tree for ZC3H3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZC3H3 gene
    CPSF4L2  CPSF42  

    Find genes that share paralogs with ZC3H3           About GenesLikeMe



    (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 ZC3H3 (see all 2677)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1858363531,2
    --144519354(+) CCACCC/TAGAGC 1 -- int10--------
    rs1903093301,2
    C--144519382(+) ACAAGC/G/TCTCGT 1 -- int10--------
    rs1150412961,2
    C,F--144519713(+) GAAGCG/ACCTTC 1 -- int12Minor allele frequency- A:0.03WA EA 238
    rs776865731,2
    C,F--144519904(+) GGGCCG/AAAAAC 1 -- ut311Minor allele frequency- A:0.09WA 118
    rs1823574031,2
    --144520120(+) AGGTGA/CGGCTT 1 -- ut310--------
    rs22941171,2
    C,F,A,H--144520147(-) TACCCC/TACAGG 1 -- ut31 ese321Minor allele frequency- T:0.29EA NA NS CSA 3842
    rs2013322311,2
    --144520212(+) AGGCCA/GGTCCC 1 -- ut310--------
    rs1499682261,2
    F--144520231(+) TCACAG/AACGTG 2 /L syn11Minor allele frequency- A:0.00NA 4444
    rs1879021741,2
    C--144520262(+) CCTATG/ACAAAG 1 -- int11Minor allele frequency- A:0.00EU 705
    rs2000722791,2
    C--144520287(+) GTGCCC/TGGAAA 1 -- int11Minor allele frequency- T:0.00EU 443

    HapMap Linkage Disequilibrium report for ZC3H3 (144519825 - 144623623 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ZC3H3 (see all 37):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2738015CNV Deletion23290073
    esv1091073CNV Deletion17803354
    esv2738014CNV Deletion23290073
    esv1005132CNV Deletion20482838
    esv2611442CNV Deletion19546169
    esv998186CNV Deletion20482838
    esv2738016CNV Deletion23290073
    esv2673374CNV Deletion23128226
    dgv7920n71CNV Loss21882294
    dgv7924n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): ZC3H3
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZC3H3
    DNA2.0 Custom Variant and Variant Library Synthesis for ZC3H3

    (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.)
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    Find genes that share disorders with ZC3H3           About GenesLikeMe

    Genetic Association Database (GAD): ZC3H3
    Human Genome Epidemiology (HuGE) Navigator: ZC3H3 (2 documents)

    Export disorders for ZC3H3 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 ZC3H3 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with ZC3H3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. (PubMed id 8590280)1, 2, 3 Nagase T.... Nomura N. (DNA Res. 1995)
    2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PubMed id 19851296)1, 4 Oguri M....Yamada Y. (Am. J. Hypertens. 2010)
    3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PubMed id 20198315)1, 4 Yoshida T....Yamada Y. (Int. J. Mol. Med. 2010)
    4. 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)
    5. A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis. (PubMed id 23509962)1 Greliche N....TrAcgouAt D.A. (BMC Med. Genet. 2013)
    6. The HECT type ubiquitin ligase NEDL2 is degraded by anaphase-promoting complex/cyclosome (APC/C)-Cdh1, and its tight regulation maintains the metaphase to anaphase transition. (PubMed id 24163370)1 Lu L....Zhang L. (J. Biol. Chem. 2013)
    7. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    8. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (Sci. Signal. 2011)
    9. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    10. A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. (PubMed id 19364924)1 Hurt J.A....Silver P.A. (J. Cell Biol. 2009)

    (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: 23144 HGNC: 28972 AceView: ZC3HDC3 Ensembl:ENSG00000014164 euGenes: HUgn23144
    ECgene: ZC3H3 H-InvDB: ZC3H3

    (According to HUGE)
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    HUGE: KIAA0150

    (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 ZC3H3 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 ZC3H3 gene:
    Search GeneIP for patents involving ZC3H3

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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