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

ZC3H3 Gene

protein-coding   GIFtS: 46
GCID: GC08M144519

Zinc Finger CCCH-Type Containing 3

(Previous name: zinc finger CCCH-type domain containing 3)
(Previous symbol: ZC3HDC3)
  Search for ZC3H3
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 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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for ZC3H3 Gene: 
ZC3H3 (zinc finger CCCH-type containing 3) is a protein-coding gene. GO annotations related to this gene include molecular_function and nucleic acid binding. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000008.10  NT_008046.16  NC_018919.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for ZC3H3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 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: 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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8IXZ2

  • ZC3H3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    ZC3H3 Protein Expression
    REFSEQ proteins: NP_055932.2  
    ENSEMBL proteins: 
     ENSP00000262577   ENSP00000436834  

    Human Recombinant Protein Products for ZC3H3: 
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    Cloud-Clone Corp. Proteins for ZC3H3 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA16115198

    ZC3H3 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

    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


    ZC3H3 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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0003676nucleic acid binding ----
    GO:0008270zinc ion binding ----
    GO:0046872metal ion binding IEA--
         
    ZC3H3 for ontologies           About GeneDecksing


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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 ZC3H3

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

    ZC3H3 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 ZC3H3

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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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    8/13 QIAGEN miScript miRNA 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
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for ZC3H3
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      QIAGEN 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 

    24/98 AceView cDNA sequences (see all 98):

    BE386102 BI554154 AW135082 AL079951 BM148116 BX341764 BQ672330 BM053056 
    AI917334 BQ671910 CK903970 BX279623 D63484 BG760659 BX341763 BE208462 
    BU166511 BX350451 AW024134 BF825869 BQ017101 CO248777 BM804295 BU931425 

    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

    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


    See ZC3H3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZC3H3

    SOURCE GeneReport for Unigene cluster: Hs.521915
        SABiosciences 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)
    About This Section

    This gene was present in the common ancestor of animals and fungi.

    Orthologs for ZC3H3 gene from 6/12 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 77.17(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 56.85(n)
    51.14(a)
      430349  NM_001031585.1  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 45.84(n)
    40.33(a)
      561182  XM_684588.5  XP_689680.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta ZC3H36
    ZC3H3
    16(a)
    1 ↔ 1
    3L(8500569-8502863)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YTH16
    Essential RNA-binding component of cleavage and po...
    24(a)
    1 → many
    XVI(741438-742064)


    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)
    About This Section
    Paralogs for ZC3H3 gene
    CPSF4L2  CPSF42  

    ZC3H3 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

    10/2677 SNPs in ZC3H3 are shown (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) 10/37 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
    SABiosciences Cancer Mutation PCR Assays
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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

    ZC3H3 for disorders           About MalaCards

    ZC3H3 for disorders           About GeneDecksing

    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)
    About This Section

    PubMed articles for ZC3H3 gene, integrated from 9 sources (see all 13):
    (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. (1995)
    2. Assessment of a polymorphism of SDK1 with hypertensio n in Japanese Individuals. (PubMed id 19851296)1, 4 Oguri M....Yamada Y. (2010)
    3. Association of genetic variants with hemorrhagic stro ke in Japanese individuals. (PubMed id 20198315)1, 4 Yoshida T....Yamada Y. (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. (2004)
    5. A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis. (PubMed id 23509962)1 Greliche N....Tregouet D.A. (2013)
    6. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. (PubMed id 19364924)1 Hurt J.A....Silver P.A. (2009)
    9. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    10. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)2 Olsen J.V....Mann M. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 23144 HGNC: 28972 AceView: ZC3HDC3 Ensembl:ENSG00000014164 euGenes: HUgn23144
    ECgene: ZC3H3 H-InvDB: ZC3H3

    (According to HUGE)
    About This Section
    HUGE: KIAA0150

    (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 ZC3H3 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 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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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     inGenious Targeting Laboratory - Custom generated mouse model solutions for ZC3H3
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
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