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ZCCHC3 Gene

protein-coding   GIFtS: 46
GCID: GC20P000278

Zinc Finger, CCHC Domain Containing 3

(Previous name: chromosome 20 open reading frame 99)
(Previous symbol: C20orf99)
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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, CCHC Domain Containing 31 2
C20orf991 2 3
Chromosome 20 Open Reading Frame 991
Zinc Finger CCHC Domain-Containing Protein 32

External Ids:    HGNC: 162301   Entrez Gene: 853642   Ensembl: ENSG000001777647   UniProtKB: Q9NUD53   

Export aliases for ZCCHC3 gene to outside databases

Previous GC identifer: GC20P000227


(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 ZCCHC3 Gene:
ZCCHC3 (zinc finger, CCHC domain containing 3) is a protein-coding gene. GO annotations related to this gene include nucleic acid binding.


(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_000020.10  NC_018931.2  NT_011387.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZCCHC3 gene promoter:
         AML1a   GATA-3   C/EBPalpha   GATA-1   GATA-2   CHOP-10   AREB6   Max   c-Myc   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZCCHC3 promoter sequence
   Search Chromatin IP Primers for ZCCHC3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZCCHC3


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

Entrez Gene cytogenetic band: 20p13-p12.2   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13-p12.2

ZCCHC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZCCHC3 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P000278:  view genomic region     (about GC identifiers)

Start:
277,737 bp from pter      End:
280,965 bp from pter
Size:
3,229 bases      Orientation:
plus 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: ZCHC3_HUMAN, Q9NUD5 (See protein sequence)
Recommended Name: Zinc finger CCHC domain-containing protein 3  
Size: 404 amino acids; 43618 Da
Secondary accessions: Q6NT79

Explore the universe of human proteins at neXtProt for ZCCHC3: NX_Q9NUD5

Explore proteomics data for ZCCHC3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys45
  • Modification sites at PhosphoSitePlus

  • See ZCCHC3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_149080.2  
    ENSEMBL proteins: 
     ENSP00000371789  

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    antibodies-online peptides for ZCCHC3

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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:
    ZCCHC: Zinc fingers, CCHC domain containing

    1 InterPro protein domain:
     IPR001878 Znf_CCHC

    Graphical View of Domain Structure for InterPro Entry Q9NUD5

    ProtoNet protein and cluster: Q9NUD5

    1 Blocks protein domain: IPB001878 C2HC-type zinc-finger signature

    UniProtKB/Swiss-Prot: ZCHC3_HUMAN, Q9NUD5
    Similarity: Contains 3 CCHC-type zinc fingers


    Find genes that share domains with ZCCHC3           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): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0008270zinc ion binding IEA--
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with ZCCHC3           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ZCCHC3

    miRNA
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    miRTarBase miRNAs that target ZCCHC3:
    hsa-mir-28-5p (MIRT049989)

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    hsa-miR-124* hsa-miR-3130-5p hsa-miR-15a hsa-miR-200a hsa-miR-10b* hsa-miR-3170 hsa-miR-3148 hsa-miR-4306
    SwitchGear 3'UTR luciferase reporter plasmidZCCHC3 3' UTR sequence
    Inhib. RNA
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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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    cytoskeleton1

    (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 ZCCHC3
    Interactions:

        Search GeneGlobe Interaction Network for ZCCHC3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for ZCCHC3 (Q9NUD53 ENSP000003717894) via UniProtKB, MINT, STRING, and/or I2D (see all 65)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PDPK1O155303I2D: score=1 
    UBCENSP000003448184STRING: ENSP00000344818
    CBX8ENSP000002693854STRING: ENSP00000269385
    KNCNENSP000003796074STRING: ENSP00000379607
    SIRT7ENSP000003294664STRING: ENSP00000329466
    About this table

    (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 ZCCHC3 (ZCHC3)



    (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 ZCCHC3 gene: 
    NM_033089.6  

    Unigene Cluster for ZCCHC3:

    Zinc finger, CCHC domain containing 3
    Hs.28608  [show with all ESTs]
    Unigene Representative Sequence: BC069238
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000382352(uc002wdf.3)
    miRNA
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    hsa-miR-124* hsa-miR-3130-5p hsa-miR-15a hsa-miR-200a hsa-miR-10b* hsa-miR-3170 hsa-miR-3148 hsa-miR-4306
    SwitchGear 3'UTR luciferase reporter plasmidZCCHC3 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat ZCCHC3

    Additional mRNA sequence: 

    AK025768.1 BC036469.2 BC069238.1 BC107584.1 

    4 DOTS entries:

    DT.99953935  DT.448586  DT.95370412  DT.100027424 

    Selected AceView cDNA sequences (see all 202):

    AI217049 BU178334 AI168327 AA745767 BM797621 CA443158 AA127770 BU619366 
    BX089974 CR596693 AA127715 AI061202 H63359 AA127778 BQ233198 AA989093 
    AA699813 AI885041 AI694812 AA033672 AI793231 AI858939 BQ001894 H01405 

    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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    ZCCHC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCCAACTAA
    ZCCHC3 Expression
    About this image

    ZCCHC3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZCCHC3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.28608
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZCCHC3

    (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 ZCCHC3 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zcchc31 , 5 zinc finger, CCHC domain containing 31, 5 84.67(n)1
    85.93(a)1
      2 (74.98 cM)5
    679171  NM_175126.41  NP_780335.11 
     1524119555 
    lizard
    (Anolis carolinensis)
    Reptilia ZCCHC36
    zinc finger, CCHC domain containing 3
    15(a)
    1 ↔ 1
    GL343830.1(166-2187)
    zebrafish
    (Danio rerio)
    Actinopterygii ZCCHC36
    zinc finger, CCHC domain containing 3
    36(a)
    1 ↔ 1
    2(14588404-14588922) ENSDARG00000078237


    ENSEMBL Gene Tree for ZCCHC3 (if available)
    TreeFam Gene Tree for ZCCHC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZCCHC3 gene

    Find genes that share paralogs with ZCCHC3           About GenesLikeMe


    3 Pseudogenes.org Pseudogenes for ZCCHC3
    PGOHUM00000242590 PGOHUM00000239508 PGOHUM00000233632


    (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 ZCCHC3 (see all 123)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1447544311,2
    C--276454(+) TTTCTC/TTTTGG 1 -- us2k10--------
    rs735724891,2
    C,F--276474(+) GATCCC/GCCCAC 1 -- us2k12Minor allele frequency- G:0.04WA 120
    rs1864579421,2
    --276580(+) TCTTCC/TACTTA 1 -- us2k10--------
    rs1478973831,2
    --276621(+) ATTATA/GTGATA 1 -- us2k10--------
    rs1399213721,2
    C--276656(+) TAAGAA/GGAATG 1 -- us2k10--------
    rs1168520161,2
    C,F--276746(+) AAGAAT/CAACAG 1 -- us2k11Minor allele frequency- C:0.03NA 120
    rs1160844491,2
    C,F--276756(+) GAGAAG/ATATGT 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1499813781,2
    C--276806(+) CGAGTA/GTGATC 1 -- us2k10--------
    rs1913053811,2
    --276919(+) ACCAAC/TACCAG 1 -- us2k10--------
    rs60476211,2
    C,F--277032(+) GCTACC/Aggccg 1 -- us2k11Minor allele frequency- A:0.10WA 118

    HapMap Linkage Disequilibrium report for ZCCHC3 (277737 - 280965 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for ZCCHC3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv469544CNV Loss16826518
    dgv65n68CNV Loss17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZCCHC3
    DNA2.0 Custom Variant and Variant Library Synthesis for ZCCHC3

    (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 ZCCHC3           About GenesLikeMe

    Genetic Association Database (GAD): ZCCHC3

    Export disorders for ZCCHC3 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 ZCCHC3 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with ZCCHC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. (PubMed id 17370265)1, 2 Denis N.J.... Figeys D. (Proteomics 2007)
    2. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PubMed id 15592455)1, 2 Rush J.... Comb M.J. (Nat. Biotechnol. 2005)
    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. (Genome Res. 2004)
    4. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    5. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    6. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C.... Cristea I.M. (Mol. Cell. Proteomics 2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    8. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 Complexes in mammalian cells. (PubMed id 21282530)1 Vandamme J.... Angrand P.O. (Mol. Cell. Proteomics 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. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)

    (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: 85364 HGNC: 16230 AceView: ZCCHC3 Ensembl:ENSG00000177764 euGenes: HUgn85364
    ECgene: ZCCHC3 H-InvDB: ZCCHC3

    (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 ZCCHC3 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 ZCCHC3 gene:
    Search GeneIP for patents involving ZCCHC3

    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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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