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ZC3H6 Gene

protein-coding   GIFtS: 43
GCID: GC02P113033

Zinc Finger CCCH-Type Containing 6

(Previous name: zinc finger CCCH-type domain containing 6)
(Previous symbol: ZC3HDC6)
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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 61 2
ZC3HDC61 2 3
Zinc Finger CCCH-Type Domain Containing 61 2
Zinc Finger CCCH Domain-Containing Protein 62
Zinc Finger CCCH Type Domain Containing 62
KIAA20353

External Ids:    HGNC: 247621   Entrez Gene: 3769402   Ensembl: ENSG000001881777   UniProtKB: P611293   

Export aliases for ZC3H6 gene to outside databases

Previous GC identifers: GC02P112774 GC02P105545


(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 ZC3H6 Gene:
ZC3H6 (zinc finger CCCH-type containing 6) is a protein-coding gene. An important paralog of this gene is ZC3H4.


(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_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZC3H6 gene promoter:
         TBP   Elk-1   Pax-5   HSF1 (long)   Gfi-1   POU2F1   COMP1   HOXA5   POU2F1a   HSF1short   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZC3H6 promoter sequence
   Search Chromatin IP Primers for ZC3H6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZC3H6


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

Entrez Gene cytogenetic band: 2q13   Ensembl cytogenetic band:  2q13   HGNC cytogenetic band: 2q13

ZC3H6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZC3H6 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P113033:  view genomic region     (about GC identifiers)

Start:
113,033,171 bp from pter      End:
113,097,640 bp from pter
Size:
64,470 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ZC3H6_HUMAN, P61129 (See protein sequence)
Recommended Name: Zinc finger CCCH domain-containing protein 6  
Size: 1189 amino acids; 131670 Da
Sequence caution: Sequence=BAC85608.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC87128.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC87128.1;
Type=Frameshift; Positions=1120;
Secondary accessions: A9JR71 Q6ZW96

Explore the universe of human proteins at neXtProt for ZC3H6: NX_P61129

Explore proteomics data for ZC3H6 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZC3H6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_940983.2  
    ENSEMBL proteins: 
     ENSP00000386764   ENSP00000340298  

    ZC3H6 Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for ZC3H6 


    (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 P61129

    ProtoNet protein and cluster: P61129

    1 Blocks protein domain: IPB000571 Zn-finger

    UniProtKB/Swiss-Prot: ZC3H6_HUMAN, P61129
    Similarity: Contains 3 C3H1-type zinc fingers


    Find genes that share domains with ZC3H6           About GenesLikeMe


    (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, 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 ZC3H6           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ZC3H6
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for ZC3H6
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for ZC3H6

    miRNA
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    Block miRNA regulation of human, mouse, rat ZC3H6 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate ZC3H6 (see all 131):
    hsa-miR-411* hsa-miR-579 hsa-miR-146a hsa-miR-938 hsa-miR-4275 hsa-miR-200b hsa-miR-877 hsa-miR-374b*
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for ZC3H6
    Predesigned siRNA for gene silencing in human, mouse, rat ZC3H6

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: ZC3H6 (NM_198581)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for ZC3H6
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat ZC3H6

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZC3H6


    (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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--

    Find genes that share ontologies with ZC3H6           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 ZC3H6
    Interactions:

        Search GeneGlobe Interaction Network for ZC3H6

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

    Selected Interacting proteins for ZC3H6 (ENSP000003867644) via UniProtKB, MINT, STRING, and/or I2D (see all 28)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTSENSP000002803624STRING: ENSP00000280362
    CPSF1ENSP000003393534STRING: ENSP00000339353
    CPSF2ENSP000002988754STRING: ENSP00000298875
    RBBP6ENSP000003178724STRING: ENSP00000317872
    SYMPKENSP000002459344STRING: ENSP00000245934
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    Find genes that share ontologies with ZC3H6           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 ZC3H6



    (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 ZC3H6 gene: 
    NM_198581.2  

    Unigene Cluster for ZC3H6:

    Zinc finger CCCH-type containing 6
    Hs.190477  [show with all ESTs]
    Unigene Representative Sequence: NM_198581
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409871 ENST00000476511 ENST00000343936(uc002thr.1 uc002thq.1)

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat ZC3H6 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate ZC3H6 (see all 131):
    hsa-miR-411* hsa-miR-579 hsa-miR-146a hsa-miR-938 hsa-miR-4275 hsa-miR-200b hsa-miR-877 hsa-miR-374b*
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
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    Predesigned siRNA for gene silencing in human, mouse, rat ZC3H6
    Clone
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    OriGene ORF clones in mouse, rat for ZC3H6
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: ZC3H6 (NM_198581)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for ZC3H6
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat ZC3H6
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ZC3H6
      QuantiTect SYBR Green Assays in human, mouse, rat ZC3H6
      QuantiFast Probe-based Assays in human, mouse, rat ZC3H6

    Additional mRNA sequence: 

    AB111887.1 AK123404.1 AK127776.1 AK131416.1 AL831901.1 BC155540.1 BC167154.1 

    6 DOTS entries:

    DT.91664316  DT.108516  DT.70105138  DT.435828  DT.100739743  DT.75176505 

    Selected AceView cDNA sequences (see all 90):

    AI697650 AA948719 AA815218 AA478854 AI816829 BE220073 BX103740 BF437135 
    AA047728 AI963731 AA825406 BM478994 AI220781 BX090791 BM979346 AL831901 
    AI733399 AI241733 AA873249 AI088556 AI791424 BE671018 AI911583 BF223587 

    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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    ZC3H6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTTTGGCGA
    ZC3H6 Expression
    About this image


    ZC3H6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
    ZC3H6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZC3H6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.190477
        Custom PCR Arrays for ZC3H6
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZC3H6

    (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.

    Orthologs for ZC3H6 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zc3h61 , 5 zinc finger CCCH type containing 61, 5 84.06(n)1
    77.62(a)1
      2 (62.63 cM)5
    787511  NM_178404.31  NP_848491.21 
     1289674025 
    chicken
    (Gallus gallus)
    Aves ZC3H61 zinc finger CCCH-type containing 6 71.32(n)
    67.52(a)
      421230  NM_001199450.1  NP_001186379.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    59(a)
    1 → many
    GL343437.1(103413-128333)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia CF592268.12   -- 78.85(n)    CF592268.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5593121 zinc finger CCCH domain-containing protein 6-like 54.35(n)
    49.38(a)
      559312  XM_682645.6  XP_687737.6 
    fruit fly
    (Drosophila melanogaster)
    Insecta su(s)6
    suppressor of sable
    10(a)
    1 → many
    X(529920-537793)
    worm
    (Caenorhabditis elegans)
    Secernentea T26A8.46
    Protein T26A8.4 (T26A8.4) mRNA, complete cds
    19(a)
    1 → many
    IV(8428961-8431493) WBGene00020827


    ENSEMBL Gene Tree for ZC3H6 (if available)
    TreeFam Gene Tree for ZC3H6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZC3H6 gene
    ZC3H42  ZC3H82  

    Find genes that share paralogs with ZC3H6           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 ZC3H6 (see all 1165)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs346239581,2
    C,F--113031217(-) CTGTCT/CCCTGT 1 -- us2k18Minor allele frequency- C:0.31NA CSA WA EA 368
    rs1808370181,2
    --113031317(+) AGAAAA/GGCCTA 1 -- us2k10--------
    rs1459610831,2
    --113031359(+) GTCCTA/GAGATT 1 -- us2k10--------
    rs1141927941,2
    C,F--113031447(+) TTATGG/ATAAAG 1 -- us2k11Minor allele frequency- A:0.02NA 120
    rs1460484821,2
    C--113031460(+) GGCTA-/TTAAGT 1 -- us2k10--------
    rs124785061,2
    C,A,H--113031564(+) AAAAAA/GGGGGC 1 -- us2k13Minor allele frequency- G:0.12NA WA 240
    rs1395055491,2
    --113031781(+) CAGGCA/GGGTAT 1 -- us2k10--------
    rs1853663951,2
    --113031802(+) ACCTCA/TGGTGA 1 -- us2k10--------
    rs1914924011,2
    --113031831(+) CCAAAA/GTGCTG 1 -- us2k10--------
    rs1831479141,2
    C--113031852(+) CGTGAA/GCCATT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZC3H6 (113033171 - 113097640 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ZC3H6 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2672162CNV Deletion23128226
    nsv819480CNV Loss19587683
    nsv874867CNV Loss21882294
    nsv874876CNV Loss21882294
    dgv4279n71CNV Loss21882294
    nsv521956CNV Loss19592680
    nsv874863CNV Loss21882294
    esv29391CNV Gain19812545
    dgv4278n71CNV Gain21882294
    nsv819303CNV Gain19587683

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZC3H6
    DNA2.0 Custom Variant and Variant Library Synthesis for ZC3H6

    (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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    1 disease from the University of Copenhagen DISEASES database for ZC3H6:
    Spina bifida

    Find genes that share disorders with ZC3H6           About GenesLikeMe


    Export disorders for ZC3H6 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 ZC3H6 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ZC3H6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

    (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: 376940 HGNC: 24762 AceView: ZC3HDC6 Ensembl:ENSG00000188177 euGenes: HUgn376940
    ECgene: ZC3H6 H-InvDB: ZC3H6

    (According to HUGE)
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    HUGE: KIAA2035

    (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 ZC3H6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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