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

ZC3H13 Gene

protein-coding   GIFtS: 49
GCID: GC13M046528

zinc finger CCCH-type containing 13

(Previous name: KIAA0853 )
(Previous symbol: KIAA0853)
 Explore 5 diseases affiliated with
ZC3H13 via our new
 Human Malady Compendium 
Biological research products
for ZC3H13
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Zinc Finger CCCH-Type Containing 131 2
KIAA08531 2 3
DKFZp434D18121
Zinc Finger CCCH Domain-Containing Protein 132

External Ids:    HGNC: 203681   Entrez Gene: 230912   Ensembl: ENSG000001232007   UniProtKB: Q5T2003   

Export aliases for ZC3H13 gene to outside databases

Previous GC identifers: GC13M045426 GC13M027333


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Gene Wiki entry for ZC3H13


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.1  NT_024524.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZC3H13 gene promoter:
         AML1a   FOXO3   HNF-4alpha2   Cdc5   HNF-4alpha1   FOXO3b   c-Ets-1   PPAR-alpha   FOXO3a   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZC3H13 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZC3H13

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZC3H13


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

Entrez Gene cytogenetic band: 13q14.13   Ensembl cytogenetic band:  13q14.13   HGNC cytogenetic band: 13q14.11

ZC3H13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZC3H13 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M046528:  view genomic region     (about GC identifiers)

Start:
46,528,600 bp from pter      End:
46,626,894 bp from pter
Size:
98,295 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: ZC3HD_HUMAN, Q5T200 (See protein sequence)
Recommended Name: Zinc finger CCCH domain-containing protein 13  
Size: 1668 amino acids; 196635 Da
Secondary accessions: A2A323 O94936 Q5T1Z9 Q7Z7J3 Q8NDT6 Q9H0L6
Alternative splicing: 2 isoforms:  Q5T200-1   Q5T200-2   (Contains a phosphoserine at position 1453. Contains a phosphoserine at position 1456. Contains a phosphoserine at position 1466)

Explore the universe of human proteins at neXtProt for ZC3H13: NX_Q5T200

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5T200

  • ZC3H13 Protein expression data from MOPED and PaxDb:    About this image 
    ZC3H13 Protein Expression
    REFSEQ proteins: NP_055885.3  
    ENSEMBL proteins: 
     ENSP00000242848   ENSP00000282007   ENSP00000416238   ENSP00000368201  

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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ZC3H13 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR000571 Znf_CCCH

    Graphical View of Domain Structure for InterPro Entry Q5T200

    ProtoNet protein and cluster: Q5T200

    1 Blocks protein family: IPB000571 Zn-finger

    UniProtKB/Swiss-Prot: ZC3HD_HUMAN, Q5T200
    Similarity: Contains 1 C3H1-type zinc finger


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IEA--
         
    ZC3H13 for ontologies           About GeneDecksing


    Phenotypes:
         6 GenomeRNAi human phenotypes for ZC3H13:
     Downregulation of NF-kappaB pa  Downregulation of NF-kappaB pa  Increased HPV18 LCR reporter a  Increased S DNA content 
     S arrest  Synthetic lethal with Ras 

    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for ZC3H13 

    miRNA
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    hsa-miR-302d hsa-miR-520e hsa-miR-302e hsa-miR-221 hsa-miR-520a-3p hsa-miR-372 hsa-miR-520d-3p hsa-miR-302b
    SwitchGear 3'UTR luciferase reporter plasmidZC3H13 3' UTR sequence
    Inhib. RNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZC3H13


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZC3H13

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

    5/37 Interacting proteins for ZC3H13 (Q5T2001, 2, 3 ENSP000002820074) via UniProtKB, MINT, STRING, and/or I2D (see all 37)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SCHIP1Q9P0W51, 3EBI-2679720,EBI-1397509 I2D: score=1 
    YWHAZP631042, 3MINT-3306813 I2D: score=1 
    CCNCP248633, ENSP000003582224I2D: score=1 STRING: ENSP00000358222
    MED1Q156483, ENSP000003006514I2D: score=1 STRING: ENSP00000300651
    MED14O602443, ENSP000003237204I2D: score=1 STRING: ENSP00000323720
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 ZC3H13
    Search CenterWatch for drugs/clinical trials and news about ZC3H13 / ZC3HD 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ZC3H13 gene: 
    NM_015070.3  

    Unigene Cluster for ZC3H13:

    Zinc finger CCCH-type containing 13
    Hs.136102  [show with all ESTs]
    Unigene Representative Sequence: AY283618
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000242848(uc010tfw.1 uc001vat.1) ENST00000282007(uc001vas.1)
    ENST00000470308 ENST00000464597 ENST00000428921 ENST00000378921(uc001vaq.2)


    miRNA
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    8/17 QIAGEN miScript miRNA Assays for microRNAs that regulate ZC3H13 (see all 17):
    hsa-miR-302d hsa-miR-520e hsa-miR-302e hsa-miR-221 hsa-miR-520a-3p hsa-miR-372 hsa-miR-520d-3p hsa-miR-302b
    SwitchGear 3'UTR luciferase reporter plasmidZC3H13 3' UTR sequence
    Inhib. RNA
    Products:
         
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ZC3H13
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    Additional cDNA sequence: 

    AB020660.1 AK001815.1 AK056422.1 AK074924.1 AK092988.1 AL136745.1 AL831833.1 AY283618.1 
    BC019000.2 BC032425.1 BC050658.2 BC062685.1 BC107864.1 

    21 DOTS entries:

    DT.65284215  DT.455108  DT.110411  DT.95258392  DT.92352302  DT.92418508  DT.100813404  DT.407460 
    DT.92436998  DT.100813397  DT.100813401  DT.120791108  DT.40274428  DT.92326246  DT.92413573  DT.95359816 
    DT.97799374  DT.100813399  DT.91747216  DT.95345320  DT.97858505 

    24/309 AceView cDNA sequences (see all 309):

    AU117997 BC050658 AA807559 W67339 BP338157 N50717 BM504539 BE551563 
    BE302735 BG940964 CA428192 BG944805 AW019885 N49498 BG943271 BG943739 
    BQ228808 CA335476 AW629264 BE796172 CA393684 BG943281 CN480622 BE766369 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for ZC3H13 (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^
    SP1:                          -                                                                                                                                 
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 21a · 21b ^ 22 ^ 23 ^ 24
    SP1:                              
    SP2:                              
    SP3:                              
    SP4:                              
    SP5:                              


    ECgene alternative splicing isoforms for ZC3H13

    (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

    ZC3H13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --
    ZC3H13 Expression
    About this image
    See ZC3H13 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZC3H13

    SOURCE GeneReport for Unigene cluster: Hs.136102
        SABiosciences Custom PCR Arrays for ZC3H13

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZC3H13

    (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 eukaryotes.

    Orthologs for ZC3H13 gene from 7/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves ZC3H131 zinc finger CCCH-type containing 13 73.57(n)
    74.52(a)
      418850  XM_417045.3  XP_417045.3 
    lizard
    (Anolis carolinensis)
    Reptilia ZC3H136
    --
    64(a)
    1 ↔ 1
    1(132110939-132147914)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.45902 Xenopus laevis transcribed sequence with weak similarity more 76.28(n)    CA793403.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc663592 hypothetical protein MGC66359 74.6(n)   393494  BC055616.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG133306
    --
    10(a)
    1 ↔ 1
    2R(9402764-9404957)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G534406
    uncharacterized protein
    8(a)
    possible ortholog
    5(21683679-21687970)
    rice
    (Oryza sativa)
    Liliopsida Os.54172 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 72.08(n)    AK068171.1 


    ENSEMBL Gene Tree for ZC3H13 (if available)
    TreeFam Gene Tree for ZC3H13 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZC3H13 gene
    SREK12  LUC7L2  SRSF112  RSRC22  LUC7L32  LUC7L22  PNISR2  RBM252  
    PRPF38B2  TRAF3IP12  

    ZC3H13 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/1432 NCBI SNPs in ZC3H13 are shown (see all 1432    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1897054761,2
    --46535978(+) TACCCC/TACAAA 1 -- ds50010--------
    rs45021171,2
    C,F,A,H--46536052(+) CTTAGT/CGCAAT 1 -- ds500115Minor allele frequency- C:0.01NS EA NA WA CSA 791
    rs1826956511,2
    --46536148(+) TATGAA/GATATG 1 -- ds50010--------
    rs1473405821,2
    --46536288(+) AAATAC/TAGATA 1 -- ds50010--------
    rs125858231,2
    C,F,H--46536291(+) TATAGA/GTAGAT 1 -- ds500123Minor allele frequency- G:0.09NS EA NA 2500
    rs2019808291,2
    C--46536323(-) GTCTTG/TTNNNN 1 -- ut310--------
    rs749365661,2
    F--46536383(+) GCAGCA/CAAAAT 1 -- ut311Minor allele frequency- C:0.06WA 118
    rs1484157611,2
    --46536472(+) AAGTAA/GGGGCC 1 -- ut310--------
    rs1425534411,2
    --46536522(+) AACTTC/GAAATG 1 -- ut310--------
    rs1872727961,2
    --46536767(+) GGCTAC/TATTAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for ZC3H13 (46528600 - 46626894 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 4 variations for ZC3H13
         4 CNVs: 101724 86816 86817 4802

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing ZC3H13
    DNA2.0 Custom Variant and Variant Library Synthesis for ZC3H13

    (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.)
    About This Section

    ZC3H13 for disorders           About GeneDecksing

    5 diseases for ZC3H13:    About MalaCards
    imperforate anus    esotropia    fanconi's anemia    anemia
    malaria

    2 diseases from the University of Copenhagen DISEASES database for ZC3H13:
    Esotropia     Imperforate anus
    Human Genome Epidemiology (HuGE) Navigator: ZC3H13 (1 document)

    Export disorders for ZC3H13 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 ZC3H13 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with ZC3H13)
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    1. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10048485)1, 2, 3 Nagase T....Ohara O. (1998)
    2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
    3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    4. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (2004)
    5. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PubMed id 15144186)1, 2 Brill L.M....Peters E.C. (2004)
    6. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    9. 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)
    10. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23091 HGNC: 20368 AceView: KIAA0853 Ensembl:ENSG00000123200 euGenes: HUgn23091
    ECgene: ZC3H13 H-InvDB: ZC3H13

    (According to HUGE)
    About This Section
    HUGE: KIAA0853

    (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 ZC3H13 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 ZC3H13 gene:
    Search GeneIP for patents involving ZC3H13

    GeneCards and IP:
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