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ZC3H13 Gene

protein-coding   GIFtS: 51

GC13M045426
zinc finger CCCH-type containing 13
(Previous name: KIAA0853 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: KIAA0853)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
DKFZp434D1812 1, 2
FLJ35669 2
KIAA0853 1, 2, 3
OTTHUMP00000018357 2
Descriptions
zinc finger CCCH-type containing 13 2
External Ids
HGNC: 203681
Entrez Gene: 230912
UniProtKB: Q5T2003
Ensembl: ENSG000001232007
Search outside databases for aliases for ZC3H13 gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
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 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the ZC3H13 gene  

Entrez Gene cytogenetic band: 13q14.12   Ensembl cytogenetic band:  13q14.12   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)

GeneLoc gene densities for chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M045426:     (about GC identifiers)

Start:
45,426,601 bp from pter
End:
45,524,895 bp from pter
Size:
98,295 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000013.9  NT_024524.13  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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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   

Post-translational modifications:

  • Phosphorylated upon DNA damage, probably by ATM or ATR1
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_055885.3  

    ENSEMBL proteins: 
    ENSP00000368201 ENSP00000242848 ENSP00000282007 


    Human Recombinant Proteins 
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    Recombinant Proteins from Abcam (ZC3H13)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 


    Antibodies for ZC3H13: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (ZC3H13), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Novus Biologicals Antibodies for ZC3H13

    Assays for ZC3H13: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    1 InterPro domain/family:
     IPR000571 Znf_CCCH


       GeneDecks  ZC3H13 for the domains selected above  
    About GeneDecksing

    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 MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (ZC3H13)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (KIAA0853)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): BC019000

                  Applied Biosystems Silencer® siRNAs for ZC3H13

                  Sigma-Aldrich siRNA for ZC3H13  
                         Sigma-Aldrich shRNA for ZC3H13  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_015070
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_015070
                                     untagged cDNA clones in CMV expression vector (see all 3): AK001815 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_015070

    3 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676 nucleic acid binding IEA--
    GO:0008270 zinc ion binding IEA--
    GO:0046872 metal ion binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section



    1 Interacting protein for ZC3H13 (Q5T2002) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YWHAZP631042MINT-3306813
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for ZC3H13

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (ZC3H13)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (KIAA0853)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): BC019000

                  Sigma-Aldrich siRNA for ZC3H13  
                         Sigma-Aldrich shRNA for ZC3H13  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_015070  

    REFSEQ mRNAs for ZC3H13 gene: 

    NM_015070.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_015070  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_015070
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_015070
                                     untagged cDNA clones in CMV expression vector (see all 3): AK001815 

    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 

    22 DOTS entries:

    DT.65284215  DT.455108  DT.110411  DT.95258392  DT.92352302  DT.92418508  DT.100813404  DT.407461 
    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 ):

    BU186837 BE551563 AA885613 AI088551 BG943739 BM699307 BM504539 BE766369 
    N50717 BG942948 AA588518 AA807559 NM_015070 AB020660 AA604101 BG943281 
    AW629264 BG942236 BG114807 CA393684 BC050658 AI695267 BX956136 AW237833 

    highest scoring ESTs for ZC3H13:

    AB020660 AI472196 AK056422 AY283618 BE247416 BF107255 BF681397 BI090938 BX504090 CA393684 

    Unigene Cluster for ZC3H13:

    Zinc finger CCCH-type containing 13
    Hs.136102  [show with all ESTs]
    Unigene Representative Sequence: AY283618


    GeneLoc Exon Structure

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

    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:                              

    About this scheme

    ECgene alternative splicing isoforms for ZC3H13

    3 Ensembl transcripts including schematic representations:
    ENST00000378921  ENST00000242848  ENST00000282007  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    ZC3H13 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for ZC3H13

    1 / 2 / 3

    9 probe-sets matching ZC3H13 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    51766_at2, 3 U95-B 1 1.00 1.00 0.84 1.59 AI472196 0.80 1.00 0.91 1

    39924_at2, 3 U95-A 1 1.00 1.00 0.76 0.88 AB020660 0.80 1.00 0.91 1

    62666_r_at2, 3 U95-C 1 0.69 1.00 0.86 0.57 N54540 0.60 1.00 0.82 1

    227536_at2, 3 U133-B 1 1.00 1.00 -- -- AI472196 0.80 1.00 0.91 1

    212402_at2, 3 U133-A 1 1.00 1.00 -- -- BE895685 0.60 1.00 0.82 1

    209851_at2, 3 U133-A 1 1.00 1.00 -- -- AL136745 0.60 1.00 0.82 1

    227536_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    212402_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    209851_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  ZC3H13 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: --

    SOURCE GeneReport for Unigene cluster: Hs.136102
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for ZC3H13 gene from 5/13 species (see all 13 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    ZC3H131   -- zinc finger CCCH-type containing 13 91.85(n)
    94.68(a)
    485453  XM_542572.2  XP_542572.2 
    cow
    (Bos taurus)
    ZC3H131   -- zinc finger CCCH-type containing 13 88.12(n)
    91.8(a)
    540735  XM_612879.3  XP_612879.2 
    rat
    (Rattus norvegicus)
    Zc3h131   -- zinc finger CCCH type containing 13 82.07(n)
    85.71(a)
    305955  XM_224295.4  XP_224295.4 
    mouse
    (Mus musculus)
    Zc3h131, 5 145
    zinc finger CCCH type containing 131, 5 82.69(n)1
    85.99(a)1
    673021  NM_026083.21  NP_080359.21 
     AI1546535  AK0111765  (see all 22)
    chicken
    (Gallus gallus)
    ZC3H131   -- zinc finger CCCH-type containing 13 73.62(n)
    74.51(a)
    418850  XM_417045.2  XP_417045.2 
    About this table        Species with no ortholog for ZC3H13

    ENSEMBL Gene Tree for ZC3H13
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

      --
    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/396 NCBI SNPs in ZC3H13 are shown (see all 396 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 123)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 13 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs45021171,2
    A,C,F,H45434053(+) CTTAGT/CGCAAT 1 -- ng514Minor allele frequency- C:0.01EU EA WA 416
    --
    rs173508331,2
    C,F,H45435758(+) TCATTA/GTACTC 1 -- ut31 ese36Minor allele frequency- G:0.42NA EU EA 440
    rs95342641,2
    C,F,H45439674(+) TTTGTA/TTCTTC 1 E/D mis19Minor allele frequency- T:0.19EU EA WA NA 894
    rs125858231,2
    C,F,H45434292(+) tatagA/Gtagat 1 -- ng5111Minor allele frequency- G:0.10EU EA WA NA 976
    rs10557681,2
    C,H45482562(-) AAAATC/AAAGCC 1 X/S non19Minor allele frequency- A:0.00MN EU EA WA 996
    --
    rs73202091,2
    H45439816(+) TTTGAG/CAACTC 1 C/S mis1 ese34Minor allele frequency- C:0.00EU EA WA 404
    --
    rs115376031,2
    H45461129(-) TCCTCG/TTCGAA 1 R/L mis1 ese34Minor allele frequency- T:0.00EU EA WA 406
    rs11340711,2
    C,F,H45460936(+) CTTTCG/ATGGCG 1 H/H syn114Minor allele frequency- A:0.17EA NS NA EU WA 2190
    rs345022261,2
    C,F45460927(+) CCTTCC/TCTCCT 1 R/R syn11Minor allele frequency- T:0.03NA 76
    rs170675181,2
    F,H45457704(+) TAATCT/CCTCAT 1 R/R syn17Minor allele frequency- C:0.03NA EU EA WA 556
    About this table

    HapMap Linkage Disequilibrium images for ZC3H13 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

      --

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/18 PubMed articles for ZC3H13 gene (see all 18 ):
    (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, 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 ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for ZC3H13:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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