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ZIM3 Gene

protein-coding   GIFtS: 45
GCID: GC19M057645

Zinc Finger, Imprinted 3

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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, Imprinted 31 2
Zinc Finger Protein 6572 3
ZNF6572 3
Zinc Finger Imprinted 32

External Ids:    HGNC: 163661   Entrez Gene: 1140262   Ensembl: ENSG000001419467   UniProtKB: Q96PE63   

Export aliases for ZIM3 gene to outside databases

Previous GC identifers: GC19M058544 GC19M058099 GC19M062321 GC19M062337 GC19M053958


(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 ZIM3 Gene:
ZIM3 (zinc finger, imprinted 3) is a protein-coding gene. An important paralog of this gene is ZNF175.

UniProtKB/Swiss-Prot: ZIM3_HUMAN, Q96PE6
Function: May be involved in transcriptional regulation




(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_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Search for regulatory transcription factor binding sites for ZIM3
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZIM3 promoter sequence
   Search Chromatin IP Primers for ZIM3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZIM3


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

Ensembl cytogenetic band:  19q13.43   HGNC cytogenetic band: 19q13.4

ZIM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZIM3 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M057645:  view genomic region     (about GC identifiers)

Start:
57,645,464 bp from pter      End:
57,656,570 bp from pter
Size:
11,107 bases      Orientation:
minus 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: ZIM3_HUMAN, Q96PE6 (See protein sequence)
Recommended Name: Zinc finger imprinted 3  
Size: 472 amino acids; 54498 Da
Secondary accessions: Q14CA6

Explore the universe of human proteins at neXtProt for ZIM3: NX_Q96PE6

Explore proteomics data for ZIM3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZIM3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_443114.1  
    ENSEMBL proteins: 
     ENSP00000269834  
    Reactome Protein details: Q96PE6

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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:
    ZNF: Zinc fingers, C2H2-type

    4 InterPro protein domains:
     IPR001909 Krueppel-associated_box
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q96PE6

    ProtoNet protein and cluster: Q96PE6

    2 Blocks protein domains:
    IPB001909 KRAB box
    IPB007086 C2H2-type zinc finger signature


    UniProtKB/Swiss-Prot: ZIM3_HUMAN, Q96PE6
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 11 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain


    Find genes that share domains with ZIM3           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZIM3_HUMAN, Q96PE6
    Function: May be involved in transcriptional regulation

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity IBA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with ZIM3           About GenesLikeMe


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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 UniProtKB/Swiss-Prot
    ZIM3_HUMAN, Q96PE6: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--

    Find genes that share ontologies with ZIM3           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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    SuperPaths for ZIM3 About    
    See pathways by source

    SuperPathContained pathways About
    1Gene Expression
    Generic Transcription Pathway0.40
    Gene Expression0.40


    Find genes that share SuperPaths with ZIM3           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for ZIM3
        Generic Transcription Pathway


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ZIM3
    Interactions:

        Search GeneGlobe Interaction Network for ZIM3

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IBA--

    Find genes that share ontologies with ZIM3           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 ZIM3



    (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 ZIM3 gene: 
    NM_052882.1  

    Unigene Cluster for ZIM3:

    Zinc finger, imprinted 3
    Hs.348622
    Unigene Representative Sequence: AF365931
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000269834(uc002qnz.1)
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    Additional mRNA sequence: 

    AF365931.1 BC069071.1 BC114446.1 BC114503.1 

    1 DOTS entry:

    DT.99953549 

    3 AceView cDNA sequences:

    AF365931 NM_052882 BC069071 

    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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    ZIM3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAGGTATCTT
    ZIM3 Expression
    About this image

    ZIM3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZIM3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.348622
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    (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 ZIM3 gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zim35 zinc finger, imprinted 3   --   7 6955685 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    30(a)
    1 → many
    GL343417.1(237294-242292)


    ENSEMBL Gene Tree for ZIM3 (if available)
    TreeFam Gene Tree for ZIM3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZIM3 gene
    ZNF1752  ZNF6742  ZNF4872  ZNF5102  ZNF6142  ZNF1572  ZNF262  ZNF6132  
    ZNF812  ZNF6492  ENSG000002673602  ZNF7822  ZNF7932  ZNF252  ZNF5682  ENSG000002365752  
    ENSG000002296312  ZNF5672  ZNF1822  ZNF37A2  ZNF2482  ZNF3002  ZNF3822  RBAK-RBAKDN2  
    Selected SIMAP similar genes for ZIM3 using alignment to 3 protein entries:     ZIM3_HUMAN (see all proteins) (see all similar genes):
    ZNF78L1    ZNF132    ZNF300P1    HZF36    ZNF397    ZSCAN23
    ZNF146    DKFZp666C237    ZNF22    kr-znf3    ZNF304    HZF30
    MGC12518    ZNF    ZNF232    ZNF271    ZNF623    ZNF660

    Find genes that share paralogs with ZIM3           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 ZIM3 (see all 479)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1469402991,2
    C--57644988(+) TGAAAA/GAAGAA 1 -- ds50010--------
    rs72589311,2
    C,F,A,H--57644995(+) AGAAAT/CGTAgg 1 -- ds500112Minor allele frequency- C:0.44EA NS NA WA 632
    rs1385277991,2
    C--57645081(+) CGAGAA/CCATCT 1 -- ds50010--------
    rs1426120631,2
    C--57645086(+) ACATCC/TTGGCC 1 -- ds50010--------
    rs1913629431,2
    --57645088(+) ATCTTA/GGCCAA 1 -- ds50010--------
    rs1434029791,2
    C--57645150(+) GGTGCA/GTGCCT 1 -- ds50010--------
    rs1173802601,2
    C,F--57645163(+) CGTCCT/CAGCTA 1 -- ds50012Minor allele frequency- C:0.07NA EA 240
    rs1850442111,2
    --57645172(+) TACTAC/TTTTGG 1 -- ds50010--------
    rs133449621,2
    C,F--57645244(+) accacC/Tgtact 1 -- ds50011Minor allele frequency- T:0.50WA 2
    rs2014966671,2
    --57645283(+) TCTCC-/AAAAAA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for ZIM3 (57645464 - 57656570 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for ZIM3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2719067CNV Deletion23290073
    esv2280796CNV Deletion18987734
    nsv528378CNV Loss19592680
    nsv817876CNV Gain17921354
    nsv912523CNV Gain21882294

    Human Gene Mutation Database (HGMD): ZIM3
    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for ZIM3

    (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 ZIM3           About GenesLikeMe


    Export disorders for ZIM3 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 ZIM3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ZIM3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain. (PubMed id 11543637)1, 2 Kim J.... Stubbs L. (Genomics 2001)
    3. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    4. 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)

    (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: 114026 HGNC: 16366 AceView: ZIM3 Ensembl:ENSG00000141946 euGenes: HUgn114026
    ECgene: ZIM3 H-InvDB: ZIM3

    (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 ZIM3 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 ZIM3 gene:
    Search GeneIP for patents involving ZIM3

    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, LSBio, eBioscience, 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 inGenious Targeting Laboratory, 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

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