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

ZKSCAN3 Gene

protein-coding   GIFtS: 48
GCID: GC06P028317

zinc finger with KRAB and SCAN domains 3

(Previous names: zinc finger protein 306, zinc finger protein 309 )
(Previous symbols: ZNF306, ZNF309)
 Explore 5 diseases affiliated with
ZKSCAN3 via our new
 Human Malady Compendium 
Biological research products
for ZKSCAN3
    

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

Aliases
Zinc Finger With KRAB And SCAN Domains 31 2     ZSCAN132 3
ZNF3061 2 3 5     ZFP3062
Zinc Finger Protein 3061 2 3     DJ874C20.11
Zinc Finger Protein 3091 2 3     Zfp-473
ZNF3091 2 3     Zinc Finger Protein With KRAB And SCAN Domains 32
ZF471 2     Zinc Finger Protein Zfp472
ZSCAN351 2     ZFP473
Zfp471 2     Zf473
Zinc Finger And SCAN Domain-Containing Protein 132 3     Zfp-473
Zinc Finger Protein 47 Homolog2 3     

External Ids:    HGNC: 138531   Entrez Gene: 803172   Ensembl: ENSG000001892987   OMIM: 6127915   UniProtKB: Q9BRR03   

Export aliases for ZKSCAN3 gene to outside databases

Previous GC identifers: GC06P028426 GC06P028124


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

UniProtKB/Swiss-Prot: ZKSC3_HUMAN, Q9BRR0
Function: Acts as a transcriptional regulator. Binds to the consensus sequence 5'-[GT][AG][AGT]GGGG-3'. Associates with
chromatin at the ITGB4 and VEGF promoters. Activates the transcription of genes associated with colon cancer
progression




(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_000006.11  NC_018917.1  NT_007592.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZKSCAN3 gene promoter:
         GCNF   LUN-1   AP-2gamma   c-Ets-1   GCNF-1   Cart-1   AP-2beta   GCNF-2   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZKSCAN3 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZKSCAN3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZKSCAN3


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

Entrez Gene cytogenetic band: 6p22.1   Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p22.1

ZKSCAN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZKSCAN3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P028317:  view genomic region     (about GC identifiers)

Start:
28,317,691 bp from pter      End:
28,334,524 bp from pter
Size:
16,834 bases      Orientation:
plus 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: ZKSC3_HUMAN, Q9BRR0 (See protein sequence)
Recommended Name: Zinc finger protein with KRAB and SCAN domains 3  
Size: 538 amino acids; 60641 Da
Subcellular location: Nucleus
Secondary accessions: B2R8W2 B3KVC0 H7BXX1 Q5VXH3 Q92972 Q9H4T3
Alternative splicing: 2 isoforms:  Q9BRR0-1   Q9BRR0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ZKSCAN3: NX_Q9BRR0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BRR0

  • ZKSCAN3 Protein expression data from MOPED and PaxDb:    About this image 
    ZKSCAN3 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001229823.1  NP_001229824.1  NP_077819.2  

    ENSEMBL proteins: 
     ENSP00000366465   ENSP00000252211   ENSP00000341883  
    Reactome Protein details: Q9BRR0
    Human Recombinant Protein Products for ZKSCAN3: 
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    Novus Biologicals ZKSCAN3 Proteins
    Novus Biologicals ZKSCAN3 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for ZKSCAN3

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IDA18940803

    ZKSCAN3 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for ZKSCAN3


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

    ZKSCAN3 for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR015880 Znf_C2H2-like
     IPR001909 Krueppel-associated_box
     IPR008916 Retrov_capsid_C
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9BRR0

    ProtoNet protein and cluster: Q9BRR0

    3 Blocks protein families:
    IPB001909 KRAB box
    IPB003309 Transcriptional regulator SCAN
    IPB007086 C2H2-type zinc finger signature


    UniProtKB/Swiss-Prot: ZKSC3_HUMAN, Q9BRR0
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 7 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain
    Similarity: Contains 1 SCAN box domain


    (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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZKSC3_HUMAN, Q9BRR0
    Function: Acts as a transcriptional regulator. Binds to the consensus sequence 5'-[GT][AG][AGT]GGGG-3'. Associates with
    chromatin at the ITGB4 and VEGF promoters. Activates the transcription of genes associated with colon cancer
    progression

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IDA18940803
    GO:0003682chromatin binding IDA18940803
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0008270zinc ion binding IEA--
         
    ZKSCAN3 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for ZKSCAN3 

    miRNA
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    hsa-miR-374b* hsa-miR-3910 hsa-miR-549 hsa-miR-124 hsa-miR-561 hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidZKSCAN3 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 ZKSCAN3


    (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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Generic Transcription Pathway
    Generic Transcription Pathway1.00
    Gene Expression0.46

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    2        Reactome Pathways for ZKSCAN3
        Generic Transcription Pathway
    Gene Expression



    ZKSCAN3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZKSCAN3

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for ZKSCAN3 (Q9BRR03 ENSP000002522114) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GRB2P629933, ENSP000003390074I2D: score=1 STRING: ENSP00000339007
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0016032viral reproduction IEA--
    GO:0045893positive regulation of transcription, DNA-dependent IDA18940803

    ZKSCAN3 for ontologies           About GeneDecksing



    (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 ZKSCAN3
    Search CenterWatch for drugs/clinical trials and news about ZKSCAN3 / ZKSC3 

    (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 ZKSCAN3 gene (3 alternative transcripts): 
    NM_001242894.1  NM_001242895.1  NM_024493.3  

    Unigene Cluster for ZKSCAN3:

    Zinc finger with KRAB and SCAN domains 3
    Hs.380930  [show with all ESTs]
    Unigene Representative Sequence: NM_001242894
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000377255 ENST00000252211(uc010jrc.3 uc003nle.4 uc003nlf.4)
    ENST00000341464

    miRNA
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    6 QIAGEN miScript miRNA Assays for microRNAs that regulate ZKSCAN3:
    hsa-miR-374b* hsa-miR-3910 hsa-miR-549 hsa-miR-124 hsa-miR-561 hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidZKSCAN3 3' UTR sequence
    Inhib. RNA
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ZKSCAN3
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    Additional cDNA sequence: 

    AK091225.1 AK122790.1 AK313532.1 BC006118.1 BT007427.1 U71601.1 

    9 DOTS entries:

    DT.208564  DT.305121  DT.100020799  DT.97833050  DT.91716187  DT.97785867  DT.92420792  DT.121321685 
    DT.97790119 

    24/33 AceView cDNA sequences (see all 33):

    BM918366 BX098589 BM762243 BE278730 AA987348 AK091225 BF896711 BG390695 
    CA395711 NM_024493 AI299042 BU678604 AK122790 BT007427 AI222318 AA580382 
    BC006118 AX746861 AI678222 BQ423950 M86009 AI124541 U71601 AA304455 

    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™, 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

    ZKSCAN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --
    ZKSCAN3 Expression
    About this image
    See ZKSCAN3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZKSCAN3

    SOURCE GeneReport for Unigene cluster: Hs.380930

    UniProtKB/Swiss-Prot: ZKSC3_HUMAN, Q9BRR0
    Tissue specificity: Expressed in colorectal cancers (at protein level)

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    In Situ
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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)
    About This Section
      --

    ENSEMBL Gene Tree for ZKSCAN3 (if available)
    TreeFam Gene Tree for ZKSCAN3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZKSCAN3 gene
    ZNF4962  ZNF4492  ZNF4462  ZSCAN92  ZKSCAN12  ZNF3972  ZNF5002  ZNF2132  
    ZSCAN302  ZNF2322  ZNF2022  ZNF2632  ZKSCAN42  ZNF1742  ZSCAN252  ZNF3962  
    ZSCAN122  ZNF3942  ZSCAN212  ZSCAN232  ZNF1652  ZSCAN162  ZKSCAN82  ZSCAN312  
    ZSCAN222  ZNF242  ZNF182  
    18/422 SIMAP similar genes for ZKSCAN3 using alignment to 1 protein entry:     ZKSC3_HUMAN(see all similar genes):
    ZKSCAN4    DKFZp686G16228    ZNF883    HZF36    ZNF320    ZNF502
    HZF30    ZNF134    ZNF135    ZNF253    ZNF585B    ZNF71
    ZNF772    ZNF782    ZNF98    DKFZp686B16128    KIAA1829    ZFS-1

    ZKSCAN3 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

    10/348 NCBI SNPs in ZKSCAN3 are shown (see all 348    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs755303531,2
    F--28315728(+) TTTGCC/TTTTAT 3 -- us2k11Minor allele frequency- T:0.07EA 120
    rs1457901901,2
    --28315739(+) TTAATG/TGCTAA 3 -- us2k10--------
    rs1910282291,2
    --28315825(+) ATTTTG/TTTTCT 3 -- us2k10--------
    rs1477447311,2
    C--28315829(+) TTTTT-/CTGTAT 3 -- us2k10--------
    rs2019337711,2
    --28315837(+) TATGA-/TTGT  
            
    TGGCT
    3 -- us2k10--------
    rs2132401,2
    C,F,A,H--28315875(+) ATGTTC/TATTAT 3 -- us2k1 tfbs320Minor allele frequency- T:0.39NS EA NA WA CSA 1894
    rs69420301,2
    C,F,A,H--28315958(+) TCTTTA/TCCATT 3 -- us2k115Minor allele frequency- T:0.49NS EA NA WA CSA 792
    rs1477886641,2
    --28315974(+) CTAGTA/CTCTTT 3 -- us2k10--------
    rs606986361,2
    C,F--28316045(+) TGTTTA/GTGCAG 3 -- us2k15Minor allele frequency- G:0.14WA NA EA 362
    rs1469709661,2
    --28316357(+) AGTTCG/TGTTTC 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZKSCAN3 (28317691 - 28334524 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for ZKSCAN3
         1 CNV: 4491

    SABiosciences Cancer Mutation PCR Assays
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    (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

    ZKSCAN3 for disorders           About GeneDecksing

    OMIM gene information: 612791    OMIM disorders: --

    5 diseases for ZKSCAN3:    About MalaCards
    colonic neoplasm    multiple myeloma    myeloma    colon cancer
    colorectal cancer


    Export disorders for ZKSCAN3 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 ZKSCAN3 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with ZKSCAN3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Computer sequence analysis of human highly conserved zinc finger modules. (PubMed id 10520746)1, 2, 3 Petroni D.... Comi P. (1998)
    2. The zinc finger transcription factor ZKSCAN3 promotes prostate cancer cell migration. (PubMed id 22531714)1, 3 Zhang X....Yang L. (2012)
    3. The previously undescribed ZKSCAN3 (ZNF306) is a novel 'driver' of colorectal cancer progression. (PubMed id 18519692)1, 2 Yang L....Boyd D.D. (2008)
    4. Unbiased Screening for Transcriptional Targets of ZKSCAN3 Identifies Integrin {beta}4 and Vascular Endothelial Growth Factor as Downstream Targets. (PubMed id 18940803)1, 2 Yang L....Boyd D.D. (2008)
    5. 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. (2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    8. Evidence of a role for the novel zinc-finger transcri ption factor ZKSCAN3 in modulating Cyclin D2 expression in multiple myeloma. (PubMed id 21057542)1 Yang L....Orlowski R.Z. (2011)
    9. Genome-wide association and large-scale follow up iden tifies 16 new loci influencing lung function. (PubMed id 21946350)1 Soler Artigas M....Tobin M.D. (2011)
    10. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PubMed id 17474147)1 Wu C....Li S.S. (2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 80317 HGNC: 13853 AceView: ZNF306 Ensembl:ENSG00000189298 euGenes: HUgn80317
    ECgene: ZKSCAN3 H-InvDB: ZKSCAN3

    (According to HUGE)
    About This Section
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    (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 ZKSCAN3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for ZKSCAN3 gene:
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