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ZBED3 Gene

protein-coding   GIFtS: 45
GCID: GC05M076367

Zinc Finger, BED-Type Containing 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, BED-Type Containing 31 2
Axin-Interacting Protein2 3
2610005H11Rik2
Zinc Finger BED Domain-Containing Protein 32
Zinc Finger, BED Domain Containing 32

External Ids:    HGNC: 207111   Entrez Gene: 843272   Ensembl: ENSG000001328467   OMIM: 6152505   UniProtKB: Q96IU23   

Export aliases for ZBED3 gene to outside databases

Previous GC identifers: GC05M076606 GC05M076411 GC05M076456 GC05M076408 GC05M071579


(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 ZBED3 Gene:
ZBED3 (zinc finger, BED-type containing 3) is a protein-coding gene. An important paralog of this gene is ZBED2.

UniProtKB/Swiss-Prot: ZBED3_HUMAN, Q96IU2
Function: Acts as a positive regulator in the activation of the canonical Wnt/beta-catenin signaling pathway by
stabilizing cytoplasmic beta-catenin. Involved in transcription activation of Wnt target gene expression (By
similarity)




(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_000005.9  NC_018916.2  NT_034772.7  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZBED3 gene promoter:
         NF-1   NF-1/L   Pax-6   Pax-2a   Tal-1beta   GATA-1   E47   Max   S8   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZBED3 promoter sequence
   Search Chromatin IP Primers for ZBED3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZBED3


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

Entrez Gene cytogenetic band: 5q13.3   Ensembl cytogenetic band:  5q13.3   HGNC cytogenetic band: 5q13.2

ZBED3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZBED3 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M076367:  view genomic region     (about GC identifiers)

Start:
76,367,897 bp from pter      End:
76,383,148 bp from pter
Size:
15,252 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ZBED3_HUMAN, Q96IU2 (See protein sequence)
Recommended Name: Zinc finger BED domain-containing protein 3  
Size: 234 amino acids; 25132 Da
Subunit: Interacts with AXIN1; the interaction is direct, enhanced by protein kinase GSK3B and casein kinase
CSNK1E activities and decreases GSK3B-induced beta-catenin serine and threonine phosphorylations (By similarity)

Explore the universe of human proteins at neXtProt for ZBED3: NX_Q96IU2

Explore proteomics data for ZBED3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZBED3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_115743.1  
    ENSEMBL proteins: 
     ENSP00000255198   ENSP00000427487  

    ZBED3 Human Recombinant Protein Products:

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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:
    ZBED: Zinc fingers, BED-type

    1 InterPro protein domain:
     IPR003656 Znf_BED_prd

    Graphical View of Domain Structure for InterPro Entry Q96IU2

    ProtoNet protein and cluster: Q96IU2

    UniProtKB/Swiss-Prot: ZBED3_HUMAN, Q96IU2
    Similarity: Contains 1 BED-type zinc finger


    Find genes that share domains with ZBED3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: ZBED3_HUMAN, Q96IU2
    Function: Acts as a positive regulator in the activation of the canonical Wnt/beta-catenin signaling pathway by
    stabilizing cytoplasmic beta-catenin. Involved in transcription activation of Wnt target gene expression (By
    similarity)

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with ZBED3           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for ZBED3:
     Wnt reporter downregulated 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ZBED3

    miRNA
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    miRTarBase miRNAs that target ZBED3:
    hsa-mir-17-5p (MIRT050888), hsa-mir-9-5p (MIRT021400), hsa-mir-124-3p (MIRT002674)

    Block miRNA regulation of human, mouse, rat ZBED3 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate ZBED3:
    hsa-miR-9
    SwitchGear 3'UTR luciferase reporter plasmidZBED3 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ZBED3
    Predesigned siRNA for gene silencing in human, mouse, rat ZBED3

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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
    ZBED3_HUMAN, Q96IU2: Cytoplasm (By similarity). Membrane (By similarity). Note=Colocalizes with AXIN1 in the
    cytoplasm (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol4
    nucleus3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol ISS--
    GO:0016020membrane ISS--

    Find genes that share ontologies with ZBED3           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 ZBED3
    Interactions:

        Search GeneGlobe Interaction Network for ZBED3

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

    1 Interacting protein for ZBED3 (ENSP000002551984) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001933negative regulation of protein phosphorylation ISS--
    GO:0016055Wnt signaling pathway IEA--
    GO:0045944positive regulation of transcription from RNA polymerase II promoter ISS--
    GO:0050821protein stabilization ISS--
    GO:0090263positive regulation of canonical Wnt signaling pathway ISS--

    Find genes that share ontologies with ZBED3           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 ZBED3



    (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 ZBED3 gene: 
    NM_032367.2  

    Unigene Cluster for ZBED3:

    Zinc finger, BED-type containing 3
    Hs.584988  [show with all ESTs]
    Unigene Representative Sequence: BU570509
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000255198(uc003kev.1) ENST00000511587 ENST00000505685
    miRNA
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    Block miRNA regulation of human, mouse, rat ZBED3 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate ZBED3:
    hsa-miR-9
    SwitchGear 3'UTR luciferase reporter plasmidZBED3 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat ZBED3
      QuantiFast Probe-based Assays in human, mouse, rat ZBED3

    Additional mRNA sequence: 

    AK223624.1 BC007239.1 

    1 DOTS entry:

    DT.454885 

    Selected AceView cDNA sequences (see all 95):

    BM741545 AI355755 AI399944 AA311214 AI810713 AI421730 NM_032367 BM727024 
    BC007239 CB119841 CA449845 AW301709 AI573007 AI522237 BU521064 BE302693 
    AA568943 BM750164 CD674177 AI810967 AI886180 AK123915 AA190953 BM683576 

    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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    ZBED3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGCCTATACA
    ZBED3 Expression
    About this image

    ZBED3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZBED3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.584988
        Custom PCR Arrays for ZBED3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZBED3

    (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 human and mouse.

    Orthologs for ZBED3 gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zbed31 , 5 zinc finger, BED domain containing 31, 5 68.48(n)1
    54.75(a)1
      13 (49.38 cM)5
    721141  NM_028106.21  NP_082382.11 
     953252375 


    ENSEMBL Gene Tree for ZBED3 (if available)
    TreeFam Gene Tree for ZBED3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZBED3 gene
    ZBED22  
    1 SIMAP similar gene for ZBED3 using alignment to 3 protein entries:     ZBED3_HUMAN (see all proteins):
    ZBED2

    Find genes that share paralogs with ZBED3           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 ZBED3 (see all 98)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs751803941,2
    C,F--76372192(+) GAGCAC/TTATGA 1 -- int11Minor allele frequency- T:0.01NA 120
    rs352475401,2
    C--76372516(+) AACTC-/T/TT  
            
    TTTTT
    1 -- int11CSA 2
    rs623625821,2
    C--76372534(+) TTTGGG/TTAAAA 1 -- ut311Minor allele frequency- T:0.50NA 2
    rs1845165521,2
    --76372556(+) TTCCAC/TGCACC 1 -- ut310--------
    rs731299341,2
    C--76372601(+) GTGTGA/GTAAGT 1 -- ut312Minor allele frequency- G:0.11WA 120
    rs10565871,2
    C,F--76372709(-) GAGCTC/TCAGGA 1 -- ut31 ese36Minor allele frequency- T:0.25MN NA CSA EA 429
    rs10565861,2
    C--76372850(-) CACACC/TCTAAG 1 -- ut31 ese34Minor allele frequency- T:0.19MN NA EA 426
    rs1894385781,2
    --76372895(+) GTAGCG/TGCTGC 1 -- ut310--------
    rs1813483761,2
    C--76372907(+) GGCCTA/GGCTTC 1 -- ut310--------
    rs1395597821,2
    C--76372981(+) GGGGTG/TGGGAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for ZBED3 (76367897 - 76383148 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for ZBED3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv4886CNV Insertion18451855
    esv29310CNV Loss19812545
    nsv469515CNV Loss16826518
    nsv823102CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for ZBED3

    (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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    OMIM gene information: 615250    OMIM disorders: --


    Find genes that share disorders with ZBED3           About GenesLikeMe

    Human Genome Epidemiology (HuGE) Navigator: ZBED3 (5 documents)

    Export disorders for ZBED3 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 ZBED3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ZBED3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PubMed id 23533661)1, 3 Hayward A.... Jern P. (PLoS ONE 2013)
    2. 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)
    3. Genetic risk reclassification for type 2 diabetes by age below or above 50 years using 40 type 2 diabetes risk single nucleotide polymorphisms. (PubMed id 20889853)1 de Miguel-Yanes J.M.... . (Diabetes Care 2011)
    4. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. (PubMed id 20581827)1 Voight B.F.... . (Nat. Genet. 2010)
    5. Identification of zinc-finger BED domain-containing 3 (Zbed3) as a novel Axin-interacting protein that activates Wnt/beta-catenin signaling. (PubMed id 19141611)1 Chen T....Li L. (J. Biol. Chem. 2009)
    6. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    7. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (PubMed id 18691976)2 Daub H.... Mann M. (Mol. Cell 2008)
    8. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
    9. 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)
    10. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. (PubMed id 8125298)1 Maruyama K. and Sugano S. (Gene 1994)

    (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: 84327 HGNC: 20711 AceView: ZBED3 Ensembl:ENSG00000132846 euGenes: HUgn84327
    ECgene: ZBED3 H-InvDB: ZBED3

    (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 ZBED3 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 ZBED3 gene:
    Search GeneIP for patents involving ZBED3

    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, eBioscience, antibodies-online, 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 genOway)
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     Block miRNA regulation of human, mouse, rat ZBED3 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing ZBED3
     DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZBED3 Predesigned siRNA for gene silencing in human, mouse, rat ZBED3
     QuantiFast Probe-based Assays in human, mouse, rat ZBED3 QuantiTect SYBR Green Assays in human, mouse, rat ZBED3
     Custom PCR Arrays for ZBED3 Search Chromatin IP Primers for ZBED3
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     SwitchGear 3'UTR luciferase reporter plasmids for ZBED3
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     genOway: Develop your customized and physiologically relevant rodent model for ZBED3
     antibodies-online antibodies for ZBED3 (23 products)
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