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Aliases for ZBED3 Gene

Aliases for ZBED3 Gene

  • Zinc Finger BED-Type Containing 3 2 3 5
  • Axin-Interacting Protein 3 4
  • Zinc Finger BED Domain-Containing Protein 3 3
  • Zinc Finger, BED Domain Containing 3 3
  • 2610005H11Rik 3

External Ids for ZBED3 Gene

Previous GeneCards Identifiers for ZBED3 Gene

  • GC05M076606
  • GC05M076411
  • GC05M076456
  • GC05M076408
  • GC05M076367
  • GC05M071579

Summaries for ZBED3 Gene

Entrez Gene Summary for ZBED3 Gene

  • This gene belongs to a class of genes that arose through hAT DNA transposition and that encode regulatory proteins. This gene is upregulated in lung cancer tissues, where the encoded protein causes an accumulation of beta-catenin and enhanced lung cancer cell invasion. In addition, the encoded protein can be secreted and be involved in resistance to insulin. [provided by RefSeq, Jul 2016]

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 for ZBED3 Gene

  • 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).

Additional gene information for ZBED3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZBED3 Gene

Genomics for ZBED3 Gene

GeneHancer (GH) Regulatory Elements for ZBED3 Gene

Promoters and enhancers for ZBED3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J077085 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.3 251 2.8 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF207 ZNF143 KLF13 SP3 ZBED3-AS1 ZBED3 ENSG00000284762 ENSG00000285000
GH05J077076 Enhancer 1 Ensembl ENCODE 0.4 +9.8 9822 1.4 CTCF RB1 ZNF223 SIN3A ZNF335 E2F1 CTBP1 POLR2A ZNF207 ZNF143 GC05M077073 RPL7P23 AGGF1 GC05M077081 SNORA47 ZBED3 ENSG00000285000
GH05J077133 Enhancer 0.8 ENCODE 0.2 -45.9 -45948 0.2 FOXA2 INSM2 SIN3A ZNF335 ZNF366 SCRT2 FOS CEBPB REST ZEB2 HMGB1P35 ENSG00000284762 ZBED3-AS1 ZBED3 ENSG00000285000
GH05J077139 Promoter 0.8 EPDnew 0.2 -51.9 -51937 0.1 GLIS1 HMBOX1 HNF4A ZIC2 SP7 ZBTB20 ZNF558 PDE8B HMGB1P35 ENSG00000284762 ZBED3-AS1 ZBED3 ENSG00000285000
GH05J077144 Enhancer 0.6 ENCODE 0.2 -57.4 -57388 0.2 CTCF ZNF654 ZNF10 TRIM22 REST ZNF2 RAD21 YY1 SP1 XRCC5 HMGB1P35 PDE8B ZBED3-AS1 LOC100422441 ZBED3 ENSG00000284762 ENSG00000285000
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZBED3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZBED3 gene promoter:
  • Tal-1beta
  • E47
  • Pax-6
  • GATA-1
  • S8
  • NF-1/L
  • NF-1
  • c-Myc
  • Max
  • Pax-2a

Genomic Locations for ZBED3 Gene

Genomic Locations for ZBED3 Gene
15,252 bases
Minus strand
15,252 bases
Minus strand

Genomic View for ZBED3 Gene

Genes around ZBED3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZBED3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZBED3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZBED3 Gene

Proteins for ZBED3 Gene

  • Protein details for ZBED3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger BED domain-containing protein 3
    Protein Accession:

    Protein attributes for ZBED3 Gene

    234 amino acids
    Molecular mass:
    25132 Da
    Quaternary structure:
    • 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.

neXtProt entry for ZBED3 Gene

Post-translational modifications for ZBED3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZBED3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZBED3 Gene

Domains & Families for ZBED3 Gene

Gene Families for ZBED3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZBED3 Gene


Suggested Antigen Peptide Sequences for ZBED3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZBED3: view

No data available for UniProtKB/Swiss-Prot for ZBED3 Gene

Function for ZBED3 Gene

Molecular function for ZBED3 Gene

UniProtKB/Swiss-Prot 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).

Phenotypes From GWAS Catalog for ZBED3 Gene

Gene Ontology (GO) - Molecular Function for ZBED3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0003677 DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZBED3: view
genes like me logo Genes that share phenotypes with ZBED3: view

Animal Model Products

miRNA for ZBED3 Gene

miRTarBase miRNAs that target ZBED3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZBED3 Gene

Localization for ZBED3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZBED3 Gene

Cytoplasm. Membrane. Note=Colocalizes with AXIN1 in the cytoplasm. {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZBED3 gene
Compartment Confidence
cytosol 4
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZBED3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol ISS --
GO:0016020 membrane ISS --
genes like me logo Genes that share ontologies with ZBED3: view

Pathways & Interactions for ZBED3 Gene

SuperPathways for ZBED3 Gene

No Data Available

Interacting Proteins for ZBED3 Gene

Selected Interacting proteins: Q96IU2-ZBED3_HUMAN for ZBED3 Gene via IID

Gene Ontology (GO) - Biological Process for ZBED3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001933 negative regulation of protein phosphorylation IEA,ISS --
GO:0016055 Wnt signaling pathway IEA --
GO:0045944 positive regulation of transcription by RNA polymerase II ISS --
GO:0050821 protein stabilization IEA,ISS --
GO:0090263 positive regulation of canonical Wnt signaling pathway ISS,IEA --
genes like me logo Genes that share ontologies with ZBED3: view

No data available for Pathways by source and SIGNOR curated interactions for ZBED3 Gene

Drugs & Compounds for ZBED3 Gene

No Compound Related Data Available

Transcripts for ZBED3 Gene

mRNA/cDNA for ZBED3 Gene

(2) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(95) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ZBED3 Gene

Zinc finger, BED-type containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZBED3 Gene

No ASD Table

Relevant External Links for ZBED3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZBED3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZBED3 Gene

Protein differential expression in normal tissues from HIPED for ZBED3 Gene

This gene is overexpressed in Urinary Bladder (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZBED3 Gene

Protein tissue co-expression partners for ZBED3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZBED3 Gene:


SOURCE GeneReport for Unigene cluster for ZBED3 Gene:


Evidence on tissue expression from TISSUES for ZBED3 Gene

  • Skin(4)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with ZBED3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZBED3 Gene

Orthologs for ZBED3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for ZBED3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia ZBED3 33
  • 86.1 (n)
(Mus musculus)
Mammalia Zbed3 16 34 33
  • 68.48 (n)
(Rattus norvegicus)
Mammalia Zbed3 33
  • 68.47 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 58 (a)
Species where no ortholog for ZBED3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for ZBED3 Gene

Gene Tree for ZBED3 (if available)
Gene Tree for ZBED3 (if available)
Evolutionary constrained regions (ECRs) for ZBED3: view image

Paralogs for ZBED3 Gene

Paralogs for ZBED3 Gene

(1) SIMAP similar genes for ZBED3 Gene using alignment to 3 proteins:

  • Q53EL5_HUMAN
genes like me logo Genes that share paralogs with ZBED3: view

Variants for ZBED3 Gene

Sequence variations from dbSNP and Humsavar for ZBED3 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000135858 -- 77,088,636(-) T/TT upstream_transcript_variant
rs1000188611 -- 77,088,903(-) A/G upstream_transcript_variant
rs1000412859 -- 77,081,871(-) A/C intron_variant
rs1000801034 -- 77,084,009(-) A/T intron_variant
rs1000870471 -- 77,082,303(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZBED3 Gene

Variant ID Type Subtype PubMed ID
esv29310 CNV loss 19812545
nsv1027236 CNV gain 25217958
nsv1145065 CNV deletion 24896259
nsv469515 CNV loss 16826518
nsv4886 CNV insertion 18451855
nsv823102 CNV gain 20364138

Variation tolerance for ZBED3 Gene

Gene Damage Index Score: 7.44; 81.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZBED3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZBED3 Gene

Disorders for ZBED3 Gene

Additional Disease Information for ZBED3

No disorders were found for ZBED3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZBED3 Gene

Publications for ZBED3 Gene

  1. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PMID: 23533661) Hayward A … Jern P (PloS one 2013) 2 3 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Prion protein is required for tumor necrosis factor α (TNFα)-triggered nuclear factor κB (NF-κB) signaling and cytokine production. (PMID: 28900035) Wu GR … Li CY (The Journal of biological chemistry 2017) 3 58
  4. The LncRNA ZBED3-AS1 induces chondrogenesis of human synovial fluid mesenchymal stem cells. (PMID: 28431932) Ou F … Zhang Z (Biochemical and biophysical research communications 2017) 3 58
  5. Circulating Zbed3 Levels in Subjects With and Without Metabolic Syndrome. (PMID: 28346859) Hu W … Fan X (Metabolic syndrome and related disorders 2017) 3 58

Products for ZBED3 Gene

Sources for ZBED3 Gene

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