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Aliases for ZBED4 Gene

Aliases for ZBED4 Gene

  • Zinc Finger BED-Type Containing 4 2 3 5
  • KIAA0637 4

External Ids for ZBED4 Gene

Previous GeneCards Identifiers for ZBED4 Gene

  • GC22P046837
  • GC22P048466
  • GC22P048568
  • GC22P048635
  • GC22P050247
  • GC22P033189

Summaries for ZBED4 Gene

GeneCards Summary for ZBED4 Gene

ZBED4 (Zinc Finger BED-Type Containing 4) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and protein dimerization activity. An important paralog of this gene is ZBED6.

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZBED4 Gene

Genomics for ZBED4 Gene

Regulatory Elements for ZBED4 Gene

Enhancers for ZBED4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22G050188 1.8 FANTOM5 ENCODE dbSUPER 28.7 +337.2 337238 5.6 HDGF PKNOX1 AGO1 SIN3A ARID4B YBX1 ZNF2 ZNF766 KLF13 ZNF263 TUBGCP6 ENSG00000272836 ZBED4 LOC105373095 MAPK12 ALG12 HDAC10 ENSG00000273253 MAPK11 PLXNB2
GH22G050626 1.3 ENCODE dbSUPER 27.3 +774.2 774181 2.4 HDGF ZNF493 ARID4B SIN3A YBX1 GLI4 ZNF2 GLIS2 KLF7 SP3 TUBGCP6 ENSG00000272836 ZBED4 LOC105373095 DENND6B ARSA ALG12 SHANK3 CPT1B MAPK8IP2
GH22G049942 2 FANTOM5 Ensembl ENCODE dbSUPER 16.2 +95.4 95400 13.5 MLX ZFP64 DMAP1 YBX1 YY1 SLC30A9 ZNF143 SP3 NFYC SSRP1 TUBGCP6 ALG12 ENSG00000272836 DENND6B ZBED4 ENSG00000273192 LOC105373095 PIM3 PANX2 TRABD
GH22G050183 1.6 FANTOM5 ENCODE dbSUPER 15.9 +332.0 331982 3.9 ATF1 ARID4B DMAP1 ZNF2 ZNF48 YY1 ZNF121 GTF3C2 GLIS2 ZNF143 TRABD LOC105373095 SELENOO ZBED4 ALG12 ENSG00000273253 ENSG00000273192 ENSG00000272836 LOC100420885 PANX2
GH22G049790 0.9 dbSUPER 24.9 -62.3 -62285 1.8 ARID4B ZNF48 ZNF2 ZNF121 GLIS2 ZNF766 ZNF143 KLF7 SP3 SP5 ZBED4 BRD1 ENSG00000229409 ENSG00000272836 LOC105373095 LOC105377205 ALG12 CRELD2 GC22M049795 PIR31802
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZBED4 on UCSC Golden Path with GeneCards custom track

Promoters for ZBED4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000147639 158 2401 FOXA2 AGO1 ARID4B SIN3A DMAP1 ZNF2 ZNF143 ZNF207 FOS ZNF263

Genomic Location for ZBED4 Gene

49,853,842 bp from pter
49,890,078 bp from pter
36,237 bases
Plus strand

Genomic View for ZBED4 Gene

Genes around ZBED4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZBED4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZBED4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZBED4 Gene

Proteins for ZBED4 Gene

  • Protein details for ZBED4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger BED domain-containing protein 4
    Protein Accession:
    Secondary Accessions:
    • B2RZH1
    • Q1ECU0
    • Q9UGG8

    Protein attributes for ZBED4 Gene

    1171 amino acids
    Molecular mass:
    130322 Da
    Quaternary structure:
    • Homodimer.
    • Sequence=BAA31612.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for ZBED4 Gene

Post-translational modifications for ZBED4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZBED4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZBED4 Gene

Domains & Families for ZBED4 Gene

Gene Families for ZBED4 Gene

Protein Domains for ZBED4 Gene

Suggested Antigen Peptide Sequences for ZBED4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZBED4: view

No data available for UniProtKB/Swiss-Prot for ZBED4 Gene

Function for ZBED4 Gene

Gene Ontology (GO) - Molecular Function for ZBED4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IBA --
GO:0005515 protein binding IPI --
genes like me logo Genes that share ontologies with ZBED4: view
genes like me logo Genes that share phenotypes with ZBED4: view

Animal Model Products

CRISPR Products

miRNA for ZBED4 Gene

miRTarBase miRNAs that target ZBED4

Inhibitory RNA Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZBED4 Gene

Localization for ZBED4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZBED4 Gene

Nucleus. Cytoplasm.

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 ZBED4 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for ZBED4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 19369242
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA,IEA 19369242
genes like me logo Genes that share ontologies with ZBED4: view

Pathways & Interactions for ZBED4 Gene

SuperPathways for ZBED4 Gene

No Data Available

Interacting Proteins for ZBED4 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: O75132-ZBED4_HUMAN ENSP00000216268 for ZBED4 Gene via IID UniProtKB STRING MINT

Gene Ontology (GO) - Biological Process for ZBED4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription from RNA polymerase II promoter IBA --
genes like me logo Genes that share ontologies with ZBED4: view

No data available for Pathways by source and SIGNOR curated interactions for ZBED4 Gene

Drugs & Compounds for ZBED4 Gene

No Compound Related Data Available

Transcripts for ZBED4 Gene

mRNA/cDNA for ZBED4 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(128) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ZBED4 Gene

Zinc finger, BED-type containing 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZBED4 Gene

No ASD Table

Relevant External Links for ZBED4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZBED4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZBED4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZBED4 Gene

This gene is overexpressed in Heart (67.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ZBED4 Gene

Protein tissue co-expression partners for ZBED4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZBED4 Gene:


SOURCE GeneReport for Unigene cluster for ZBED4 Gene:


mRNA Expression by UniProt/SwissProt for ZBED4 Gene:

Tissue specificity: Widely expressed with highest levels in testis, kidney and spinal cord and brain corpus callosum. Expressed in the retina, found in the cone photoreceptors, Mueller cells, cone pedicles and in the innermost retinal layer.

Evidence on tissue expression from TISSUES for ZBED4 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with ZBED4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZBED4 Gene

Orthologs for ZBED4 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZBED4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZBED4 34 35
  • 98.95 (n)
(Mus musculus)
Mammalia Zbed4 35
  • 83 (a)
(Monodelphis domestica)
Mammalia ZBED4 35
  • 82 (a)
(Canis familiaris)
Mammalia ZBED4 34 35
  • 81.64 (n)
(Rattus norvegicus)
Mammalia Zbed4 34
  • 80.86 (n)
(Ornithorhynchus anatinus)
Mammalia ZBED4 35
  • 76 (a)
(Gallus gallus)
Aves ZBED4 34 35
  • 72.96 (n)
(Anolis carolinensis)
Reptilia ZBED4 35
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zbed4 34
  • 65.72 (n)
Str.6285 34
(Danio rerio)
Actinopterygii zbed4 34 35
  • 60.61 (n)
Dr.17906 34
fruit fly
(Drosophila melanogaster)
Insecta CG13775 35
  • 21 (a)
(Caenorhabditis elegans)
Secernentea K09A11.1 35
  • 22 (a)
C53D6.6 35
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 28 (a)
Species where no ortholog for ZBED4 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • 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 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)
  • wheat (Triticum aestivum)

Evolution for ZBED4 Gene

Gene Tree for ZBED4 (if available)
Gene Tree for ZBED4 (if available)

Paralogs for ZBED4 Gene

Paralogs for ZBED4 Gene

genes like me logo Genes that share paralogs with ZBED4: view

Variants for ZBED4 Gene

Sequence variations from dbSNP and Humsavar for ZBED4 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000111270 -- 49,861,578(+) ACAGG(C/T)GCATG intron-variant
rs1000129127 -- 49,872,619(+) CAACC(A/T)CTTGG intron-variant
rs1000149486 -- 49,879,006(+) CGGGT(G/T)TGGTG intron-variant
rs1000163812 -- 49,861,390(+) GCCTG(C/T)CTCAG intron-variant
rs1000171927 -- 49,858,402(+) CCGGA(A/G)TCTTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ZBED4 Gene

Variant ID Type Subtype PubMed ID
esv1290042 CNV deletion 17803354
esv2724709 CNV deletion 23290073
esv2724710 CNV deletion 23290073
esv2724711 CNV deletion 23290073
esv2724712 CNV deletion 23290073
esv3558370 CNV deletion 23714750
esv3568484 CNV loss 25503493
esv997091 CNV deletion 20482838
nsv1072652 CNV deletion 25765185
nsv1126636 CNV deletion 24896259
nsv1130792 CNV deletion 24896259
nsv1136697 CNV deletion 24896259
nsv191151 CNV deletion 16902084
nsv191243 CNV deletion 16902084
nsv471221 CNV loss 18288195
nsv829328 CNV gain 20364138

Variation tolerance for ZBED4 Gene

Residual Variation Intolerance Score: 14.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.93; 35.91% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZBED4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZBED4 Gene

Disorders for ZBED4 Gene

Relevant External Links for ZBED4

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZBED4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZBED4 Gene

Publications for ZBED4 Gene

  1. ZBED4, a BED-type zinc-finger protein in the cones of the human retina. (PMID: 19369242) Saghizadeh M. … Farber D.B. (Invest. Ophthalmol. Vis. Sci. 2009) 3 4 22 64
  2. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PMID: 23533661) Hayward A. … Jern P. (PLoS ONE 2013) 2 3 64
  3. Support of association between BRD1 and both schizophrenia and bipolar affective disorder. (PMID: 19693800) Nyegaard M. … rglum A.D. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2010) 3 46 64
  4. Human DNA replication-related element binding factor (hDREF) self- association via hATC domain is necessary for its nuclear accumulation and DNA binding. (PMID: 17209048) Yamashita D. … Hirose F. (J. Biol. Chem. 2007) 3 4 64
  5. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins J.E. … Dunham I. (Genome Biol. 2004) 3 4 64

Products for ZBED4 Gene

Sources for ZBED4 Gene

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