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ZBED4 zinc finger BED-type containing 4 [ Homo sapiens (human) ]

Gene ID: 9889, updated on 2-Nov-2024

Summary

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Official Symbol
ZBED4provided by HGNC
Official Full Name
zinc finger BED-type containing 4provided by HGNC
Primary source
HGNC:HGNC:20721
See related
Ensembl:ENSG00000100426 MIM:612552; AllianceGenome:HGNC:20721
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables identical protein binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 4.8), colon (RPKM 4.3) and 25 other tissues See more
Orthologs
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Genomic context

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See ZBED4 in Genome Data Viewer
Location:
22q13.33
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (49852850..49890080)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50357143..50394562)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50247492..50283728)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene bromodomain containing 1 Neighboring gene suppressor of cytokine signaling 2 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50218197-50218776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13923 Neighboring gene uncharacterized LOC105377205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13924 Neighboring gene basic proline-rich protein-like Neighboring gene sterile alpha motif domain-containing protein 1-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13927 Neighboring gene uncharacterized LOC124905147 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50250325-50250985 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50252588-50253125 Neighboring gene ALG12 alpha-1,6-mannosyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50281931-50282432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50294104-50294824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50294825-50295544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50295545-50296264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50316438-50317008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50317009-50317578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13931 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13932 Neighboring gene cysteine rich with EGF like domains 2 Neighboring gene Sharpr-MPRA regulatory region 8073 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50336353-50337079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50337080-50337805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50340469-50341056 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50343989-50344576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50344577-50345162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50346923-50347508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13939 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13941 Neighboring gene microRNA 6821 Neighboring gene Pim-3 proto-oncogene, serine/threonine kinase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. ZBED4, a novel retinal protein expressed in cones and Müller cells. Farber DB, et al. Adv Exp Med Biol, 2010. PMID 20238005
  2. Support of association between BRD1 and both schizophrenia and bipolar affective disorder. Nyegaard M, et al. Am J Med Genet B Neuropsychiatr Genet, 2010 Mar 5. PMID 19693800
  3. No association of BRD1 and ZBED4 polymorphisms with schizophrenia in the Chinese Han population. Xu F, et al. Psychiatr Genet, 2018 Aug. PMID 29794561
  4. ZBED4, a BED-type zinc-finger protein in the cones of the human retina. Saghizadeh M, et al. Invest Ophthalmol Vis Sci, 2009 Aug. PMID 19369242, Free PMC Article
  5. Human DNA replication-related element binding factor (hDREF) self-association via hATC domain is necessary for its nuclear accumulation and DNA binding. Yamashita D, et al. J Biol Chem, 2007 Mar 9. PMID 17209048

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. There was no association between SNPs in the BRD1 and ZBED4 genes and schizophrenia in the Chinese population.
    Title: No association of BRD1 and ZBED4 polymorphisms with schizophrenia in the Chinese Han population.
  2. ZBED4, a novel protein that in human retina is localized to cone photoreceptors and glial Muller cells.
    Title: ZBED4, a novel retinal protein expressed in cones and Müller cells.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Support of association between BRD1 and both schizophrenia and bipolar affective disorder.
  4. ZBED4 cellular/subcellular localization and domains suggest a regulatory role for this protein, which may exert its effects in cones and Muller cells through multiple ways of action.
    Title: ZBED4, a BED-type zinc-finger protein in the cones of the human retina.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription cis-regulatory region binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in photoreceptor inner segment IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger BED domain-containing protein 4
Names
zinc finger, BED domain containing 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_014838.3 → NP_055653.2  zinc finger BED domain-containing protein 4

    See identical proteins and their annotated locations for NP_055653.2

    Status: VALIDATED

    Source sequence(s)
    AA809789, AL117328, DB457646
    Consensus CDS
    CCDS33677.1
    UniProtKB/Swiss-Prot
    B2RZH1, O75132, Q1ECU0, Q9UGG8
    Related
    ENSP00000216268.4, ENST00000216268.6
    Conserved Domains (2) summary
    pfam02892
    Location:118 → 166
    zf-BED; BED zinc finger
    pfam05699
    Location:1088 → 1164
    Dimer_Tnp_hAT; hAT family C-terminal dimerisation region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    49852850..49890080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441685.1 → XP_047297641.1  zinc finger BED domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    B2RZH1, O75132, Q1ECU0, Q9UGG8

  2. XM_047441686.1 → XP_047297642.1  zinc finger BED domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    B2RZH1, O75132, Q1ECU0, Q9UGG8

  3. XM_047441684.1 → XP_047297640.1  zinc finger BED domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    B2RZH1, O75132, Q1ECU0, Q9UGG8

  4. XM_024452312.2 → XP_024308080.1  zinc finger BED domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    B2RZH1, O75132, Q1ECU0, Q9UGG8
    Conserved Domains (2) summary
    pfam02892
    Location:118 → 166
    zf-BED; BED zinc finger
    pfam05699
    Location:1088 → 1164
    Dimer_Tnp_hAT; hAT family C-terminal dimerisation region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    50357143..50394562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326250.1 → XP_054182225.1  zinc finger BED domain-containing protein 4 isoform X1

  2. XM_054326251.1 → XP_054182226.1  zinc finger BED domain-containing protein 4 isoform X1

  3. XM_054326248.1 → XP_054182223.1  zinc finger BED domain-containing protein 4 isoform X1

  4. XM_054326249.1 → XP_054182224.1  zinc finger BED domain-containing protein 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75132.2 GenPept UniProtKB/Swiss-Prot:O75132

Gene LinkOut

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