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

    Gene ID: 9889, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 4.8), colon (RPKM 4.3) and 25 other tissues See more
    Orthologs
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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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    NEW Try the new Transcript table

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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