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    ZBED1 zinc finger BED-type containing 1 [ Homo sapiens (human) ]

    Gene ID: 9189, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZBED1provided by HGNC
    Official Full Name
    zinc finger BED-type containing 1provided by HGNC
    Primary source
    HGNC:HGNC:447
    See related
    Ensembl:ENSG00000214717 Ensembl:ENSG00000292345 MIM:300178; AllianceGenome:HGNC:447
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALTE; DREF; TRAMP; hDREF
    Summary
    This gene is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. It was earlier identified as a gene with similarity to Ac transposable elements, however, was found not to have transposase activity. Later studies show that this gene product is localized in the nucleus and functions as a transcription factor. It binds to DNA elements found in the promoter regions of several genes related to cell proliferation, such as histone H1, hence may have a role in regulating genes related to cell proliferation. Alternatively spliced transcript variants with different 5' untranslated region have been found for this gene. [provided by RefSeq, Jan 2010]
    Expression
    Ubiquitous expression in kidney (RPKM 10.8), colon (RPKM 10.6) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZBED1 in Genome Data Viewer
    Location:
    X;Y
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (2486435..2500976, complement)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (2486435..2500976, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (2099191..2113734, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (2163179..2177723, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (2404476..2419017, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (2354476..2369017, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985677 Neighboring gene H3K27ac hESC enhancer GRCh37_chrY:1956524-1957311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2035872-2036372 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:1993758-1994466 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrY:2010123-2010650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2170834-2171344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2171345-2171853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2180646-2181480 Neighboring gene dehydrogenase/reductase X-linked Neighboring gene uncharacterized LOC124905239 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chrX:2309773-2310384 and GRCh37_chrY:2259846-2260410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2311094-2311904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2467730-2468457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2501116-2501616 Neighboring gene H3K4me1 hESC enhancers GRCh37_chrX:2501617-2502117 and GRCh37_chrY:2451809-2452308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:2476579-2477103 Neighboring gene long intergenic non-protein coding RNA 3112 Neighboring gene microRNA 6089

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985677 Neighboring gene H3K27ac hESC enhancer GRCh37_chrY:1956524-1957311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2035872-2036372 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:1993758-1994466 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrY:2010123-2010650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2170834-2171344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2171345-2171853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2180646-2181480 Neighboring gene dehydrogenase/reductase X-linked Neighboring gene uncharacterized LOC124905239 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chrX:2309773-2310384 and GRCh37_chrY:2259846-2260410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2311094-2311904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2467730-2468457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2501116-2501616 Neighboring gene H3K4me1 hESC enhancers GRCh37_chrX:2501617-2502117 and GRCh37_chrY:2451809-2452308 Neighboring gene long intergenic non-protein coding RNA 3112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:2476579-2477103 Neighboring gene long intergenic non-protein coding RNA 102 Neighboring gene microRNA 6089 Neighboring gene CD99 molecule pseudogene 1

    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. ZBED1 Regulates Genes Important for Multiple Biological Processes of the Placenta. Johansen S, et al. Genes (Basel), 2022 Jan 12. PMID 35052473, Free PMC Article
    2. Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene. Ohshima N, et al. J Biol Chem, 2003 Jun 20. PMID 12663651
    3. Human DREF/ZBED1 is a nuclear protein widely expressed in multiple cell types derived from all three primary germ layers. Hansen SV, et al. PLoS One, 2018. PMID 30304065, Free PMC Article
    4. A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases. Esposito T, et al. Hum Mol Genet, 1999 Jan. PMID 9887332
    5. hDREF regulates cell proliferation and expression of ribosomal protein genes. Yamashita D, et al. Mol Cell Biol, 2007 Mar. PMID 17220279, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZBED1 Regulates Genes Important for Multiple Biological Processes of the Placenta.
      Title: ZBED1 Regulates Genes Important for Multiple Biological Processes of the Placenta.
    2. The pseudoautosomal region of human X and Y chromosome encoded ZBED1 protein was predicted to interact with at least 10 proteins encoded on the somatic chromosomes.
      Title: Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions.
    3. ZBED1 is not a cell proliferation-associated factor such as Drosophila DREF, and our study adds to the cumulative understanding of the functions of ZBED1 in human cells and tissues.
      Title: Human DREF/ZBED1 is a nuclear protein widely expressed in multiple cell types derived from all three primary germ layers.
    4. These findings identify DREF as a novel adenovirus E1A C terminus binding partner and provide evidence supporting a role for DREF in viral replication.
      Title: Adenovirus E1A targets the DREF nuclear factor to regulate virus gene expression, DNA replication, and growth.
    5. expression of hDREF/KIAA0785 may have a role in regulation of human genes related to cell proliferation
      Title: Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene.
    6. self-association of hDREF via the hATC domain is necessary for its nuclear accumulation and DNA binding.
      Title: Human DNA replication-related element binding factor (hDREF) self-association via hATC domain is necessary for its nuclear accumulation and DNA binding.
    7. hDREF is an important transcription factor for cell proliferation which plays roles in cell cycle-dependent regulation of a number of ribosomal protein genes
      Title: hDREF regulates cell proliferation and expression of ribosomal protein genes.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0785

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables SUMO ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables SUMO transferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    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 sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transcription coregulator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation by host of viral genome replication IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein autosumoylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein sumoylation TAS
    Traceable Author Statement
    more info
    		  
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		  
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 SUMO-protein ligase ZBED1
    Names
    Ac-like transposable element
    BED-type zinc finger domain-containing protein 1
    DNA replication-related element binding factor
    dREF homolog
    zinc finger BED domain-containing protein 1

    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.

    Genomic

    1. NG_016364.1 RefSeqGene

      Range
      4992..19533
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171135.2 → NP_001164606.1  E3 SUMO-protein ligase ZBED1

      See identical proteins and their annotated locations for NP_001164606.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      AB018328, AC079176, BC015030, BM980254, DA625185
      Consensus CDS
      CCDS14118.1
      UniProtKB/Swiss-Prot
      O96006, Q96BY4
      Related
      ENSP00000370616.3, ENSP00000518653.1, ENST00000381218.8, ENST00000711169.1
      Conserved Domains (3) summary
      pfam02892
      Location:23 → 72
      zf-BED; BED zinc finger
      pfam05699
      Location:571 → 650
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam14372
      Location:412 → 480
      DUF4413; Domain of unknown function (DUF4413)

    2. NM_001171136.2 → NP_001164607.1  E3 SUMO-protein ligase ZBED1

      See identical proteins and their annotated locations for NP_001164607.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript. Variants 1-3 encode the same protein.
      Source sequence(s)
      AB018328, AC079176, BC015030, BM980254, DA625185
      Consensus CDS
      CCDS14118.1
      UniProtKB/Swiss-Prot
      O96006, Q96BY4
      Related
      ENSP00000498725.1, ENSP00000518654.1, ENST00000652001.1, ENST00000711171.1
      Conserved Domains (3) summary
      pfam02892
      Location:23 → 72
      zf-BED; BED zinc finger
      pfam05699
      Location:571 → 650
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam14372
      Location:412 → 480
      DUF4413; Domain of unknown function (DUF4413)

    3. NM_004729.4 → NP_004720.1  E3 SUMO-protein ligase ZBED1

      See identical proteins and their annotated locations for NP_004720.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate acceptor splice site at the 3' terminal exon compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      AB018328, AC079176, BM980254, DA625185
      Consensus CDS
      CCDS14118.1
      UniProtKB/Swiss-Prot
      O96006, Q96BY4
      Related
      ENSP00000370620.2, ENSP00000518656.1, ENST00000381222.8, ENST00000711173.1
      Conserved Domains (3) summary
      pfam02892
      Location:23 → 72
      zf-BED; BED zinc finger
      pfam05699
      Location:571 → 650
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam14372
      Location:412 → 480
      DUF4413; Domain of unknown function (DUF4413)

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      2486435..2500976 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      2486435..2500976 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      2099191..2113734 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      2163179..2177723 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O96006.1 GenPept UniProtKB/Swiss-Prot:O96006

    Gene LinkOut

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

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