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

    Gene ID: 9189, updated on 4-Jul-2021

    Summary

    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 MIM:300178
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See ZBED1 in Genome Data Viewer
    Location:
    X;Y
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (2486435..2500976, complement)
    109.20210514 current GRCh38.p13 (GCF_000001405.39) Y NC_000024.10 (2486435..2500976, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (2404476..2419017, complement)
    105.20201022 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 LOC105379413 Neighboring gene uncharacterized LOC107985677 Neighboring gene dehydrogenase/reductase X-linked Neighboring gene uncharacterized LOC101928092 Neighboring gene microRNA 6089

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379413 Neighboring gene uncharacterized LOC107985677 Neighboring gene dehydrogenase/reductase X-linked Neighboring gene uncharacterized LOC101928092 Neighboring gene microRNA 6089

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0785

    Gene Ontology Provided by GOA

    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
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    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)

    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_001171135.2NP_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
      UniProtKB/TrEMBL
      A0A024RBU4
      Related
      ENSP00000370616.3, ENST00000381218.8
      Conserved Domains (3) summary
      pfam02892
      Location:2372
      zf-BED; BED zinc finger
      pfam05699
      Location:571650
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam14372
      Location:412480
      DUF4413; Domain of unknown function (DUF4413)
    2. NM_001171136.2NP_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
      UniProtKB/TrEMBL
      A0A024RBU4
      Related
      ENSP00000498725.1, ENST00000652001.1
      Conserved Domains (3) summary
      pfam02892
      Location:2372
      zf-BED; BED zinc finger
      pfam05699
      Location:571650
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam14372
      Location:412480
      DUF4413; Domain of unknown function (DUF4413)
    3. NM_004729.4NP_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
      UniProtKB/TrEMBL
      A0A024RBU4
      Related
      ENSP00000370620.2, ENST00000381222.8
      Conserved Domains (3) summary
      pfam02892
      Location:2372
      zf-BED; BED zinc finger
      pfam05699
      Location:571650
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region
      pfam14372
      Location:412480
      DUF4413; Domain of unknown function (DUF4413)

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p13 Primary Assembly

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