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    ZBED6 zinc finger BED-type containing 6 [ Homo sapiens (human) ]

    Gene ID: 100381270, updated on 8-Mar-2024

    Summary

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    Official Symbol
    ZBED6provided by HGNC
    Official Full Name
    zinc finger BED-type containing 6provided by HGNC
    Primary source
    HGNC:HGNC:33273
    See related
    Ensembl:ENSG00000257315 MIM:613512; AllianceGenome:HGNC:33273
    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
    MGR
    Summary
    The protein encoded by this transposon-derived intronless gene is a transcriptional repressor that binds to the consensus sequence 5'-GCTCGC-3'. The encoded protein has been shown to repress IGF2 transcription. This gene is located within the first intron of the ZC3H11A gene. [provided by RefSeq, Jul 2016]
    Orthologs
    mouse all
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    Genomic context

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    See ZBED6 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (203795623..203854124)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (203058813..203118077)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (203764751..203823252)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATPase plasma membrane Ca2+ transporting 4 Neighboring gene uncharacterized LOC102723543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203722055-203722656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2355 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:203741871-203742446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2356 Neighboring gene lymphocyte transmembrane adaptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2357 Neighboring gene uncharacterized LOC128031836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203772353-203772854 Neighboring gene charged multivesicular body protein 5 pseudogene Neighboring gene zinc finger CCCH-type containing 11A Neighboring gene MPRA-validated peak661 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:203810670-203811170 Neighboring gene ribosomal protein L35a pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 5904 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203831257-203831832 Neighboring gene small nuclear ribonucleoprotein polypeptide E Neighboring gene keratin 8 pseudogene 29

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Transcriptional modulator ZBED6 affects cell cycle and growth of human colorectal cancer cells. Akhtar Ali M, et al. Proc Natl Acad Sci U S A, 2015 Jun 23. PMID 26056301, Free PMC Article
    2. Studying phenotypic evolution in domestic animals: a walk in the footsteps of Charles Darwin. Andersson L. Cold Spring Harb Symp Quant Biol, 2009. PMID 20375320
    3. Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells. Wang X, et al. Proc Natl Acad Sci U S A, 2013 Oct 1. PMID 24043816, Free PMC Article
    4. A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth. Butter F, et al. EMBO Rep, 2010 Apr. PMID 20134481, Free PMC Article
    5. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. Markljung E, et al. PLoS Biol, 2009 Dec. PMID 20016685, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of ZBED6 Protects Against Sepsis-Induced Muscle Atrophy by Upregulating DOCK3-Mediated RAC1/PI3K/AKT Signaling Pathway in Pigs.
      Title: Loss of ZBED6 Protects Against Sepsis-Induced Muscle Atrophy by Upregulating DOCK3-Mediated RAC1/PI3K/AKT Signaling Pathway in Pigs.
    2. results of this study show that the effect of ZBED6 on tumor development depends on the genetic background and the transcriptional state of its target genes
      Title: Transcriptional modulator ZBED6 affects cell cycle and growth of human colorectal cancer cells.
    3. Mouse MGR (Zbed6) is a repressor of Igf2.
      Title: A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth.
    4. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation.
      Title: ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1.
    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)

    Genotypes

    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 factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of muscle cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of insulin secretion involved in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		  
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger BED domain-containing protein 6

    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_001174108.2 → NP_001167579.1  zinc finger BED domain-containing protein 6

      See identical proteins and their annotated locations for NP_001167579.1

      Status: REVIEWED

      Source sequence(s)
      AC114402
      Consensus CDS
      CCDS55673.1
      UniProtKB/Swiss-Prot
      P86452
      Conserved Domains (2) summary
      smart00614
      Location:135 → 182
      ZnF_BED; BED zinc finger
      pfam05699
      Location:868 → 948
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region

    2. NM_001395895.1 → NP_001382824.1  zinc finger BED domain-containing protein 6

      Status: REVIEWED

      Source sequence(s)
      AC114402
      Consensus CDS
      CCDS55673.1
      UniProtKB/Swiss-Prot
      P86452
      Related
      ENSP00000447879.1, ENST00000550078.3
      Conserved Domains (2) summary
      smart00614
      Location:135 → 182
      ZnF_BED; BED zinc finger
      pfam05699
      Location:868 → 948
      Dimer_Tnp_hAT; hAT family C-terminal dimerization region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      203795623..203854124
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      203058813..203118077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P86452.1 GenPept UniProtKB/Swiss-Prot:P86452

    Gene LinkOut

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