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    Bend3 BEN domain containing 3 [ Mus musculus (house mouse) ]

    Gene ID: 331623, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Bend3provided by MGI
    Official Full Name
    BEN domain containing 3provided by MGI
    Primary source
    MGI:MGI:2677212
    See related
    Ensembl:ENSMUSG00000038214 AllianceGenome:MGI:2677212
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    mKIAA1553
    Summary
    Predicted to enable rDNA binding activity. Predicted to be involved in negative regulation of macromolecule biosynthetic process; positive regulation of ATP metabolic process; and protein homooligomerization. Predicted to be located in heterochromatin; nucleolus; and nucleoplasm. Is expressed in 8-cell stage embryo; blastocyst; and compacted morula. Orthologous to human BEND3 (BEN domain containing 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 3.0), limb E14.5 (RPKM 2.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Bend3 in Genome Data Viewer
    Location:
    10 B2; 10 23.0 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (43355130..43391413)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (43479134..43515417)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene prenyl (solanesyl) diphosphate synthase, subunit 2 Neighboring gene STARR-positive B cell enhancer mm9_chr10:43098751-43099051 Neighboring gene ribosomal protein S19, pseudogene 11 Neighboring gene STARR-seq mESC enhancer starr_26505 Neighboring gene STARR-positive B cell enhancer mm9_chr10:43137256-43137557 Neighboring gene STARR-positive B cell enhancer ABC_E9031 Neighboring gene STARR-seq mESC enhancer starr_26511 Neighboring gene ribosomal protein L41 pseudogene Neighboring gene predicted gene, 47889 Neighboring gene presequence translocase associated motor 16 like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation. Yakhou L, et al. Nucleic Acids Res, 2023 Oct 27. PMID 37650637, Free PMC Article
    2. Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation. Zhang J, et al. Science, 2022 Mar 4. PMID 35143257
    3. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Saksouk N, et al. Mol Cell, 2014 Nov 20. PMID 25457167
    4. H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst. Pailles M, et al. Sci Rep, 2022 Aug 16. PMID 35974030, Free PMC Article
    5. An Oct4-centered protein interaction network in embryonic stem cells. van den Berg DLC, et al. Cell Stem Cell, 2010 Apr 2. PMID 20362541, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation.
      Title: A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation.
    2. Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.
      Title: Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.
    3. BEND3 is a key factor in mediating a switch from constitutive to facultative heterochromatin.
      Title: Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2) 

    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 MGI

    Function Evidence Code Pubs
    enables rDNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables rDNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables rDNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA methylation-dependent constitutive heterochromatin formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA methylation-dependent constitutive heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of ATP metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of ATP metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein homooligomerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein homooligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in rDNA heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rDNA heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in rDNA heterochromatin formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in heterochromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    BEN domain-containing protein 3

    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_001359600.1 → NP_001346529.1  BEN domain-containing protein 3

      Status: VALIDATED

      Source sequence(s)
      AK122525, AK143099, BY732040
      Consensus CDS
      CCDS35892.1
      UniProtKB/Swiss-Prot
      Q6PAL0, Q80TC0
      Conserved Domains (1) summary
      smart01025
      Location:734 → 813
      BEN; The BEN domain is found in diverse animal proteins

    2. NM_001359601.1 → NP_001346530.1  BEN domain-containing protein 3

      Status: VALIDATED

      Source sequence(s)
      AC121926, AK122525, AK143099, BY732040
      Consensus CDS
      CCDS35892.1
      UniProtKB/Swiss-Prot
      Q6PAL0, Q80TC0
      Conserved Domains (1) summary
      smart01025
      Location:734 → 813
      BEN; The BEN domain is found in diverse animal proteins

    3. NM_199028.2 → NP_950193.1  BEN domain-containing protein 3

      See identical proteins and their annotated locations for NP_950193.1

      Status: VALIDATED

      Source sequence(s)
      AK122525, BC060240
      Consensus CDS
      CCDS35892.1
      UniProtKB/Swiss-Prot
      Q6PAL0, Q80TC0
      Related
      ENSMUSP00000127351.2, ENSMUST00000167488.9
      Conserved Domains (1) summary
      smart01025
      Location:734 → 813
      BEN; The BEN domain is found in diverse animal proteins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      43355130..43391413
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030245146.2 → XP_030101006.1  BEN domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q6PAL0, Q80TC0
      Conserved Domains (1) summary
      smart01025
      Location:734 → 813
      BEN; The BEN domain is found in diverse animal proteins

    2. XM_006512770.5 → XP_006512833.1  BEN domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006512833.1

      UniProtKB/Swiss-Prot
      Q6PAL0, Q80TC0
      Conserved Domains (1) summary
      smart01025
      Location:734 → 813
      BEN; The BEN domain is found in diverse animal proteins

    3. XM_030245147.2 → XP_030101007.1  BEN domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q6PAL0, Q80TC0
      Conserved Domains (1) summary
      smart01025
      Location:734 → 813
      BEN; The BEN domain is found in diverse animal proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PAL0.1 GenPept UniProtKB/Swiss-Prot:Q6PAL0

    Gene LinkOut

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

    Other Literature Sources
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