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    BEND3 BEN domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 57673, updated on 10-Dec-2024

    Summary

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    Official Symbol
    BEND3provided by HGNC
    Official Full Name
    BEN domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:23040
    See related
    Ensembl:ENSG00000178409 MIM:616374; AllianceGenome:HGNC:23040
    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
    Also known as
    KIAA1553
    Summary
    Enables rDNA binding activity. Involved in negative regulation of macromolecule biosynthetic process; positive regulation of ATP metabolic process; and protein homooligomerization. Located in heterochromatin; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in stomach (RPKM 1.1), testis (RPKM 1.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BEND3 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107065182..107115515, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108244038..108294460, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (107386386..107436719, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17435 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:107312640-107312741 Neighboring gene CD24 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107361561-107362452 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107382561-107383456 Neighboring gene mitochondrial transcription rescue factor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:107414410-107414593 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107426683-107427338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17439 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107437205-107437968 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:107437969-107438734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24902 Neighboring gene RNA, U6 small nuclear 1299, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107470292-107470792 Neighboring gene decaprenyl diphosphate synthase subunit 2 Neighboring gene ribosomal protein S24 pseudogene 12

    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
    • 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. BEND3 mediates transcriptional repression and heterochromatin organization. Khan A, et al. Transcription, 2015. PMID 26507581, Free PMC Article
    2. BEND3 safeguards pluripotency by repressing differentiation-associated genes. Kurniawan F, et al. Proc Natl Acad Sci U S A, 2022 Mar 1. PMID 35217604, Free PMC Article
    3. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization. Shiheido H, et al. Biochem Biophys Res Commun, 2015 Feb 20. PMID 25600804
    4. Characterization of the NTPR and BD1 interacting domains of the human PICH-BEND3 complex. Pitchai GP, et al. Acta Crystallogr F Struct Biol Commun, 2016 Aug. PMID 27487930, Free PMC Article
    5. BEND3 is involved in the human-specific repression of calreticulin: Implication for the evolution of higher brain functions in human. Aghajanirefah A, et al. Gene, 2016 Jan 15. PMID 26481236

    See all (65) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BEND3 safeguards pluripotency by repressing differentiation-associated genes.
      Title: BEND3 safeguards pluripotency by repressing differentiation-associated genes.
    2. Data indicate BEND3 as a new interaction partner for PICH in mitosis, and have defined the residues within a TPR-BEN domain interface that mediate this interaction.
      Title: A novel TPR-BEN domain interaction mediates PICH-BEND3 association.
    3. Characterization of the NTPR and BD1 interacting domains of the human PICH-BEND3 complex has been reported.
      Title: Characterization of the NTPR and BD1 interacting domains of the human PICH-BEND3 complex.
    4. Data shows that BEND3 associates with chromatin remodeling complexes to modulate gene expression and heterochromatin organization.
      Title: BEND3 mediates transcriptional repression and heterochromatin organization.
    5. propose that there is a link between binding of BEND3 to the CALR rs138452745 C-allele and removal of NFI binding site from this nucleotide, and the evolution of human-specific higher brain functions
      Title: BEND3 is involved in the human-specific repression of calreticulin: Implication for the evolution of higher brain functions in human.
    6. Data show that SUMOylated BANP, E5R, and Nac1 (BEN) domain 3 (BEND3) stabilizes NoRC component TTF-1-interacting protein 5 (Tip5)via association with ubiquitin specific protease 21 (USP21) debiquitinase.
      Title: BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase.
    7. Three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential for its nuclear localization, suggesting that these residues play a role as a functional nuclear localization signals.
      Title: Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization.
    8. associates with heterochromatin and represses transcription
      Title: A BEN-domain-containing protein associates with heterochromatin and represses transcription.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1553

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rDNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables rDNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA methylation-dependent constitutive heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of ATP metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein homooligomerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rDNA heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rDNA heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    BEN domain-containing protein 3
    Names
    BANP, E5R, and Nac1 (BEN) domain 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_001080450.3 → NP_001073919.1  BEN domain-containing protein 3

      See identical proteins and their annotated locations for NP_001073919.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AB046773, AL355586, BC131628
      Consensus CDS
      CCDS34507.1
      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Related
      ENSP00000411268.2, ENST00000429433.3
      Conserved Domains (1) summary
      smart01025
      Location:737 → 816
      BEN; The BEN domain is found in diverse animal proteins

    2. NM_001367314.1 → NP_001354243.1  BEN domain-containing protein 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AL355586
      Consensus CDS
      CCDS34507.1
      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Related
      ENSP00000358038.1, ENST00000369042.6
      Conserved Domains (1) summary
      smart01025
      Location:737 → 816
      BEN; The BEN domain is found in diverse animal proteins

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      107065182..107115515 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536005.4 → XP_011534307.1  BEN domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_011534307.1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Conserved Domains (1) summary
      smart01025
      Location:737 → 816
      BEN; The BEN domain is found in diverse animal proteins

    2. XM_005267080.5 → XP_005267137.1  BEN domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005267137.1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
      Conserved Domains (1) summary
      smart01025
      Location:737 → 816
      BEN; The BEN domain is found in diverse animal proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      108244038..108294460 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356110.1 → XP_054212085.1  BEN domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9

    2. XM_054356111.1 → XP_054212086.1  BEN domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A2RRH2, Q5T5X7, Q9HCL9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T5X7.1 GenPept UniProtKB/Swiss-Prot:Q5T5X7

    Gene LinkOut

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

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