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

Gene ID: 57673, updated on 11-Apr-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 several processes, including histone modification; negative regulation of macromolecule metabolic process; and protein homooligomerization. Located in heterochromatin; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in stomach (RPKM 1.1), testis (RPKM 1.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q21
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107065182..107115515, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108244038..108294460, complement)
105.20220307 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 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
  2. BEND3 mediates transcriptional repression and heterochromatin organization. Khan A, et al. Transcription, 2015. PMID 26507581, 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 (56) 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)

Genotypes

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 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
part_of 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_2023_10

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

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