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    UBN1 ubinuclein 1 [ Homo sapiens (human) ]

    Gene ID: 29855, updated on 2-Nov-2024

    Summary

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    Official Symbol
    UBN1provided by HGNC
    Official Full Name
    ubinuclein 1provided by HGNC
    Primary source
    HGNC:HGNC:12506
    See related
    Ensembl:ENSG00000118900 MIM:609771; AllianceGenome:HGNC:12506
    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
    VT; VT4
    Summary
    Cellular senescence is a hallmark of tumor suppression and tissue aging. Senescent cells contain domains of heterochromatin, called senescence-associated heterochromatin foci (SAHF), that repress proliferation-promoting genes. The protein encoded by this gene binds to proliferation-promoting genes and is required for SAHF formation, enhancing methylation of histone H3. [provided by RefSeq, Oct 2016]
    Expression
    Broad expression in testis (RPKM 22.1), bone marrow (RPKM 13.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UBN1 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4847481..4882401)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4876971..4911890)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (4897482..4932402)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4852142-4852642 Neighboring gene Sharpr-MPRA regulatory region 4562 Neighboring gene rogdi atypical leucine zipper Neighboring gene glyoxylate reductase 1 homolog Neighboring gene uncharacterized LOC124903638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4897448-4898290 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:4901871-4903070 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:4908973-4910172 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4920799-4920984 Neighboring gene MPRA-validated peak2474 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4935135-4935635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4945259-4946104 Neighboring gene uncharacterized LOC124903637 Neighboring gene periplakin Neighboring gene uncharacterized LOC105371064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4968443-4968998

    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 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. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. Ricketts MD, et al. J Biol Chem, 2019 Jun 7. PMID 31040182, Free PMC Article
    2. Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells. Jaiswal A, et al. Sci Rep, 2023 Nov 10. PMID 37949972, Free PMC Article
    3. The nuclear and adherent junction complex component protein ubinuclein negatively regulates the productive cycle of Epstein-Barr virus in epithelial cells. Gruffat H, et al. J Virol, 2011 Jan. PMID 21084479, Free PMC Article
    4. Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex. Ricketts MD, et al. Nat Commun, 2015 Jul 10. PMID 26159857, Free PMC Article
    5. A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function. Ricketts MD, et al. J Mol Biol, 2017 Jun 30. PMID 27871933, Free PMC Article

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells.
      Title: Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells.
    2. UBN1 may be capable of binding two H3.3/H4 molecules to facilitate (H3.3/H4)2 tetramer formation in a pathway to nucleosome deposition that may also involve UBN1-mediated DNA binding by the HIRA complex.
      Title: The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity.
    3. analysis of the trimeric HIRA, UBN1 and CABIN1 H3.3 histone chaperone complex
      Title: Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit.
    4. study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA histone chaperone complex.
      Title: Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex.
    5. NHRD domain of UBN1 as being an essential region for HIRA interaction and chromatin organization by the HUCA complex
      Title: Identification of an ubinuclein 1 region required for stability and function of the human HIRA/UBN1/CABIN1/ASF1a histone H3.3 chaperone complex.
    6. a 184-amino acid region (from amino acids 39 to 223) at the N-terminal region of Ubn-1 was responsible for the interaction with the PDZ2 domain of ZO-1
      Title: Identification of new interacting partners of the shuttling protein ubinuclein (Ubn-1).
    7. Data show that, like HIRA, UBN1, and ASF1a, CABIN1 is involved in heterochromatinization of the genome of senescent human cells.
      Title: Human CABIN1 is a functional member of the human HIRA/UBN1/ASF1a histone H3.3 chaperone complex.
    8. By a chromatin immunoprecipitation (ChIP) assay, the authors show that Ubn-1 blocks EB1-human herpesvirus 4 DNA interaction.
      Title: The nuclear and adherent junction complex component protein ubinuclein negatively regulates the productive cycle of Epstein-Barr virus in epithelial cells.
    9. Analyses have revealed that in most cells ubinuclein occurred in the nucleoplasm, but in cells forming tight junctions it is recruited to the plaque structure of the zonula occludens.
      Title: Characterization of the ubinuclein protein as a new member of the nuclear and adhesion complex components (NACos).
    10. Hpc2-related domain of UBN1, UBN2, and Hpc2p is an evolutionarily conserved HIRA/Hir-binding domain, which directly interacts with the N-terminal WD repeats of HIRA/Hir.
      Title: Human UBN1 is an ortholog of yeast Hpc2p and has an essential role in the HIRA/ASF1a chromatin-remodeling pathway in senescent cells.
    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

    Pathways from PubChem

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    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in PML body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in bicellular tight junction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear body 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
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubinuclein-1
    Names
    HIRA-binding protein
    ubiquitously expressed nuclear protein

    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.

    Genomic

    1. NG_051820.2 RefSeqGene

      Range
      5002..39922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001079514.3 → NP_001072982.1  ubinuclein-1 isoform a

      See identical proteins and their annotated locations for NP_001072982.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC020663, AC027687
      Consensus CDS
      CCDS10525.1
      UniProtKB/Swiss-Prot
      B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7
      Related
      ENSP00000262376.5, ENST00000262376.11
      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 573
      UBN_AB; Ubinuclein conserved middle domain

    2. NM_001288656.1 → NP_001275585.1  ubinuclein-1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the 3' coding region, compared to variant 2. The encoded isoform (b) is shorter, compared to isoform a.
      Source sequence(s)
      AF108460, AK300131, AU120544, BC013750, BG822152, BQ186272, CB242197, CV574190
      Consensus CDS
      CCDS73822.1
      UniProtKB/Swiss-Prot
      Q9NPG3
      Related
      ENSP00000468740.1, ENST00000590769.5
      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 573
      UBN_AB; Ubinuclein conserved middle domain

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      4847481..4882401
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522465.3 → XP_011520767.1  ubinuclein-1 isoform X5

      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 573
      UBN_AB; Ubinuclein conserved middle domain

    2. XM_017023190.3 → XP_016878679.1  ubinuclein-1 isoform X4

    3. XM_047434040.1 → XP_047289996.1  ubinuclein-1 isoform X6

    4. XM_005255277.5 → XP_005255334.1  ubinuclein-1 isoform X1

      See identical proteins and their annotated locations for XP_005255334.1

      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 573
      UBN_AB; Ubinuclein conserved middle domain

    5. XM_005255279.5 → XP_005255336.1  ubinuclein-1 isoform X3

      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 525
      UBN_AB; Ubinuclein conserved middle domain

    6. XM_017023192.3 → XP_016878681.1  ubinuclein-1 isoform X9

    7. XM_011522467.3 → XP_011520769.1  ubinuclein-1 isoform X10

      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 569
      UBN_AB; Ubinuclein conserved middle domain

    8. XM_047434037.1 → XP_047289993.1  ubinuclein-1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7
      Related
      ENSP00000379894.3, ENST00000396658.8

    9. XM_047434039.1 → XP_047289995.1  ubinuclein-1 isoform X4

    10. XM_005255278.4 → XP_005255335.1  ubinuclein-1 isoform X1

      See identical proteins and their annotated locations for XP_005255335.1

      Conserved Domains (2) summary
      pfam08729
      Location:119 → 168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360 → 573
      UBN_AB; Ubinuclein conserved middle domain

    11. XM_047434038.1 → XP_047289994.1  ubinuclein-1 isoform X3

    12. XM_047434041.1 → XP_047289997.1  ubinuclein-1 isoform X7

    13. XM_047434042.1 → XP_047289998.1  ubinuclein-1 isoform X8

    RNA

    1. XR_007064874.1 RNA Sequence

    2. XR_007064875.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      4876971..4911890
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380192.1 → XP_054236167.1  ubinuclein-1 isoform X5

    2. XM_054380190.1 → XP_054236165.1  ubinuclein-1 isoform X4

    3. XM_054380193.1 → XP_054236168.1  ubinuclein-1 isoform X6

    4. XM_054380195.1 → XP_054236170.1  ubinuclein-1 isoform X9

    5. XM_054380196.1 → XP_054236171.1  ubinuclein-1 isoform X10

    6. XM_054380189.1 → XP_054236164.1  ubinuclein-1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7

    7. XM_054380191.1 → XP_054236166.1  ubinuclein-1 isoform X4

    8. XM_054380194.1 → XP_054236169.1  ubinuclein-1 isoform X8

    RNA

    1. XR_008489082.1 RNA Sequence

    2. XR_008489083.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016936.3: Suppressed sequence

      Description
      NM_016936.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NPG3.2 GenPept UniProtKB/Swiss-Prot:Q9NPG3

    Gene LinkOut

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

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