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    UBN1 ubinuclein 1 [ Homo sapiens (human) ]

    Gene ID: 29855, updated on 28-Oct-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001079514.3NP_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:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360573
      UBN_AB; Ubinuclein conserved middle domain
    2. NM_001288656.1NP_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:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360573
      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_011522465.3XP_011520767.1  ubinuclein-1 isoform X5

      Conserved Domains (2) summary
      pfam08729
      Location:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360573
      UBN_AB; Ubinuclein conserved middle domain
    2. XM_017023190.3XP_016878679.1  ubinuclein-1 isoform X4

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

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

      See identical proteins and their annotated locations for XP_005255334.1

      Conserved Domains (2) summary
      pfam08729
      Location:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360573
      UBN_AB; Ubinuclein conserved middle domain
    5. XM_005255279.5XP_005255336.1  ubinuclein-1 isoform X3

      Conserved Domains (2) summary
      pfam08729
      Location:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360525
      UBN_AB; Ubinuclein conserved middle domain
    6. XM_017023192.3XP_016878681.1  ubinuclein-1 isoform X9

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

      Conserved Domains (2) summary
      pfam08729
      Location:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360569
      UBN_AB; Ubinuclein conserved middle domain
    8. XM_047434037.1XP_047289993.1  ubinuclein-1 isoform X2

      UniProtKB/Swiss-Prot
      B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7
      Related
      ENSP00000379894.3, ENST00000396658.8
    9. XM_047434039.1XP_047289995.1  ubinuclein-1 isoform X4

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

      See identical proteins and their annotated locations for XP_005255335.1

      Conserved Domains (2) summary
      pfam08729
      Location:119168
      HUN; HPC2 and ubinuclein domain
      pfam14075
      Location:360573
      UBN_AB; Ubinuclein conserved middle domain
    11. XM_047434038.1XP_047289994.1  ubinuclein-1 isoform X3

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

    13. XM_047434042.1XP_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_054380192.1XP_054236167.1  ubinuclein-1 isoform X5

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

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

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

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

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

      UniProtKB/Swiss-Prot
      B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7
    7. XM_054380191.1XP_054236166.1  ubinuclein-1 isoform X4

    8. XM_054380194.1XP_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.