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Aliases for UBN1 Gene

Aliases for UBN1 Gene

  • Ubinuclein 1 2 3 5
  • Ubiquitously Expressed Nuclear Protein 3 4
  • HIRA-Binding Protein 3 4
  • Ubinuclein-1 3
  • Protein VT4 4
  • VT4 3
  • VT 3

External Ids for UBN1 Gene

Previous GeneCards Identifiers for UBN1 Gene

  • GC16P004921
  • GC16P004898
  • GC16P004838
  • GC16P004897

Summaries for UBN1 Gene

Entrez Gene Summary for UBN1 Gene

  • 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]

GeneCards Summary for UBN1 Gene

UBN1 (Ubinuclein 1) is a Protein Coding gene. Among its related pathways are Cellular Senescence and DNA Damage/Telomere Stress Induced Senescence. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is UBN2.

UniProtKB/Swiss-Prot for UBN1 Gene

  • Acts as a novel regulator of senescence. Involved in the formation of senescence-associated heterochromatin foci (SAHF), which represses expression of proliferation-promoting genes. Binds to proliferation-promoting genes. May be required for replication-independent chromatin assembly.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UBN1 Gene

Genomics for UBN1 Gene

Regulatory Elements for UBN1 Gene

Enhancers for UBN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16F004628 1 FANTOM5 Ensembl 29.8 -218.0 -217979 0.6 ZNF48 UBN1 MGRN1 NUDT16L1 CORO7 GLYR1 RN7SL850P
GH16F004872 0.5 ENCODE 26.3 +27.7 27727 3.2 ELF3 MLX ARID4B SIN3A DMAP1 ZSCAN9 RAD21 ZNF48 RARA SLC30A9 UBN1 GLYR1 NUDT16L1 PPL ZNF500 SEPT12 PIR38578 PIR48909
GH16F004867 0.2 ENCODE 23.2 +22.2 22235 3.6 PKNOX1 SIN3A ZIC2 CTBP1 ZNF366 FOS RCOR1 ZNF687 MAZ ZHX2 UBN1 SEPT12 ZNF500 GLYR1 NUDT16L1 PPL SMIM22 ENSG00000267077 MGRN1 PIR48909
GH16F004862 0.4 FANTOM5 18.3 +16.1 16127 0.2 ATF3 HLF CEBPA RAD21 YY1 UBN1 SEPT12 MGRN1 CORO7 GLYR1 GC16P004860 PIR31758 PIR48909
GH16F004401 0.3 FANTOM5 13.9 -445.2 -445220 0.1 BACH1 CEBPG ZIC2 ZNF644 ZNF335 IRF9 ZNF766 SCRT2 PATZ1 TRIM24 UBN1 MGRN1 CORO7 GLYR1 CORO7-PAM16 VASN
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around UBN1 on UCSC Golden Path with GeneCards custom track

Promoters for UBN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000503008 1335 3601 PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207

Genomic Location for UBN1 Gene

Chromosome:
16
Start:
4,846,665 bp from pter
End:
4,882,401 bp from pter
Size:
35,737 bases
Orientation:
Plus strand

Genomic View for UBN1 Gene

Genes around UBN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UBN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UBN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UBN1 Gene

Proteins for UBN1 Gene

  • Protein details for UBN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPG3-UBN1_HUMAN
    Recommended name:
    Ubinuclein-1
    Protein Accession:
    Q9NPG3
    Secondary Accessions:
    • B7Z6D3
    • D3DUE8
    • Q13079
    • Q9P1P7

    Protein attributes for UBN1 Gene

    Size:
    1134 amino acids
    Molecular mass:
    121520 Da
    Quaternary structure:
    • Component of a complex that includes at least ASF1A, CABIN1, HIRA, histone H3.3 and UBN1. Interacts with Epstein-Barr virus BZLF1. Interacts with HIRA (via WD repeat domain); the interaction is direct. Interacts with ASF1A, CEBPA, TJP1, TJP2 and TJP3.

    Three dimensional structures from OCA and Proteopedia for UBN1 Gene

    Alternative splice isoforms for UBN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UBN1 Gene

Post-translational modifications for UBN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for UBN1

No data available for DME Specific Peptides for UBN1 Gene

Domains & Families for UBN1 Gene

Gene Families for UBN1 Gene

Protein Domains for UBN1 Gene

Suggested Antigen Peptide Sequences for UBN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NPG3

UniProtKB/Swiss-Prot:

UBN1_HUMAN :
  • Belongs to the ubinuclein family.
Family:
  • Belongs to the ubinuclein family.
genes like me logo Genes that share domains with UBN1: view

Function for UBN1 Gene

Molecular function for UBN1 Gene

UniProtKB/Swiss-Prot Function:
Acts as a novel regulator of senescence. Involved in the formation of senescence-associated heterochromatin foci (SAHF), which represses expression of proliferation-promoting genes. Binds to proliferation-promoting genes. May be required for replication-independent chromatin assembly.

Gene Ontology (GO) - Molecular Function for UBN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 10725330
GO:0005515 protein binding IPI 18823282
genes like me logo Genes that share ontologies with UBN1: view
genes like me logo Genes that share phenotypes with UBN1: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for UBN1 Gene

Localization for UBN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for UBN1 Gene

Nucleus, nucleoplasm. Nucleus, PML body. Cell junction, tight junction. Note=Localized as a nuclear speckled-like pattern in proliferating primary fibroblasts. Colocalizes with HIRA, PML and SP100 in PML bodies of senescent cells. Colocalizes with TJP1 and CLDN1. Detected along the upper granular cell layer of epidermis. When overexpressed, accumulates in the nucleus in cells showing defective cytokinesis.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for UBN1 Gene COMPARTMENTS Subcellular localization image for UBN1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for UBN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,TAS 10725330
GO:0005654 nucleoplasm TAS --
GO:0005923 bicellular tight junction ISS --
GO:0016605 PML body IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with UBN1: view

Pathways & Interactions for UBN1 Gene

genes like me logo Genes that share pathways with UBN1: view

Gene Ontology (GO) - Biological Process for UBN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
GO:0006357 regulation of transcription from RNA polymerase II promoter TAS 10725330
GO:0010923 negative regulation of phosphatase activity IDA 19389623
GO:0016032 viral process IEA --
genes like me logo Genes that share ontologies with UBN1: view

No data available for SIGNOR curated interactions for UBN1 Gene

Transcripts for UBN1 Gene

Unigene Clusters for UBN1 Gene

Ubinuclein 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for UBN1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a ·
SP1: - -
SP2: -
SP3:
SP4: -
SP5: -
SP6: -

ExUns: 19b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for UBN1 Gene

GeneLoc Exon Structure for
UBN1
ECgene alternative splicing isoforms for
UBN1

Expression for UBN1 Gene

mRNA expression in normal human tissues for UBN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for UBN1 Gene

This gene is overexpressed in Whole Blood (x4.2).

Protein differential expression in normal tissues from HIPED for UBN1 Gene

This gene is overexpressed in Plasma (55.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for UBN1 Gene



NURSA nuclear receptor signaling pathways regulating expression of UBN1 Gene:

UBN1

SOURCE GeneReport for Unigene cluster for UBN1 Gene:

Hs.440219

mRNA Expression by UniProt/SwissProt for UBN1 Gene:

Q9NPG3-UBN1_HUMAN
Tissue specificity: Ubiquitous. Also expressed in numerous tumors and cancer cell lines.
genes like me logo Genes that share expression patterns with UBN1: view

Primer Products

No data available for Protein tissue co-expression partners for UBN1 Gene

Orthologs for UBN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for UBN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia UBN1 34 35
  • 99.65 (n)
dog
(Canis familiaris)
Mammalia UBN1 34 35
  • 88.18 (n)
rat
(Rattus norvegicus)
Mammalia Ubn1 34
  • 85.94 (n)
mouse
(Mus musculus)
Mammalia Ubn1 34 16 35
  • 85.76 (n)
cow
(Bos Taurus)
Mammalia UBN1 34 35
  • 85.44 (n)
oppossum
(Monodelphis domestica)
Mammalia UBN1 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UBN1 35
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves UBN1 34 35
  • 72.25 (n)
lizard
(Anolis carolinensis)
Reptilia UBN1 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ubn1 34
  • 55.36 (n)
zebrafish
(Danio rerio)
Actinopterygii UBN1 35
  • 40 (a)
OneToOne
Dr.7295 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5464 34
fruit fly
(Drosophila melanogaster)
Insecta yemalpha 35
  • 19 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 34 (a)
OneToMany
Species where no ortholog for UBN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for UBN1 Gene

ENSEMBL:
Gene Tree for UBN1 (if available)
TreeFam:
Gene Tree for UBN1 (if available)

Paralogs for UBN1 Gene

Paralogs for UBN1 Gene

(1) SIMAP similar genes for UBN1 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for UBN1 Gene

genes like me logo Genes that share paralogs with UBN1: view

Variants for UBN1 Gene

Sequence variations from dbSNP and Humsavar for UBN1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs765004815 Likely pathogenic 4,874,766(+) ACAGC(A/T)TGCCA reference, missense
rs1001302 -- 4,864,763(-) TCTCT(C/T)TGATT intron-variant
rs1045643 -- 4,881,512(+) GTATA(C/T)GGTGT utr-variant-3-prime
rs1049223 -- 4,882,658(-) TCTCA(C/T)TGGTA intron-variant, downstream-variant-500B, utr-variant-3-prime
rs10500326 -- 4,868,325(+) TAATA(G/T)AGAGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for UBN1 Gene

Variant ID Type Subtype PubMed ID
esv2422516 CNV deletion 17116639
esv25186 CNV gain 19812545
esv26756 CNV gain+loss 19812545
esv3637707 CNV gain 21293372
esv998381 CNV deletion 20482838
nsv1046986 CNV gain 25217958
nsv1720 CNV deletion 18451855
nsv510674 CNV deletion 20534489

Variation tolerance for UBN1 Gene

Residual Variation Intolerance Score: 2.94% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.34; 63.17% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UBN1 Gene

Human Gene Mutation Database (HGMD)
UBN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
UBN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UBN1 Gene

Disorders for UBN1 Gene

Relevant External Links for UBN1

Genetic Association Database (GAD)
UBN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UBN1

No disorders were found for UBN1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for UBN1 Gene

Publications for UBN1 Gene

  1. Ubinuclein, a novel nuclear protein interacting with cellular and viral transcription factors. (PMID: 10725330) Aho S. … Uitto J. (J. Cell Biol. 2000) 2 3 4 22 64
  2. Characterization of the ubinuclein protein as a new member of the nuclear and adhesion complex components (NACos). (PMID: 18823282) Aho S. … Gruffat H. (Biol. Cell 2009) 3 4 22 64
  3. Human UBN1 is an ortholog of yeast Hpc2p and has an essential role in the HIRA/ASF1a chromatin-remodeling pathway in senescent cells. (PMID: 19029251) Banumathy G. … Adams P.D. (Mol. Cell. Biol. 2009) 3 4 64
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for UBN1 Gene

Sources for UBN1 Gene

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