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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 DNA Damage/Telomere Stress Induced Senescence and Cellular Senescence (REACTOME). Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. 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.

Additional gene information for UBN1 Gene

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

Genomics for UBN1 Gene

GeneHancer (GH) Regulatory Elements for UBN1 Gene

Promoters and enhancers for UBN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I004845 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 558.9 +0.9 922 3.2 HDGF PKNOX1 CLOCK FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 UBN1 GLYR1 SEPT12 ROGDI LOC102724927 ALG1 ENSG00000267077 SMIM22 PIR33451
GH16I004473 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 14.7 -370.5 -370497 5.4 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 NMRAL1 HMOX2 CREBBP ZNF500 CDIP1 UBN1 NUDT16L1 ENSG00000261938 MGRN1 GC16P004473
GH16I004424 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 14.7 -420.6 -420571 3.3 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ENSG00000277170 DNAJA3 CORO7 NMRAL1 CREBBP ZNF500 ZNF597 ANKS3 UBN1 HMOX2
GH16I004800 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 13.4 -43.8 -43813 5.7 PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF766 FOS ZNF263 ROGDI GC16M004803 CREBBP SEPT12 ENSG00000267077 ZNF500 UBN1 EEF2KMT PAM16 GLYR1
GH16I004692 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 13.2 -152.4 -152442 4.3 HDGF PKNOX1 SMAD1 ATF1 ARNT ZNF493 ARID4B SIN3A DMAP1 ZNF48 NUDT16L1 ZNF500 MGRN1 EEF2KMT CREBBP UBN1 ANKS3 ALG1 GLYR1 HMOX2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around UBN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the UBN1 gene promoter:

Genomic Locations for UBN1 Gene

Genomic Locations for UBN1 Gene
chr16:4,846,665-4,882,401
(GRCh38/hg38)
Size:
35,737 bases
Orientation:
Plus strand
chr16:4,896,666-4,932,363
(GRCh37/hg19)

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

No Post-translational modifications

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.

Phenotypes From GWAS Catalog for UBN1 Gene

Gene Ontology (GO) - Molecular Function for UBN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity 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

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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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UBN1 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for UBN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IEA 10725330
GO:0005654 nucleoplasm TAS,IDA --
GO:0005923 bicellular tight junction ISS --
GO:0016604 nuclear body IDA --
GO:0016605 PML body 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 by RNA polymerase II TAS 10725330
GO:0010923 negative regulation of phosphatase activity IDA --
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

Drugs & Compounds for UBN1 Gene

No Compound Related Data Available

Transcripts for UBN1 Gene

Unigene Clusters for UBN1 Gene

Ubinuclein 1:
Representative Sequences:

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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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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.

Evidence on tissue expression from TISSUES for UBN1 Gene

  • Liver(4.2)
  • Nervous system(3.2)
genes like me logo Genes that share expression patterns with UBN1: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.65 (n)
dog
(Canis familiaris)
Mammalia UBN1 33 34
  • 88.18 (n)
rat
(Rattus norvegicus)
Mammalia Ubn1 33
  • 85.94 (n)
mouse
(Mus musculus)
Mammalia Ubn1 33 16 34
  • 85.76 (n)
cow
(Bos Taurus)
Mammalia UBN1 33 34
  • 85.44 (n)
oppossum
(Monodelphis domestica)
Mammalia UBN1 34
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UBN1 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves UBN1 33 34
  • 72.25 (n)
lizard
(Anolis carolinensis)
Reptilia UBN1 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ubn1 33
  • 55.36 (n)
zebrafish
(Danio rerio)
Actinopterygii UBN1 34
  • 40 (a)
OneToOne
Dr.7295 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5464 33
fruit fly
(Drosophila melanogaster)
Insecta yemalpha 34
  • 19 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs765004815 likely-pathogenic, Non-immune hydrops fetalis 4,874,766(+) T/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000040940 -- 4,862,545(+) T/A intron_variant
rs1000079466 -- 4,853,701(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000095915 -- 4,870,784(+) A/C intron_variant
rs1000114284 -- 4,863,499(+) A/G 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)

Additional Variant Information 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

Additional Disease Information for 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 (The Journal of cell biology 2000) 2 3 4 22 58
  2. Characterization of the ubinuclein protein as a new member of the nuclear and adhesion complex components (NACos). (PMID: 18823282) Aho S … Gruffat H (Biology of the cell 2009) 3 4 22 58
  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 PD (Molecular and cellular biology 2009) 3 4 58
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for UBN1 Gene

Sources for UBN1 Gene

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