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Aliases for NOP53 Gene

Aliases for NOP53 Gene

  • NOP53 Ribosome Biogenesis Factor 2 3 5
  • Glioma Tumor Suppressor Candidate Region Gene 2 Protein 3 4
  • Protein Interacting With Carboxyl Terminus 1 3 4
  • GLTSCR2 3 4
  • PICT-1 3 4
  • PICT1 3 4
  • P60 3 4
  • Glioma Tumor Suppressor Candidate Region Gene 2 2
  • Ribosome Biogenesis Protein NOP53 3
  • GLT 4

External Ids for NOP53 Gene

Previous HGNC Symbols for NOP53 Gene

  • GLTSCR2

Summaries for NOP53 Gene

GeneCards Summary for NOP53 Gene

NOP53 (NOP53 Ribosome Biogenesis Factor) is a Protein Coding gene. Diseases associated with NOP53 include Human Herpesvirus 8 and Keratosis, Seborrheic. Among its related pathways are Translational Control and PI3K / Akt Signaling.

UniProtKB/Swiss-Prot for NOP53 Gene

  • Nucleolar protein which is involved in the integration of the 5S RNP into the ribosomal large subunit during ribosome biogenesis (PubMed:24120868). In ribosome biogenesis, may also play a role in rRNA transcription (PubMed:27729611). Also functions as a nucleolar sensor that regulates the activation of p53/TP53 in response to ribosome biogenesis perturbation, DNA damage and other stress conditions (PubMed:21741933, PubMed:24120868, PubMed:27829214). DNA damage or perturbation of ribosome biogenesis disrupt the interaction between NOP53 and RPL11 allowing RPL11 transport to the nucleoplasm where it can inhibit MDM2 and allow p53/TP53 activation (PubMed:24120868, PubMed:27829214). It may also positively regulate the function of p53/TP53 in cell cycle arrest and apoptosis through direct interaction, preventing its MDM2-dependent ubiquitin-mediated proteasomal degradation (PubMed:22522597). Originally identified as a tumor suppressor, it may also play a role in cell proliferation and apoptosis by positively regulating the stability of PTEN, thereby antagonizing the PI3K-AKT/PKB signaling pathway (PubMed:15355975, PubMed:16971513, PubMed:27729611). May also inhibit cell proliferation and increase apoptosis through its interaction with NF2 (PubMed:21167305). May negatively regulate NPM1 by regulating its nucleoplasmic localization, oligomerization and ubiquitin-mediated proteasomal degradation (PubMed:25818168). Thereby, may prevent NPM1 interaction with MYC and negatively regulate transcription mediated by the MYC-NPM1 complex (PubMed:25956029). May also regulate cellular aerobic respiration (PubMed:24556985). In the cellular response to viral infection, may play a role in the attenuation of interferon-beta through the inhibition of DDX58/RIG-1 (PubMed:27824081).

Gene Wiki entry for NOP53 Gene

Additional gene information for NOP53 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NOP53 Gene

Genomics for NOP53 Gene

GeneHancer (GH) Regulatory Elements for NOP53 Gene

Promoters and enhancers for NOP53 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
GH19J047741 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 671.9 -1.6 -1601 5 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF416 ZNF143 ZNF548 NOP53 ZC3H4 BICRA ENSG00000269321 SELENOW GRWD1 RASIP1 BSPH1 CA11 TPRX2P
GH19J047746 Enhancer 0.5 ENCODE dbSUPER 662.7 +1.6 1563 0.5 SIN3A NOP53 SELENOW PIR37560
GH19J047225 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 75.3 -516.1 -516141 8.2 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 BBC3 BICRA ENSG00000268810 NOP53-AS1 CCDC9 NOP53 ENSG00000269321 SNORD23 PPP5D1 INAFM1
GH19J047242 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 55.8 -501.7 -501731 2.5 CLOCK ZFP64 DMAP1 YBX1 YY1 ZNF213 E2F8 ZNF143 ZNF548 MCM3 BBC3 ZC3H4 BICRA ENSG00000268810 NOP53-AS1 CCDC9 NOP53 ENSG00000269321 SLC1A5 SNORD23
GH19J048644 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 45.2 +900.4 900408 2.9 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 ZNF2 ZBTB7B POLR2B CA11 SNORD35A GRWD1 SNORD35B ALDH16A1 NOP53-AS1 PRR12 NOP53 SNRNP70 RPS11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NOP53 on UCSC Golden Path with GeneCards custom track

Genomic Locations for NOP53 Gene

Genomic Locations for NOP53 Gene
chr19:47,745,522-47,757,066
(GRCh38/hg38)
Size:
11,545 bases
Orientation:
Plus strand
chr19:48,248,779-48,260,323
(GRCh37/hg19)
Size:
11,545 bases
Orientation:
Plus strand

Genomic View for NOP53 Gene

Genes around NOP53 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NOP53 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NOP53 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NOP53 Gene

Proteins for NOP53 Gene

  • Protein details for NOP53 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZM5-NOP53_HUMAN
    Recommended name:
    Ribosome biogenesis protein NOP53
    Protein Accession:
    Q9NZM5
    Secondary Accessions:
    • Q9BTC6
    • Q9HAX6
    • Q9NPP1
    • Q9NPR4
    • Q9UFI2

    Protein attributes for NOP53 Gene

    Size:
    478 amino acids
    Molecular mass:
    54389 Da
    Quaternary structure:
    • Homooligomer (PubMed:24735870, PubMed:26903295). Interacts with PTEN; regulates PTEN phosphorylation and increases its stability (PubMed:15355975). Interacts with RPL11; retains RPL11 into the nucleolus (PubMed:24556985, PubMed:27829214). Interacts with CDKN2A/isoform tumor suppressor ARF; the interaction is direct and promotes ARF nucleoplasmic relocalization and ubiquitin-mediated proteasomal degradation (PubMed:27323397). Interacts with NPM1; the interaction is direct and competitive with MYC (PubMed:25956029). Interacts with NF2 (via FERM domain); the interaction is direct (PubMed:21167305). Interacts with p53/TP53 (via the oligomerization region); the interaction is direct and may prevent the MDM2-mediated proteasomal degradation of p53/TP53 (PubMed:22522597). Interacts with DDX58; may regulate DDX58 through USP15-mediated Lys-63-linked deubiquitination (PubMed:27824081). Interacts with UBTF (PubMed:27729611).
    • (Microbial infection) Interacts with herpes simplex virus 1 early proteins ICP22 and ICP0.
    • (Microbial infection) Interacts with Human herpesvirus 8 protein ORF16; may sequester ORF16 in host nucleolus and reduce its antiapoptotic activity.

neXtProt entry for NOP53 Gene

Post-translational modifications for NOP53 Gene

  • Ubiquitin-mediated proteasomal degradation is regulated by c-JUN. It is associated with relocalization to the nucleoplasm and decreased homooligomerization.
  • Phosphorylated upon DNA damage probably by ATM and DNA-PK; may regulate NOP53 degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NOP53 Gene

No data available for DME Specific Peptides for NOP53 Gene

Domains & Families for NOP53 Gene

Gene Families for NOP53 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NOP53 Gene

Blocks:
InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9NZM5

UniProtKB/Swiss-Prot:

NOP53_HUMAN :
  • Belongs to the NOP53 family.
Family:
  • Belongs to the NOP53 family.
genes like me logo Genes that share domains with NOP53: view

Function for NOP53 Gene

Molecular function for NOP53 Gene

UniProtKB/Swiss-Prot Function:
Nucleolar protein which is involved in the integration of the 5S RNP into the ribosomal large subunit during ribosome biogenesis (PubMed:24120868). In ribosome biogenesis, may also play a role in rRNA transcription (PubMed:27729611). Also functions as a nucleolar sensor that regulates the activation of p53/TP53 in response to ribosome biogenesis perturbation, DNA damage and other stress conditions (PubMed:21741933, PubMed:24120868, PubMed:27829214). DNA damage or perturbation of ribosome biogenesis disrupt the interaction between NOP53 and RPL11 allowing RPL11 transport to the nucleoplasm where it can inhibit MDM2 and allow p53/TP53 activation (PubMed:24120868, PubMed:27829214). It may also positively regulate the function of p53/TP53 in cell cycle arrest and apoptosis through direct interaction, preventing its MDM2-dependent ubiquitin-mediated proteasomal degradation (PubMed:22522597). Originally identified as a tumor suppressor, it may also play a role in cell proliferation and apoptosis by positively regulating the stability of PTEN, thereby antagonizing the PI3K-AKT/PKB signaling pathway (PubMed:15355975, PubMed:16971513, PubMed:27729611). May also inhibit cell proliferation and increase apoptosis through its interaction with NF2 (PubMed:21167305). May negatively regulate NPM1 by regulating its nucleoplasmic localization, oligomerization and ubiquitin-mediated proteasomal degradation (PubMed:25818168). Thereby, may prevent NPM1 interaction with MYC and negatively regulate transcription mediated by the MYC-NPM1 complex (PubMed:25956029). May also regulate cellular aerobic respiration (PubMed:24556985). In the cellular response to viral infection, may play a role in the attenuation of interferon-beta through the inhibition of DDX58/RIG-1 (PubMed:27824081).
UniProtKB/Swiss-Prot Induction:
Down-regulated by nucleolar stress through ubiquitin-independent proteasomal degradation (at protein level) (PubMed:24923447). Up-regulated upon mitochondrial stress (at protein level) (PubMed:24556985). Expression of the protein might be regulated by DNA damage but results are not consistent (PubMed:21741933, PubMed:27829214).

Phenotypes From GWAS Catalog for NOP53 Gene

Gene Ontology (GO) - Molecular Function for NOP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002039 p53 binding IPI 22522597
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 15355975
GO:0008097 5S rRNA binding IDA 24120868
GO:0042802 identical protein binding IDA 24735870
genes like me logo Genes that share ontologies with NOP53: view
genes like me logo Genes that share phenotypes with NOP53: view

Animal Models for NOP53 Gene

MGI Knock Outs for NOP53:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NOP53 Gene

Localization for NOP53 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NOP53 Gene

Nucleus, nucleolus. Nucleus, nucleoplasm. Note=In the nucleolus may be more specifically localized to the fibrillar center (PubMed:27729611). Mainly nucleolar it relocalizes to the nucleoplasm under specific conditions including ribosomal stress enabling it to interact and regulate nucleoplasmic proteins like p53/TP53 (PubMed:22522597, PubMed:24923447, PubMed:27323397, PubMed:26903295). Also detected in the cytosol (PubMed:24923447, PubMed:27824081). {ECO:0000269 PubMed:22522597, ECO:0000269 PubMed:24923447, ECO:0000269 PubMed:26903295, ECO:0000269 PubMed:27323397, ECO:0000269 PubMed:27729611, ECO:0000269 PubMed:27824081}.

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 NOP53 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NOP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA 27729611
GO:0005622 intracellular NAS 10196275
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IEA,IDA 22522597
GO:0005730 nucleolus IDA 20042497
genes like me logo Genes that share ontologies with NOP53: view

Pathways & Interactions for NOP53 Gene

genes like me logo Genes that share pathways with NOP53: view

Pathways by source for NOP53 Gene

1 KEGG pathway for NOP53 Gene
2 Cell Signaling Technology pathways for NOP53 Gene

Gene Ontology (GO) - Biological Process for NOP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000027 ribosomal large subunit assembly IMP 24120868
GO:0000055 ribosomal large subunit export from nucleus IBA --
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 25956029
GO:0001932 regulation of protein phosphorylation IMP 15355975
GO:0006281 DNA repair IMP 21741933
genes like me logo Genes that share ontologies with NOP53: view

No data available for SIGNOR curated interactions for NOP53 Gene

Drugs & Compounds for NOP53 Gene

No Compound Related Data Available

Transcripts for NOP53 Gene

mRNA/cDNA for NOP53 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NOP53 Gene

No ASD Table

Relevant External Links for NOP53 Gene

GeneLoc Exon Structure for
NOP53
ECgene alternative splicing isoforms for
NOP53

Expression for NOP53 Gene

NURSA nuclear receptor signaling pathways regulating expression of NOP53 Gene:

NOP53

mRNA Expression by UniProt/SwissProt for NOP53 Gene:

Q9NZM5-NOP53_HUMAN
Tissue specificity: Expressed at high levels in heart and pancreas, moderate levels in placenta, liver, skeletal muscle, and kidney, and low levels in brain and lung.

Evidence on tissue expression from TISSUES for NOP53 Gene

  • Nervous system(4.6)
  • Muscle(4.5)
  • Eye(4.4)
  • Lung(4.3)
  • Skin(4.3)
  • Intestine(4.1)
  • Pancreas(3.8)
  • Kidney(3.1)
  • Stomach(3.1)
  • Blood(2.4)
  • Spleen(2.4)
  • Thyroid gland(2.4)
  • Lymph node(2.3)
  • Bone(2.2)
  • Liver(2.2)
  • Adrenal gland(2)
  • Bone marrow(2)
  • Heart(2)

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NOP53 Gene

Orthologs for NOP53 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NOP53 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GLTSCR2 34 33
  • 99.09 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GLTSCR2 34 33
  • 86.15 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GLTSCR2 34 33
  • 85.36 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gltscr2 34 33
  • 81.24 (n)
OneToOne
Nop53 16
rat
(Rattus norvegicus)
Mammalia Gltscr2 33
  • 80.61 (n)
oppossum
(Monodelphis domestica)
Mammalia GLTSCR2 34
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GLTSCR2 34
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 56 (a)
OneToMany
-- 34
  • 36 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia gltscr2 33
  • 55.21 (n)
Str.527 33
zebrafish
(Danio rerio)
Actinopterygii gltscr2 34 33
  • 56.75 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000270 33
  • 48.8 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG1785 34 33
  • 48.09 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea CELE_Y39B6A.33 33
  • 41.21 (n)
Y39B6A.33 34
  • 25 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR126W 33
  • 44.27 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F11506g 33
  • 39.74 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP53 33
  • 37.43 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05233 33
  • 48.81 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rrp16 33
  • 39.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4906 34
  • 39 (a)
OneToOne
Species where no ortholog for NOP53 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for NOP53 Gene

ENSEMBL:
Gene Tree for NOP53 (if available)
TreeFam:
Gene Tree for NOP53 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NOP53: view image

Paralogs for NOP53 Gene

Pseudogenes.org Pseudogenes for NOP53 Gene

genes like me logo Genes that share paralogs with NOP53: view

No data available for Paralogs for NOP53 Gene

Variants for NOP53 Gene

Sequence variations from dbSNP and Humsavar for NOP53 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000011170 -- 47,745,891(+) T/G intron_variant
rs1000072814 -- 47,744,508(+) C/A upstream_transcript_variant
rs1000235016 -- 47,748,932(+) C/A/T intron_variant
rs1000519381 -- 47,748,041(+) A/C/G intron_variant
rs1000585417 -- 47,748,755(+) C/G/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NOP53 Gene

Variant ID Type Subtype PubMed ID
esv3644559 CNV gain 21293372
nsv1058351 CNV gain 25217958
nsv1059189 CNV gain 25217958

Variation tolerance for NOP53 Gene

Residual Variation Intolerance Score: 88.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.36; 70.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NOP53 Gene

Human Gene Mutation Database (HGMD)
NOP53
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NOP53

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NOP53 Gene

Disorders for NOP53 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NOP53 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
human herpesvirus 8
  • kaposi sarcoma
keratosis, seborrheic
  • keratosis, seborrheic, somatic
- elite association - COSMIC cancer census association via MalaCards
Search NOP53 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NOP53

genes like me logo Genes that share disorders with NOP53: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NOP53 Gene

Publications for NOP53 Gene

  1. Critical role of PICT-1, a tumor suppressor candidate, in phosphatidylinositol 3,4,5-trisphosphate signals and tumorigenic transformation. (PMID: 16971513) Okahara F … Maehama T (Molecular biology of the cell 2006) 2 3 4 22 58
  2. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. (PMID: 24120868) Sloan KE … Watkins NJ (Cell reports 2013) 2 3 4 58
  3. GLTSCR2/PICT-1, a putative tumor suppressor gene product, induces the nucleolar targeting of the Kaposi's sarcoma-associated herpesvirus KS-Bcl-2 protein. (PMID: 20042497) Kalt I … Sarid R (Journal of virology 2010) 3 4 22 58
  4. The putative tumor suppressor gene GLTSCR2 induces PTEN-modulated cell death. (PMID: 17657248) Yim JH … Park JH (Cell death and differentiation 2007) 2 3 22 58
  5. A transcript map of the chromosome 19q-arm glioma tumor suppressor region. (PMID: 10708517) Smith JS … Jenkins RB (Genomics 2000) 2 3 4 58

Products for NOP53 Gene

Sources for NOP53 Gene

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