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Aliases for NOP58 Gene

Aliases for NOP58 Gene

  • NOP58 Ribonucleoprotein 2 3 5
  • Nucleolar Protein 5 3 4
  • NOP5 3 4
  • NOP58 Ribonucleoprotein Homolog (Yeast) 2
  • NOP58 Ribonucleoprotein Homolog 3
  • Nucleolar Protein NOP5/NOP58 3
  • Nucleolar Protein 58 3
  • NOP5/NOP58 3
  • HSPC120 3
  • NOL5 4

External Ids for NOP58 Gene

Previous GeneCards Identifiers for NOP58 Gene

  • GC02P202839
  • GC02P203130
  • GC02P194979

Summaries for NOP58 Gene

Entrez Gene Summary for NOP58 Gene

  • The protein encoded by this gene is a core component of box C/D small nucleolar ribonucleoproteins. Some box C/D small nucleolar RNAs (snoRNAs), such as U3, U8, and U14, are dependent upon the encoded protein for their synthesis. This protein is SUMOylated, which is necessary for high affinity binding to snoRNAs. [provided by RefSeq, Nov 2015]

GeneCards Summary for NOP58 Gene

NOP58 (NOP58 Ribonucleoprotein) is a Protein Coding gene. Among its related pathways are SUMOylation and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include snoRNA binding.

UniProtKB/Swiss-Prot for NOP58 Gene

  • Required for 60S ribosomal subunit biogenesis (By similarity). Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such as U3, U8 and U14 snoRNAs.

Gene Wiki entry for NOP58 Gene

Additional gene information for NOP58 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NOP58 Gene

Genomics for NOP58 Gene

GeneHancer (GH) Regulatory Elements for NOP58 Gene

Promoters and enhancers for NOP58 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
GH02I202264 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 564.8 +0.6 590 3.9 HDGF HNRNPUL1 PKNOX1 SMAD1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 NOP58 LOC100420110 RPL12P16 CYP20A1 NBEAL1 ENSG00000273456 FAM117B PIR47513 GC02P202236
GH02I202030 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 34.8 -230.5 -230522 9.8 CLOCK ATF1 ZNF133 SIN3A ZNF2 ZNF48 YY1 ETS1 GLIS2 ZNF213 FZD7 ENSG00000273209 NOP58 CDK15 KIAA2012 CARF LOC100420110 LOC729224 RNU6-440P FAM117B
GH02I202910 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 15.8 +646.3 646285 3.2 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B ZNF207 GC02M202910 CARF WDR12 NBEAL1 NOP58 RPL12P16 CYP20A1 GC02M202888
GH02I203237 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.5 +973.6 973554 3.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 POLR2B CYP20A1 PIR57218 GC02M203237 NOP58 CARF ICA1L
GH02I201778 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 12.6 -485.4 -485401 3.9 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 YY1 SLC30A9 ZNF207 FOS ALS2 GC02M201778 ORC2 CLK1 NOP58 LOC100420110 RPS2P16
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NOP58 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NOP58 gene promoter:

Genomic Locations for NOP58 Gene

Genomic Locations for NOP58 Gene
chr2:202,265,716-202,303,666
(GRCh38/hg38)
Size:
37,951 bases
Orientation:
Plus strand
chr2:203,130,439-203,168,389
(GRCh37/hg19)

Genomic View for NOP58 Gene

Genes around NOP58 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NOP58 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NOP58 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NOP58 Gene

Proteins for NOP58 Gene

  • Protein details for NOP58 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2X3-NOP58_HUMAN
    Recommended name:
    Nucleolar protein 58
    Protein Accession:
    Q9Y2X3
    Secondary Accessions:
    • Q53SA4
    • Q6PK08
    • Q9P036
    • Q9UFN3

    Protein attributes for NOP58 Gene

    Size:
    529 amino acids
    Molecular mass:
    59578 Da
    Quaternary structure:
    • Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles; the core proteins SNU13, NOP56, NOP58 and FBL assemble stepwise onto the snoRNA. Interacts with NOLC1/Nopp140. Interacts with NUFIP1, RUVBL1 AND RUVBL2; RUVBL1:RUVBL2 seem to bridge the association of NOP58 with NUFIP1. Interacts with PIH1D1 (PubMed:17636026).

neXtProt entry for NOP58 Gene

Post-translational modifications for NOP58 Gene

  • Sumoylation is essential for high-affinity binding to snoRNAs.
  • Ubiquitination at isoforms=206, Lys221, isoforms=310, isoforms=323, Lys337, and Lys365

Other Protein References for NOP58 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NOP58 Gene

Domains & Families for NOP58 Gene

Gene Families for NOP58 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for NOP58 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y2X3

UniProtKB/Swiss-Prot:

NOP58_HUMAN :
  • Belongs to the NOP5/NOP56 family.
Family:
  • Belongs to the NOP5/NOP56 family.
genes like me logo Genes that share domains with NOP58: view

Function for NOP58 Gene

Molecular function for NOP58 Gene

UniProtKB/Swiss-Prot Function:
Required for 60S ribosomal subunit biogenesis (By similarity). Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such as U3, U8 and U14 snoRNAs.

Phenotypes From GWAS Catalog for NOP58 Gene

Gene Ontology (GO) - Molecular Function for NOP58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001094 TFIID-class transcription factor binding IPI 17636026
GO:0003723 RNA binding IDA,HDA 22658674
GO:0005515 protein binding IPI 17636026
GO:0030515 snoRNA binding IDA 17636026
GO:0051117 ATPase binding IPI 17636026
genes like me logo Genes that share ontologies with NOP58: view
genes like me logo Genes that share phenotypes with NOP58: view

Animal Model Products

miRNA for NOP58 Gene

miRTarBase miRNAs that target NOP58

Clone Products

  • Addgene plasmids for NOP58

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NOP58 Gene

Localization for NOP58 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NOP58 Gene

Nucleus, nucleolus. Nucleus, nucleoplasm.

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 NOP58 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (4)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NOP58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA,TAS 10925205
GO:0005732 small nucleolar ribonucleoprotein complex IDA 17636026
genes like me logo Genes that share ontologies with NOP58: view

Pathways & Interactions for NOP58 Gene

genes like me logo Genes that share pathways with NOP58: view

Gene Ontology (GO) - Biological Process for NOP58 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000154 rRNA modification IBA --
GO:0006364 rRNA processing TAS 10925205
GO:0016049 cell growth TAS 10925205
GO:0042254 ribosome biogenesis IEA --
GO:0048254 snoRNA localization IMP 17636026
genes like me logo Genes that share ontologies with NOP58: view

No data available for SIGNOR curated interactions for NOP58 Gene

Drugs & Compounds for NOP58 Gene

No Compound Related Data Available

Transcripts for NOP58 Gene

Unigene Clusters for NOP58 Gene

NOP58 ribonucleoprotein:
Representative Sequences:

Clone Products

  • Addgene plasmids for NOP58

Alternative Splicing Database (ASD) splice patterns (SP) for NOP58 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^
SP1: - - - - - -
SP2: - - - - - - - -
SP3: - - -
SP4: - -
SP5: - - - -
SP6: - - -
SP7: - - - -
SP8:
SP9:

ExUns: 17a · 17b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for NOP58 Gene

GeneLoc Exon Structure for
NOP58
ECgene alternative splicing isoforms for
NOP58

Expression for NOP58 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NOP58 Gene

Protein differential expression in normal tissues from HIPED for NOP58 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (10.6), CD8 Tcells (7.5), Tlymphocyte (6.9), and Blymphocyte (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NOP58 Gene



Protein tissue co-expression partners for NOP58 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NOP58 Gene:

NOP58

SOURCE GeneReport for Unigene cluster for NOP58 Gene:

Hs.471104

mRNA Expression by UniProt/SwissProt for NOP58 Gene:

Q9Y2X3-NOP58_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for NOP58 Gene

  • Nervous system(4.5)
  • Blood(4.4)
  • Skin(4.4)
  • Liver(4.3)
  • Adrenal gland(2)
  • Pancreas(2)
  • Stomach(2)
genes like me logo Genes that share expression patterns with NOP58: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NOP58 Gene

Orthologs for NOP58 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NOP58 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NOP58 33 34
  • 99.68 (n)
cow
(Bos Taurus)
Mammalia NOP58 33 34
  • 91.68 (n)
mouse
(Mus musculus)
Mammalia Nop58 33 16 34
  • 91.3 (n)
dog
(Canis familiaris)
Mammalia NOP58 33 34
  • 91.18 (n)
rat
(Rattus norvegicus)
Mammalia Nop58 33
  • 90.55 (n)
oppossum
(Monodelphis domestica)
Mammalia NOP58 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NOP58 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves NOP58 33 34
  • 76.55 (n)
lizard
(Anolis carolinensis)
Reptilia NOP58 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nop58 33
  • 70.26 (n)
MGC75641 33
African clawed frog
(Xenopus laevis)
Amphibia LOC398558 33
zebrafish
(Danio rerio)
Actinopterygii nop58 33 34
  • 71.6 (n)
Dr.282 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.14025 33
fruit fly
(Drosophila melanogaster)
Insecta nop5 33 34
  • 61.17 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002171 33
  • 59.35 (n)
worm
(Caenorhabditis elegans)
Secernentea nol-5 33 34
  • 59.09 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08613g 33
  • 55.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP58 33 34 36
  • 54.96 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR328C 33
  • 54.27 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G05060 33
  • 60.24 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2939 33
rice
(Oryza sativa)
Liliopsida Os03g0350300 33
  • 61.79 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.721 33
corn
(Zea mays)
Liliopsida Zm.10383 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 61 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC23G3.06 33
  • 58.12 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU03396 33
  • 52.81 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14972 33
Species where no ortholog for NOP58 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for NOP58 Gene

ENSEMBL:
Gene Tree for NOP58 (if available)
TreeFam:
Gene Tree for NOP58 (if available)

Paralogs for NOP58 Gene

(1) SIMAP similar genes for NOP58 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for NOP58 Gene

genes like me logo Genes that share paralogs with NOP58: view

No data available for Paralogs for NOP58 Gene

Variants for NOP58 Gene

Sequence variations from dbSNP and Humsavar for NOP58 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000026848 -- 202,293,614(+) C/G intron_variant
rs1000053207 -- 202,280,513(+) A/C intron_variant
rs1000126627 -- 202,280,668(+) T/C intron_variant
rs1000136804 -- 202,287,357(+) C/T intron_variant
rs1000174334 -- 202,276,201(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NOP58 Gene

Variant ID Type Subtype PubMed ID
esv3593992 CNV loss 21293372

Variation tolerance for NOP58 Gene

Residual Variation Intolerance Score: 7.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.98; 20.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NOP58 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NOP58

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NOP58 Gene

Disorders for NOP58 Gene

Additional Disease Information for NOP58

No disorders were found for NOP58 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NOP58 Gene

Publications for NOP58 Gene

  1. Isolation and characterization of a novel PDGF-induced human gene. (PMID: 10925205) Nelson SA … LaRochelle WJ (Gene 2000) 2 3 4 58
  2. Human Nop5/Nop58 is a component common to the box C/D small nucleolar ribonucleoproteins. (PMID: 10606270) Lyman SK … Baserga SJ (RNA (New York, N.Y.) 1999) 2 3 4 58
  3. A proteomic screen for nucleolar SUMO targets shows SUMOylation modulates the function of Nop5/Nop58. (PMID: 20797632) Westman BJ … Lamond AI (Molecular cell 2010) 3 4 58
  4. Evidence that the AAA+ proteins TIP48 and TIP49 bridge interactions between 15.5K and the related NOP56 and NOP58 proteins during box C/D snoRNP biogenesis. (PMID: 19620283) McKeegan KS … Watkins NJ (Molecular and cellular biology 2009) 3 4 58
  5. A dynamic scaffold of pre-snoRNP factors facilitates human box C/D snoRNP assembly. (PMID: 17636026) McKeegan KS … Watkins NJ (Molecular and cellular biology 2007) 3 4 58

Products for NOP58 Gene

  • Addgene plasmids for NOP58

Sources for NOP58 Gene

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