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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NOP58 Gene

protein-coding   GIFtS: 54
GCID: GC02P203130

NOP58 ribonucleoprotein

(Previous name: NOP58 ribonucleoprotein homolog (yeast) )
 Explore 2 diseases affiliated with
NOP58 via our new
 Human Malady Compendium 
Biological research products
for NOP58
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
NOP58 Ribonucleoprotein1 2     NOP5/NOP582
NOP51 2 3     NOP58 Ribonucleoprotein Homolog2
Nucleolar Protein 52 3     Nucleolar Protein 582
HSPC1201     Nucleolar Protein NOP5/NOP582
NOP58 Ribonucleoprotein Homolog (Yeast)1     NOL53

External Ids:    HGNC: 299261   Entrez Gene: 516022   Ensembl: ENSG000000550447   UniProtKB: Q9Y2X33   

Export aliases for NOP58 gene to outside databases

Previous GC identifers: GC02P202839 GC02P194979


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: NOP58_HUMAN, Q9Y2X3
Function: Required for 60S ribosomal subunit biogenesis (By similarity)

Gene Wiki entry for NOP58 (NOP5/NOP58)


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_005403.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NOP58 gene promoter:
         CREB   ATF-2   deltaCREB   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNOP58 promoter sequence
   Search SABiosciences Chromatin IP Primers for NOP58

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NOP58


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q33.1   Ensembl cytogenetic band:  2q33.1   HGNC cytogenetic band: 2q33.1

NOP58 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NOP58 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P203130:  view genomic region     (about GC identifiers)

Start:
203,130,439 bp from pter      End:
203,168,389 bp from pter
Size:
37,951 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: NOP58_HUMAN, Q9Y2X3 (See protein sequence)
Recommended Name: Nucleolar protein 58  
Size: 529 amino acids; 59578 Da
Subunit: Interacts with NOLC1/Nopp140 (By similarity). Component of box C/D small nucleolar ribonucleoprotein (snoRNP)
particles
Subcellular location: Nucleus, nucleolus
Secondary accessions: Q53SA4 Q6PK08 Q9P036 Q9UFN3

Explore the universe of human proteins at neXtProt for NOP58: NX_Q9Y2X3

Post-translational modifications:

  • Sumoylation is essential for high-affinity binding to snoRNAs1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9Y2X3

  • NOP58 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_057018.1  
    ENSEMBL proteins: 
     ENSP00000264279   ENSP00000388905   ENSP00000388126  

    Human Recombinant Protein Products: 
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for NOP58

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730nucleolus TAS10925205
    GO:0005732small nucleolar ribonucleoprotein complex IDA17636026
    GO:0005737cytoplasm IDA--
    GO:0015030Cajal body IDA16687569


    NOP58 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    NOP58 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR002687 SnoRNA-bd_dom
     IPR012974 NOP5_N
     IPR012976 NOSIC

    Graphical View of Domain Structure for InterPro Entry Q9Y2X3

    ProtoNet protein and cluster: Q9Y2X3

    3 Blocks protein families:
    IPB002687 Pre-mRNA processing ribonucleoprotein
    IPB012974 NOP5
    IPB012976 NOSIC


    UniProtKB/Swiss-Prot: NOP58_HUMAN, Q9Y2X3
    Similarity: Belongs to the NOP5/NOP56 family
    Similarity: Contains 1 Nop domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: NOP58_HUMAN, Q9Y2X3
    Function: Required for 60S ribosomal subunit biogenesis (By similarity)

    miRNA
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    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI17636026
    GO:0030515snoRNA binding IDA17636026


    NOP58 for ontologies           About GeneDecksing


    4 GenomeRNAi human phenotypes for NOP58:
     Decreased Hepatitis C virus re  Decreased viability of wild-ty  Nuclear 60S biogenesis defects  Nucleoplasmic pre-40S maturati 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Ribosome biogenesis in eukaryotes
    Ribosome biogenesis in eukaryotes1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for NOP58):
        Ribosome biogenesis in eukaryotes


    NOP58 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NOP58

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/225 Interacting proteins for NOP58 (Q9Y2X32, 3 ENSP000002642794) via UniProtKB, MINT, STRING, and/or I2D (see all 225)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006364rRNA processing TAS10925205
    GO:0006608snRNP protein import into nucleus ISS10679015
    GO:0016049cell growth TAS10925205


    NOP58 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for NOP58
    Search CenterWatch for drugs/clinical trials and news about NOP58 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for NOP58 gene: 
    NM_015934.3  

    Unigene Cluster for NOP58:

    NOP58 ribonucleoprotein
    Hs.471104  [show with all ESTs]
    Unigene Representative Sequence: NM_015934
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000264279(uc002uzb.3) ENST00000426814 ENST00000488403(uc010zhv.1)
    ENST00000492740 ENST00000472050 ENST00000467734 ENST00000492688 ENST00000478941
    ENST00000433543 ENST00000478508

    miRNA
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    hsa-miR-520d-5p hsa-miR-524-5p hsa-miR-548u
    SwitchGear 3'UTR luciferase reporter plasmidNOP58 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AF123534.1 AF161469.1 AF263608.1 AK023975.1 AK300844.1 AK307396.1 AL117554.1 BC001707.1 
    BC009306.2 BC018805.1 BC032592.2 

    20 DOTS entries:

    DT.109893  DT.75160265  DT.120937859  DT.92446016  DT.120937862  DT.120937895  DT.100822922  DT.92446010 
    DT.100058877  DT.100889290  DT.120937865  DT.97860485  DT.100725164  DT.120937864  DT.75192847  DT.91962525 
    DT.40132877  DT.92338234  DT.95114801  DT.95114803 

    24/279 AceView cDNA sequences (see all 279):

    AW471159 AW778951 BM480265 BC018805 F36488 CB159666 CF994214 BE018636 
    BP362997 AF123534 BQ223313 BQ960327 BC001707 AA307595 BI324981 BM474530 
    BC032592 CR618609 BM994688 BX354341 BM770920 BM761515 AI564329 AI435592 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for NOP58 (see all 9)    About this scheme

    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:                                -           -     -                       -                                                                                 

    ExUns: 17a · 17b
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for NOP58

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    NOP58 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TACCAGCACA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See NOP58 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NOP58

    SOURCE GeneReport for Unigene cluster: Hs.471104

    UniProtKB/Swiss-Prot: NOP58_HUMAN, Q9Y2X3
    Tissue specificity: Ubiquitous

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for NOP58 gene from 9/40 species (see all 40)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves NOP581 NOP58 ribonucleoprotein homolog (yeast) 74.24(n)
    78.82(a)
      424087  XM_421942.3  XP_421942.1 
    lizard
    (Anolis carolinensis)
    Reptilia NOP586
    --
    82(a)
    1 ↔ 1
    GL343208.1(3818333-3833324)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3985582 similar to nucleolar protein NOP5/NOP58 75.54(n)    BC041223.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.2822 Danio rerio, clone IMAGE2639288, mRNA, partial cds 74.68(n)    BC061961.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta nop51 CG10206-PA 59.74(n)
    63.14(a)
      33966  NM_058064.4  NP_477412.1 
    worm
    (Caenorhabditis elegans)
    Secernentea nol-51 Protein NOL-5 59.12(n)
    56.79(a)
      171901  NM_058733.5  NP_491134.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes NOP58(YOR310C)4
    NOP581
    Protein involved in pre-rRNA processing, 18S rRNA synthesis, more4
    Nop58p1
    55.16(n)1
    49.6(a)1
      15(898360-896825)4
    8544871, 4  NP_014955.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G050601 putative nucleolar protein 5-2 59.88(n)
    59.49(a)
      819668  NM_111378.3  NP_187157.1 
    rice
    (Oryza sativa)
    Liliopsida AK073164.12   -- 72.61(n)    AK073164.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NOP58 gene
    1 SIMAP similar gene for NOP58 using alignment to 3 protein entries:     NOP58_HUMAN (see all proteins):
    NOP56

    NOP58 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for NOP58
    PGOHUM00000248904


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/618 NCBI SNPs in NOP58 are shown (see all 618    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1916264021,2
    --203128583(+) GGGCCC/TGGGAA 1 -- us2k10--------
    rs1849188231,2
    --203128651(+) TTAATC/TCCAGT 1 -- us2k10--------
    rs568695591,2
    --203128739(+) GCTCAC/TGCCTG 1 -- us2k11Minor allele frequency- T:0.00CSA 1
    rs1897533231,2
    --203128775(+) GGTGGA/GTGGAT 1 -- us2k10--------
    rs356896011,2
    C,F,--203128816(+) GACCAT/GCATGG 1 -- us2k16Minor allele frequency- G:0.20NA WA CSA EA 247
    rs1499632031,2
    --203128958(+) ATCATA/GCCACT 1 -- us2k10--------
    rs1450582421,2
    --203128996(+) AACTCC/TGTCTC 1 -- us2k10--------
    rs350173601,2
    C--203129024(+) AAAAA-/AGACAT 1 -- us2k10--------
    rs1931326291,2
    --203129060(+) TGGGGC/TCATTT 1 -- us2k10--------
    rs768710941,2
    C,--203129119(+) TAATAA/CTTCAT 1 -- us2k13Minor allele frequency- C:0.32NA EA 242

    HapMap Linkage Disequilibrium report for NOP58 (203130439 - 203168389 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NOP58: --

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    NOP58 for disorders           About GeneDecksing

    2 diseases for NOP58:    About MalaCards
    treacher collins syndrome    malaria

    1 disease from the University of Copenhagen DISEASES database for NOP58:
    Kennedy's disease

    Export disorders for NOP58 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for NOP58 gene, integrated from 9 sources (see all 49):
    (articles sorted by number of sources associating them with NOP58)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of a novel PDGF-induced human gene. (PubMed id 10925205)1, 2, 3 Nelson S.A.... LaRochelle W.J. (2000)
    2. Human Nop5/Nop58 is a component common to the box C/D small nucleolar ribonucleoproteins. (PubMed id 10606270)1, 2, 3 Lyman S.K....Baserga S.J. (1999)
    3. A proteomic screen for nucleolar SUMO targets shows S UMOylation modulates the function of Nop5/Nop58. (PubMed id 20797632)1, 2 Westman B.J....Lamond A.I. (2010)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    6. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (2002)
    7. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2 Zhang Q.-H.... Chen Z. (2000)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    9. Host cell interactome of HIV-1 Rev includes RNA helica ses involved in multiple facets of virus production. (PubMed id 22174317)1 Naji S....Gerace L. (2012)
    10. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 51602 HGNC: 29926 AceView: NOP5\/NOP58 Ensembl:ENSG00000055044 euGenes: HUgn51602
    ECgene: NOP58 Kegg: 51602 H-InvDB: NOP58

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for NOP58 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for NOP58 gene:
    Search GeneIP for patents involving NOP58

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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