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NPM2 Gene

protein-coding   GIFtS: 50
GCID: GC08P021881

Nucleophosmin/Nucleoplasmin 2

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Nucleophosmin/Nucleoplasmin 21 2
nucleoplasmin-22

External Ids:    HGNC: 79301   Entrez Gene: 103612   Ensembl: ENSG000001588067   OMIM: 6080735   UniProtKB: Q86SE83   

Export aliases for NPM2 gene to outside databases

Previous GC identifers: GC00U990477 GC08U900224 GC08P021903 GC08P021904 GC08P021939 GC08P020424


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for NPM2 Gene:
NPM2 (nucleophosmin/nucleoplasmin 2) is a protein-coding gene. GO annotations related to this gene include histone binding and nucleic acid binding. An important paralog of this gene is NPM3.

UniProtKB/Swiss-Prot: NPM2_HUMAN, Q86SE8
Function: Core histones chaperone involved in chromatin reprogramming, specially during fertilization and early
embryonic development. Probably involved in sperm DNA decondensation during fertilization




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000008.10  NT_167187.2  NC_018919.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NPM2 gene promoter:
         HFH-3   FOXD3   GATA-1   FOXL1   Evi-1   FOXI1   FOXJ2 (long isoform)   HFH-1   FOXJ2   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNPM2 promoter sequence
   Search Chromatin IP Primers for NPM2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NPM2


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

Entrez Gene cytogenetic band: 8p21.3   Ensembl cytogenetic band:  8p21.3   HGNC cytogenetic band: 8p21.3

NPM2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPM2 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P021881:  view genomic region     (about GC identifiers)

Start:
21,881,636 bp from pter      End:
21,894,408 bp from pter
Size:
12,773 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: NPM2_HUMAN, Q86SE8 (See protein sequence)
Recommended Name: Nucleoplasmin-2  
Size: 214 amino acids; 24152 Da
Subunit: Homopentamer, when bound to H2A-H2B dimers only. Homodecamer of two stacked pentamers, when bound to
H2A-H2B dimers and H3-H4 tetramers simultaneously
1 PDB 3D structure from and Proteopedia for NPM2:
3T30 (3D)    
Secondary accessions: B3KSU0 D3DSQ8

Explore the universe of human proteins at neXtProt for NPM2: NX_Q86SE8

Explore proteomics data for NPM2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See NPM2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001273609.1  NP_001273610.1  NP_877724.1  

    ENSEMBL proteins: 
     ENSP00000429984   ENSP00000429413   ENSP00000381032   ENSP00000428016   ENSP00000427741  
     ENSP00000289820   ENSP00000370941  

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    ProSpec Recombinant Protein for NPM2
    Cloud-Clone Corp. Proteins for NPM2

     
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    antibodies-online proteins for NPM2 (5 products) 

     
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    antibodies-online kits for NPM2 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR024057 Nucleoplasmin_core_dom
     IPR004301 Nucleoplasmin

    Graphical View of Domain Structure for InterPro Entry Q86SE8

    ProtoNet protein and cluster: Q86SE8

    1 Blocks protein domain: IPB004301 Nucleoplasmin

    UniProtKB/Swiss-Prot: NPM2_HUMAN, Q86SE8
    Domain: The acidic tract A2 mediates histone binding
    Similarity: Belongs to the nucleoplasmin family


    Find genes that share domains with NPM2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NPM2_HUMAN, Q86SE8
    Function: Core histones chaperone involved in chromatin reprogramming, specially during fertilization and early
    embryonic development. Probably involved in sperm DNA decondensation during fertilization

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0019899enzyme binding IEA--
    GO:0042393histone binding TAS12581654
         
    Find genes that share ontologies with NPM2           About GenesLikeMe


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Npm2):
     embryogenesis  reproductive system 

    Find genes that share phenotypes with NPM2           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Npm2tm1Zuk for NPM2

       genOway: Develop your customized and physiologically relevant rodent model for NPM2

    miRNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NPM2_HUMAN, Q86SE8: Nucleus (By similarity). Note=Found in the oocyte nucleus before nuclear membrane breakdown,
    after which it is redistributed to the cytoplasm (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000789cytoplasmic chromatin IDA12714744
    GO:0000790nuclear chromatin IDA12714744
    GO:0005634nucleus IDA12714744
    GO:0005730nucleolus ----

    Find genes that share ontologies with NPM2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NPM2
    Interactions:

        Search GeneGlobe Interaction Network for NPM2

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for NPM2 (ENSP000002898204) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RNF2ENSP000003564804STRING: ENSP00000356480
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006338chromatin remodeling IDA12714744
    GO:0007096regulation of exit from mitosis IMP12714744
    GO:0007338single fertilization IMP12714744
    GO:0009790embryo development IMP12714744
    GO:0009994oocyte differentiation IEP12714744

    Find genes that share ontologies with NPM2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NPM2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for NPM2 gene (3 alternative transcripts): 
    NM_001286680.1  NM_001286681.1  NM_182795.1  

    Unigene Cluster for NPM2:

    Nucleophosmin/nucleoplasmin 2
    Hs.131055  [show with all ESTs]
    Unigene Representative Sequence: AK127602
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000520125 ENST00000521157 ENST00000397940(uc003xac.3 uc003xad.3)
    ENST00000522813 ENST00000518119 ENST00000520180 ENST00000289820(uc003xae.3 uc003xaf.3)
    ENST00000381530 ENST00000522953 ENST00000520456 ENST00000519373 ENST00000524322

    miRNA
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NPM2
      QuantiTect SYBR Green Assays in human, mouse, rat NPM2
      QuantiFast Probe-based Assays in human, mouse, rat NPM2

    Additional mRNA sequence: 

    AK094267.1 AK127602.1 AY262113.1 AY262114.1 BC068078.1 

    7 DOTS entries:

    DT.301347  DT.100744955  DT.95265579  DT.100021410  DT.121484015  DT.121484020  DT.121484021 

    Selected AceView cDNA sequences (see all 33):

    BF594409 BQ684634 BM055230 BQ878692 BI913169 CK904862 AY262113 AI391464 
    AK094267 AY262114 NM_182795 BQ684424 BC068078 CR603169 BI914922 AI016313 
    BI439005 BU155917 BX422822 BF057162 BQ878312 AW002370 BF592761 BQ682257 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for NPM2 (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10
    SP1:                                -     -                                             
    SP2:                                                                                    
    SP3:                                                                                    
    SP4:                                                                    -     -         
    SP5:              -                 -     -                                             


    ECgene alternative splicing isoforms for NPM2

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NPM2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CACACGCACA
    NPM2 Expression
    About this image


    NPM2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Secondary Oocyte Antral Follicle
             Secondary follicles
     
     Gonad
             Secondary Oocyte Antral Follicle
    NPM2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NPM2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.131055
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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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for NPM2 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Npm21 , 5 nucleophosmin/nucleoplasmin 21, 5 74.82(n)1
    67.55(a)1
      14 (36.42 cM)5
    3284401  NM_181345.31  NP_851990.21 
     706473025 
    lizard
    (Anolis carolinensis)
    Reptilia NPM26
    nucleophosmin/nucleoplasmin 2
    39(a)
    1 ↔ 1
    GL343322.1(718561-728008)
    African clawed frog
    (Xenopus laevis)
    Amphibia npm-A2 nucleoplasmin 71.1(n)    X04766.1 
    zebrafish
    (Danio rerio)
    Actinopterygii npm2b6
    nucleophosmin/nucleoplasmin, 2b
    36(a)
    1 ↔ 1
    10(45752921-45759514) ENSDARG00000053963


    ENSEMBL Gene Tree for NPM2 (if available)
    TreeFam Gene Tree for NPM2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NPM2 gene
    NPM32  NPM12  
    2 SIMAP similar genes for NPM2 using alignment to 4 protein entries:     NPM2_HUMAN (see all proteins):
    NPM3    NPM1

    Find genes that share paralogs with NPM2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NPM2 (see all 351)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1913332611,2
    --21880454(+) CACTTC/TGGGAG 1 -- us2k10--------
    rs1842878311,2
    --21880539(+) AAAAAC/TATGAA 1 -- us2k10--------
    rs1454832921,2
    --21880582(+) ACCCAA/GCTACT 1 -- us2k10--------
    rs1510301621,2
    C--21880615(+) CGCTTC/GAACAT 1 -- us2k10--------
    rs1169046641,2
    C,F--21880642(+) AGTGAG/CCTGAG 1 -- us2k12Minor allele frequency- C:0.05NA EA 240
    rs1461886141,2
    C--21880658(+) CCACC-/GCA   
       CTCCA
    GCACT
    1 -- us2k10--------
    rs2004562331,2
    C--21880697(+) AAAAA-/AGAAAA 1 -- us2k10--------
    rs1882211251,2
    --21880716(+) AAAGAA/GAAGAA 1 -- us2k10--------
    rs29573361,2
    C,H--21880725(-) caacaT/Atattt 1 -- us2k14Minor allele frequency- A:0.00NS EA 396
    rs557982331,2
    C,F--21880741(+) ACCCCA/CGTTAC 1 -- us2k11Minor allele frequency- C:0.10NA 120

    HapMap Linkage Disequilibrium report for NPM2 (21881636 - 21894408 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for NPM2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv528590CNV Loss19592680
    nsv831263CNV Loss17160897
    dgv7756n71CNV Loss21882294
    essv21913CNV CNV17122850
    essv19243CNV CNV17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NPM2
    DNA2.0 Custom Variant and Variant Library Synthesis for NPM2

    (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.)
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    OMIM gene information: 608073    OMIM disorders: --


    Find genes that share disorders with NPM2           About GenesLikeMe

    Genetic Association Database (GAD): NPM2
    Human Genome Epidemiology (HuGE) Navigator: NPM2 (1 document)

    Export disorders for NPM2 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)
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    PubMed articles for NPM2 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with NPM2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Roles of NPM2 in chromatin and nucleolar organization in oocytes and embryos. (PubMed id 12714744)1, 2, 3 Burns K.H.... Matzuk M.M. (Science 2003)
    2. Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos. (PubMed id 21863821)1, 2 Platonova O.... Akey C.W. (Biochemistry 2011)
    3. Centrosome-related genes, genetic variation, and risk of breast cancer. (PubMed id 20508983)1, 4 Olson J.E....Couch F.J. (Breast Cancer Res. Treat. 2011)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. New insights into the nucleophosmin/nucleoplasmin family of nuclear chaperones. (PubMed id 17187372)2, 9 Frehlick L.J.... Ausio J. (Bioessays 2007)
    6. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)
    7. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    8. Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activities. (PubMed id 22968912)1 Finn R.M....AusiA^ J. (FASEB J. 2012)
    9. Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling. (PubMed id 22362753)1 Okuwaki M....Nagata K. (Nucleic Acids Res. 2012)
    10. Genome-wide screen of promoter methylation identifies novel markers in melanoma. (PubMed id 19491193)1 Koga Y....Weissman S.M. (Genome Res. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 10361 HGNC: 7930 AceView: NPM2 Ensembl:ENSG00000158806 euGenes: HUgn10361
    ECgene: NPM2 H-InvDB: NPM2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for NPM2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NPM2 gene:
    Search GeneIP for patents involving NPM2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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