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    NPM1 nucleophosmin 1 [ Homo sapiens (human) ]

    Gene ID: 4869, updated on 26-Sep-2021

    Summary

    Official Symbol
    NPM1provided by HGNC
    Official Full Name
    nucleophosmin 1provided by HGNC
    Primary source
    HGNC:HGNC:7910
    See related
    Ensembl:ENSG00000181163 MIM:164040
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    B23; NPM
    Summary
    The protein encoded by this gene is involved in several cellular processes, including centrosome duplication, protein chaperoning, and cell proliferation. The encoded phosphoprotein shuttles between the nucleolus, nucleus, and cytoplasm, chaperoning ribosomal proteins and core histones from the nucleus to the cytoplasm. This protein is also known to sequester the tumor suppressor ARF in the nucleolus, protecting it from degradation until it is needed. Mutations in this gene are associated with acute myeloid leukemia. Dozens of pseudogenes of this gene have been identified. [provided by RefSeq, Aug 2017]
    Expression
    Ubiquitous expression in ovary (RPKM 256.2), lymph node (RPKM 146.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NPM1 in Genome Data Viewer
    Location:
    5q35.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (171387116..171410900)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (170814120..170837904)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA pseudogene 71 Neighboring gene ribosomal protein L10 pseudogene 8 Neighboring gene microRNA 3912 Neighboring gene fibroblast growth factor 18 Neighboring gene uncharacterized LOC105377721 Neighboring gene uncharacterized LOC105377720

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev HIV-1 Rev interacting protein, nucleophosmin 1 (NPM1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with NPM1 is decreased by RRE PubMed
    rev HIV-1 Rev has a nucleolar distribution which is similar to B23.1, but with different trafficking rates PubMed
    rev interaction of B23 with Rev has been implicated in the cytotoxic activity of Rev PubMed
    rev amino acids 38-52 of Rev have been implicated in the association with B32 PubMed
    rev B23 is associated with the nucleolar localization of Rev PubMed
    rev during nuclear import B23 forms a specific binding complex with Rev which is dissociated by RRE RNA and phosphorylation by casein kinase II (CK2) PubMed
    rev B23 stimulates the nuclear import of Rev, an effect that is increased when B23 is phosphorylated by casein kinase II (CK2) PubMed
    Tat tat Nucleophosmin (NPM1, nucleolar phosphoprotein B23, numatrin) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
    tat HIV-1 Tat complexes with LARP7, MEPCE, SART3, NPM1, PPM1G, hnRNP-F, and 7SK RNA to form a Tat-7SK RNP complex to control HIV-1 transcription PubMed
    tat HIV-1 Tat upregulates the expression of nucleophosmin (NPM1, nucleolar phosphoprotein B23, numatrin) in Jurkat cells PubMed
    tat Acetylation of human histone chaperone NPK1 regulates nuclear localization of HIV-1 Tat and modulates Tat-mediated LTR-transactivation PubMed
    tat Overexpression of NPM1 enhances HIV-1 Tat-mediated transactivation by reducing the histone H1 occupancy on the chromatinized template of HIV-1 LTR PubMed
    tat The nucleolar shuttle protein B23 binds to HIV-1 Tat and data indicates B23 is necessary for the nucleolar localization of Tat PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of nucleophosmin (NPM1, nucleolar phosphoprotein B23, numatrin) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC104254

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables NF-kappaB binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables Tat protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein N-terminus binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables rRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ribosomal large subunit binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ribosomal small subunit binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables unfolded protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell aging IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell volume homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to UV IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in centrosome cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in intracellular protein transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of centrosome duplication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nucleocytoplasmic transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nucleocytoplasmic transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell cycle G2/M phase transition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of centrosome duplication IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein localization to nucleolus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of translation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein localization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein stabilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in rRNA export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of DNA damage response, signal transduction by p53 class mediator IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cell growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of centriole replication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of centrosome duplication IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of eIF2 alpha phosphorylation by dsRNA IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of endodeoxyribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of endoribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of mRNA stability involved in cellular response to UV IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ribosomal large subunit biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in ribosomal large subunit export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in ribosomal small subunit biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in ribosomal small subunit export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in ribosome assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in focal adhesion HDA PubMed 
    located_in granular component IEA
    Inferred from Electronic Annotation
    more info
     
    part_of large ribosomal subunit IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-DNA complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of small ribosomal subunit IEA
    Inferred from Electronic Annotation
    more info
     
    located_in spindle pole centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    nucleophosmin
    Names
    nucleolar protein NO38
    nucleophosmin (nucleolar phosphoprotein B23, numatrin)
    nucleophosmin/nucleoplasmin family, member 1
    testicular tissue protein Li 128

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016018.1 RefSeqGene

      Range
      5001..28181
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_458

    mRNA and Protein(s)

    1. NM_001037738.3NP_001032827.1  nucleophosmin isoform 3

      See identical proteins and their annotated locations for NP_001032827.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) utilizes an alternate 3'-terminal exon, compared to variant 1, resulting in a shorter protein (isoform 3) with a distinct C-terminus.
      Source sequence(s)
      AC091980, AC093246, BC107754
      Consensus CDS
      CCDS43399.1
      UniProtKB/Swiss-Prot
      P06748
      UniProtKB/TrEMBL
      A0A140VJQ2
      Related
      ENSP00000377408.2, ENST00000393820.2
      Conserved Domains (1) summary
      pfam03066
      Location:18117
      Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
    2. NM_001355006.2NP_001341935.1  nucleophosmin isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. Variants 1 and 7 both encode the same isoform (1).
      Source sequence(s)
      AC093246, AY347529
      Consensus CDS
      CCDS4376.1
      Related
      ENSP00000428755.1, ENST00000517671.5
      Conserved Domains (2) summary
      pfam03066
      Location:18117
      Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
      pfam16276
      Location:245291
      NPM1-C; Nucleophosmin C-terminal domain
    3. NM_001355007.2NP_001341936.1  nucleophosmin isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC091980, AC093246
      Related
      ENSP00000429485.2, ENST00000521672.6
      Conserved Domains (2) summary
      pfam03066
      Location:152
      Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
      pfam16276
      Location:181229
      NPM1-C; Nucleophosmin C-terminal domain
    4. NM_001355009.2NP_001341938.1  nucleophosmin isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) lacks an internal segment and has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC091980, AC093246
      Related
      ENSP00000503717.1, ENST00000679233.1
      Conserved Domains (1) summary
      pfam03066
      Location:18116
      Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
    5. NM_001355010.2NP_001341939.1  nucleophosmin isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several alternate internal exons compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC091980, AC093246, BU661768
      Conserved Domains (1) summary
      pfam16276
      Location:118166
      NPM1-C; Nucleophosmin C-terminal domain
    6. NM_002520.7NP_002511.1  nucleophosmin isoform 1

      See identical proteins and their annotated locations for NP_002511.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 7 both encode the same isoform (1).
      Source sequence(s)
      AC091980, AC093246
      Consensus CDS
      CCDS4376.1
      UniProtKB/Swiss-Prot
      P06748
      UniProtKB/TrEMBL
      A0A0S2Z491
      Related
      ENSP00000296930.5, ENST00000296930.10
      Conserved Domains (2) summary
      pfam03066
      Location:18117
      Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
      pfam16276
      Location:245291
      NPM1-C; Nucleophosmin C-terminal domain
    7. NM_199185.4NP_954654.1  nucleophosmin isoform 2

      See identical proteins and their annotated locations for NP_954654.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2) that lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC093246, BC009623, BC021983, HM005441
      Consensus CDS
      CCDS4377.1
      UniProtKB/Swiss-Prot
      P06748
      UniProtKB/TrEMBL
      A0A0S2Z4G7
      Related
      ENSP00000341168.6, ENST00000351986.10
      Conserved Domains (2) summary
      pfam03066
      Location:18116
      Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
      pfam16276
      Location:216264
      NPM1-C; Nucleophosmin C-terminal domain

    RNA

    1. NR_149149.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate splice junction and lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC091980, AC093246
      Related
      ENST00000678774.1

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      171387116..171410900
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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