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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
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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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