Format

Send to:

Choose Destination

NPM1 nucleophosmin 1 [ Homo sapiens (human) ]

Gene ID: 4869, updated on 13-Jan-2019

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

Genomic context

See NPM1 in Genome Data Viewer
Location:
5q35.1
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (171387116..171410884)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (170814652..170837888)

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 FunctionsWhat'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 BioSystems

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
NF-kappaB binding IDA
Inferred from Direct Assay
more info
PubMed 
NF-kappaB binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Tat protein binding IDA
Inferred from Direct Assay
more info
PubMed 
activating transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
core promoter binding IDA
Inferred from Direct Assay
more info
PubMed 
histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
ribosomal large subunit binding IDA
Inferred from Direct Assay
more info
PubMed 
ribosomal small subunit binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
unfolded protein binding IDA
Inferred from Direct Assay
more info
PubMed 
unfolded protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
CENP-A containing nucleosome assembly TAS
Traceable Author Statement
more info
 
DNA repair IDA
Inferred from Direct Assay
more info
PubMed 
cell aging IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell aging ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to UV IDA
Inferred from Direct Assay
more info
PubMed 
centrosome cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
centrosome cycle ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular protein transport TAS
Traceable Author Statement
more info
PubMed 
negative regulation of apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of centrosome duplication IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein kinase activity by regulation of protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
nucleocytoplasmic transport IDA
Inferred from Direct Assay
more info
PubMed 
nucleocytoplasmic transport TAS
Traceable Author Statement
more info
PubMed 
nucleosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell cycle G2/M phase transition IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
protein complex oligomerization IDA
Inferred from Direct Assay
more info
PubMed 
protein localization IDA
Inferred from Direct Assay
more info
PubMed 
rRNA export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of centriole replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of centrosome duplication IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of eIF2 alpha phosphorylation by dsRNA IDA
Inferred from Direct Assay
more info
PubMed 
regulation of endodeoxyribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
regulation of endoribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
regulation of mRNA stability involved in cellular response to UV IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
ribosomal large subunit biogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribosomal large subunit export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribosomal small subunit biogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribosomal small subunit export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribosome assembly TAS
Traceable Author Statement
more info
PubMed 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
centrosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
centrosome ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
focal adhesion HDA PubMed 
membrane HDA PubMed 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
protein-DNA complex IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
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)

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_001037738.2NP_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, BC107754
    Consensus CDS
    CCDS43399.1
    UniProtKB/Swiss-Prot
    P06748
    UniProtKB/TrEMBL
    A0A140VJQ2
    Related
    ENSP00000377408.2, ENST00000393820.2
    Conserved Domains (1) summary
    pfam03066
    Location:18116
    Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
  2. NM_001355006.1NP_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:18116
    Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
    pfam16276
    Location:245293
    NPM1-C; Nucleophosmin C-terminal domain
  3. NM_001355007.1NP_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
    Conserved Domains (2) summary
    pfam03066
    Location:152
    Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
    pfam16276
    Location:181229
    NPM1-C; Nucleophosmin C-terminal domain
  4. NM_001355009.1NP_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
    Conserved Domains (1) summary
    pfam03066
    Location:18116
    Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
  5. NM_001355010.1NP_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_002520.6NP_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, BC002398
    Consensus CDS
    CCDS4376.1
    UniProtKB/Swiss-Prot
    P06748
    UniProtKB/TrEMBL
    A0A0S2Z491
    Related
    ENSP00000296930.5, ENST00000296930.9
    Conserved Domains (2) summary
    pfam03066
    Location:18116
    Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
    pfam16276
    Location:245293
    NPM1-C; Nucleophosmin C-terminal domain
  7. NM_199185.3NP_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)
    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_149149.1 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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    171387116..171410884
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center