Npm1 nucleophosmin 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 25498, updated on 27-Nov-2024

Summary

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Official Symbol: Npm1provided by RGD
Official Full Name: nucleophosmin 1provided by RGD
Primary source: RGD:3192
See related: EnsemblRapid:ENSRNOG00000004616 AllianceGenome:RGD:3192
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: B23NP
Summary: Enables several functions, including anion binding activity; p53 binding activity; and protein kinase B binding activity. Involved in several processes, including negative regulation of apoptotic process; rRNA metabolic process; and regulation of DNA replication. Located in nuclear matrix and nucleoplasm. Human ortholog(s) of this gene implicated in acute myeloid leukemia. Orthologous to human NPM1 (nucleophosmin 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 1624.4), Spleen (RPKM 1421.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Npm1 in Genome Data Viewer

Location:: 10q12

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (18245739..18255913, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (17741512..17751626, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (18080949..18091062, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

study suggests that although neurons need NPM1 for survival, an increase in its expression beyond physiological levels and its translocation to the cytoplasm leads to death through abortive cell cycle induction.
Title: Regulation of Neuronal Survival by Nucleophosmin 1 (NPM1) Is Dependent on Its Expression Level, Subcellular Localization, and Oligomerization Status.
The S-nitrosylation of B23 enhanced B23-SIAH1 binding and mediated the neuroprotective actions of B23 by abrogating the E3 ligase activity of SIAH1.
Title: S-nitrosylation of B23/nucleophosmin by GAPDH protects cells from the SIAH1-GAPDH death cascade.
These results suggest a key role for NPM in promoting neuronal survival and a novel mechanism of neuronal degeneration triggered by nucleolar stress.
Title: Nucleolar stress characterized by downregulation of nucleophosmin: a novel cause of neuronal degeneration.
Nuclear localization of B23 and CK2 is dynamically regulated in response to altered growth status in the cell.
Title: Protein B23/nucleophosmin/numatrin nuclear dynamics in relation to protein kinase CK2 and apoptotic activity in prostate cells.
Npm1 may act as an alarmin: implications for sepsis are reported.
Title: Nucleophosmin may act as an alarmin: implications for severe sepsis.
ATP-B23 interaction is required for the stability of the B23 protein and regulates cell survival, confining B23 within the nucleolus in PC12 cells.
Title: Disruption of ATP binding destabilizes NPM/B23 and inhibits anti-apoptotic function.
Akt2, but not other isoforms, specifically regulates B23 sumoylation and protein stability
Title: Nuclear Akt interacts with B23/NPM and protects it from proteolytic cleavage, enhancing cell survival.
B23 distinctively binds Ebp1 isoforms and regulates cell proliferation and survival through p42 and p48, respectively.
Title: Ebp1 association with nucleophosmin/B23 is essential for regulating cell proliferation and suppressing apoptosis.
polyamines modulate cytoplasmic HuR levels in intestinal epithelial cells, in turn controlling the stability of the NPM and p53 mRNAs and influencing NPM and p53 protein levels
Title: Polyamine depletion increases cytoplasmic levels of RNA-binding protein HuR leading to stabilization of nucleophosmin and p53 mRNAs.
These results indicate that B23 is a shuttle protein involved in cell cycle and cell proliferation associated with nuclear matrix.
Title: Nucleophosmin/B23 is a proliferate shuttle protein associated with nuclear matrix.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Npm1-rs (e-PCR), detects polymorphism
- UniSTS:144053

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables NF-kappaB binding	ISO Inferred from Sequence Orthology more info
enables NF-kappaB binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables Tat protein binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables core promoter sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables p53 binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphatidylinositol-3,4,5-trisphosphate binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase B binding	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein kinase inhibitor activity	ISO Inferred from Sequence Orthology more info
enables protein kinase inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info
enables rRNA binding	IEA Inferred from Electronic Annotation more info
enables rRNA binding	ISO Inferred from Sequence Orthology more info
enables ribosomal large subunit binding	ISO Inferred from Sequence Orthology more info
enables ribosomal small subunit binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables unfolded protein binding	ISO Inferred from Sequence Orthology more info
enables unfolded protein binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in cardiac muscle hypertrophy	IEP Inferred from Expression Pattern more info	PubMed
involved_in cell volume homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell volume homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to testosterone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular senescence	ISO Inferred from Sequence Orthology more info
involved_in cellular senescence	ISS Inferred from Sequence or Structural Similarity more info
involved_in centrosome cycle	ISO Inferred from Sequence Orthology more info
involved_in centrosome cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IDA Inferred from Direct Assay more info	PubMed
involved_in liver regeneration	IEP Inferred from Expression Pattern more info	PubMed
involved_in macrophage differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cardiac muscle cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of centrosome duplication	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within nucleocytoplasmic transport	ISO Inferred from Sequence Orthology more info
involved_in nucleocytoplasmic transport	ISO Inferred from Sequence Orthology more info
involved_in nucleosome assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA replication	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-directed DNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of catalytic activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell cycle G2/M phase transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell cycle G2/M phase transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of centrosome duplication	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of centrosome duplication	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of protein kinase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein localization to nucleolus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of protein localization to nucleolus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein localization to nucleolus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein ubiquitination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of translation	ISS Inferred from Sequence or Structural Similarity more info
involved_in post-transcriptional regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-transcriptional regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in protein localization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein stabilization	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	ISO Inferred from Sequence Orthology more info
involved_in rRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA damage response, signal transduction by p53 class mediator	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA damage response, signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of centriole replication	ISO Inferred from Sequence Orthology more info
involved_in regulation of centriole replication	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of centrosome duplication	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of centrosome duplication	ISO Inferred from Sequence Orthology more info
involved_in regulation of eIF2 alpha phosphorylation by dsRNA	ISO Inferred from Sequence Orthology more info
involved_in regulation of eIF2 alpha phosphorylation by dsRNA	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of endodeoxyribonuclease activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of endodeoxyribonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of endoribonuclease activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of endoribonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA stability involved in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of protein stability	ISO Inferred from Sequence Orthology more info
involved_in ribosomal large subunit biogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal large subunit biogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ribosomal large subunit biogenesis	ISO Inferred from Sequence Orthology more info
involved_in ribosomal large subunit export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal large subunit export from nucleus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ribosomal large subunit export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in ribosomal small subunit biogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal small subunit biogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ribosomal small subunit biogenesis	ISO Inferred from Sequence Orthology more info
involved_in ribosomal small subunit export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal small subunit export from nucleus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ribosomal small subunit export from nucleus	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in granular component	IEA Inferred from Electronic Annotation more info
located_in granular component	ISO Inferred from Sequence Orthology more info
part_of large ribosomal subunit	IEA Inferred from Electronic Annotation more info
part_of large ribosomal subunit	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-DNA complex	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info
part_of small ribosomal subunit	IEA Inferred from Electronic Annotation more info
part_of small ribosomal subunit	ISO Inferred from Sequence Orthology more info
located_in spindle pole centrosome	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nucleophosmin

Names: NPM; nucleolar phosphoprotein B23; nucleolar protein B23.1; nucleolar protein NO38; nucleophosmin (nucleolar phosphoprotein B23, numatrin); numatrin

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001430108.1 → NP_001417037.1 nucleophosmin isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6HDG3
NM_001430109.1 → NP_001417038.1 nucleophosmin isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010
NM_012992.4 → NP_037124.1 nucleophosmin isoform 1

See identical proteins and their annotated locations for NP_037124.1

Status: PROVISIONAL

Source sequence(s)

BC060579

UniProtKB/Swiss-Prot

P13084, Q63698, Q64269

UniProtKB/TrEMBL

A6HDG2, D3ZXI2

Related

ENSRNOP00000006591.5, ENSRNOT00000006591.9

Conserved Domains (2) summary

pfam03066
Location:18 → 117

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain

pfam16276
Location:243 → 289

NPM1-C; Nucleophosmin C-terminal domain