Details for: NIP7

Gene ID: 51388

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: NIP7

Ensembl ID: ENSG00000132603

Description: nucleolar pre-rRNA processing protein NIP7

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • GABAergic neuron CL0000617
    CSI 9.54
    rCSI 31.95%
    PRS 73.02
  • neural progenitor cell CL0011020
    CSI 8.48
    rCSI 37.31%
    PRS 76.42
  • effector CD8-positive, alpha-beta T cell CL0001050
    CSI 6.81
    rCSI 5.18%
    PRS 96.33
  • plasmablast CL0000980
    CSI 5.23
    rCSI 4.12%
    PRS 90.66
  • placental villous trophoblast CL2000060
    CSI 4.87
    rCSI 7.53%
    PRS 86.22
  • lung macrophage CL1001603
    CSI 4.26
    rCSI 9.51%
    PRS 92.62
  • precursor B cell CL0000817
    CSI 3.84
    rCSI 3.36%
    PRS 92.36
  • small pre-B-II cell CL0000954
    CSI 3.8
    rCSI 3.65%
    PRS 95.58
  • basal cell CL0000646
    CSI 3.46
    rCSI 4.63%
    PRS 85.13
  • stem cell CL0000034
    CSI 3.42
    rCSI 3.3%
    PRS 82.74
  • mesenchymal cell CL0008019
    CSI 3.36
    rCSI 8.53%
    PRS 82.06
  • pro-B cell CL0000826
    CSI 2.93
    rCSI 2.43%
    PRS 89.45
  • CD4-positive helper T cell CL0000492
    CSI 2.84
    rCSI 2.15%
    PRS 95.68
  • common myeloid progenitor CL0000049
    CSI 2.84
    rCSI 2.29%
    PRS 89.34
  • erythroid progenitor cell CL0000038
    CSI 2.78
    rCSI 15.94%
    PRS 90.53
  • plasmacytoid dendritic cell, human CL0001058
    CSI 2.78
    rCSI 1.94%
    PRS 90.93
  • vascular associated smooth muscle cell CL0000359
    CSI 2.77
    rCSI 8.98%
    PRS 85.67
  • naive T cell CL0000898
    CSI 2.75
    rCSI 1.91%
    PRS 96.69
  • CD4-positive, CD25-positive, alpha-beta regulatory T cell CL0000792
    CSI 2.67
    rCSI 2.62%
    PRS 96.37
  • immature B cell CL0000816
    CSI 2.64
    rCSI 1.96%
    PRS 94.64
  • class switched memory B cell CL0000972
    CSI 2.64
    rCSI 1.97%
    PRS 95.4
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 2.63
    rCSI 2.38%
    PRS 86.36
  • perivascular cell CL4033054
    CSI 2.57
    rCSI 3.51%
    PRS 91.01
  • activated CD4-positive, alpha-beta T cell CL0000896
    CSI 2.44
    rCSI 2.25%
    PRS 96.78
  • granulocyte monocyte progenitor cell CL0000557
    CSI 2.43
    rCSI 2.1%
    PRS 90.3
  • hematopoietic stem cell CL0000037
    CSI 2.4
    rCSI 1.6%
    PRS 89.48
  • early lymphoid progenitor CL0000936
    CSI 2.37
    rCSI 2.08%
    PRS 91.36
  • colon epithelial cell CL0011108
    CSI 2.32
    rCSI 2.43%
    PRS 85.13
  • ciliated epithelial cell CL0000067
    CSI 2.31
    rCSI 2.03%
    PRS 78.39
  • multi-ciliated epithelial cell CL0005012
    CSI 2.3
    rCSI 2.3%
    PRS 81.88
  • keratinocyte CL0000312
    CSI 2.3
    rCSI 1.93%
    PRS 88.94
  • neural crest cell CL0011012
    CSI 2.28
    rCSI 1.8%
    PRS 79.21
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 2.24
    rCSI 2.28%
    PRS 93.74
  • mesodermal cell CL0000222
    CSI 2.17
    rCSI 2.61%
    PRS 86.25
  • intestinal epithelial cell CL0002563
    CSI 2.08
    rCSI 2.18%
    PRS 85.2
  • lung ciliated cell CL1000271
    CSI 2.01
    rCSI 2.33%
    PRS 81.35
  • CD8-positive, alpha-beta cytotoxic T cell CL0000794
    CSI 2
    rCSI 2.38%
    PRS 96.77
  • epithelial cell of lung CL0000082
    CSI 1.97
    rCSI 1.63%
    PRS 88.71
  • mature B cell CL0000785
    CSI 1.95
    rCSI 1.7%
    PRS 94.34
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 1.93
    rCSI 2.47%
    PRS 84.09
  • mature alpha-beta T cell CL0000791
    CSI 1.86
    rCSI 6.75%
    PRS 97.53
  • dendritic cell, human CL0001056
    CSI 1.79
    rCSI 2.75%
    PRS 93.77
  • radial glial cell CL0000681
    CSI 1.72
    rCSI 2.39%
    PRS 86.02
  • transit amplifying cell of colon CL0009011
    CSI 1.65
    rCSI 1.94%
    PRS 88.38
  • basal cell of prostate epithelium CL0002341
    CSI 1.63
    rCSI 4.71%
    PRS 91.39
  • peripheral nervous system neuron CL2000032
    CSI 1.54
    rCSI 2.1%
    PRS 80.77
  • club cell CL0000158
    CSI 1.54
    rCSI 2.26%
    PRS 82.9
  • common dendritic progenitor CL0001029
    CSI 1.39
    rCSI 1.74%
    PRS 93.41
  • effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL0001062
    CSI 1.18
    rCSI 5.94%
    PRS 95.45
  • memory T cell CL0000813
    CSI 1.13
    rCSI 2.17%
    PRS 97.26
  • large pre-B-II cell CL0000957
    CSI 0.81
    rCSI 2.31%
    PRS 89.5
  • primitive red blood cell CL0002355
    CSI 0.8
    rCSI 4.31%
    PRS 90.59
  • pancreatic stellate cell CL0002410
    CSI 0.53
    rCSI 3.1%
    PRS 89.74
  • pluripotent stem cell CL0002248
    CSI 0.2
    rCSI 5.89%
    PRS 93.47
  • epithelial cell of urethra CL1000296
    CSI 0.19
    rCSI 4.7%
    PRS 91.52

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [NIP7](/details-gene/51388) (Nucleolar pre-rRNA processing protein NIP7) is a protein-coding gene located on chromosome 16q22.1. It encodes a highly conserved nucleolar protein essential for the biogenesis of the 60S ribosomal subunit. As a core component of the cellular protein synthesis machinery, [NIP7](/details-gene/51388) is fundamentally involved in processing precursor ribosomal RNA ([rRNA](https://reactome.org/content/detail/R-HSA-72312)). Its expression pattern reflects this essential function, with significant enrichment observed in cells characterized by high metabolic activity, rapid proliferation, or complex protein synthesis demands. These include diverse cell types such as [GABAergic neuron](/details-cell/CL0000617), [neural progenitor cell](/details-cell/CL0011020), and activated immune cells like [effector CD8-positive, alpha-beta T cell](/details-cell/CL0001050), underscoring its critical role in supporting fundamental cellular growth and function. ## Cellular Roles and Expression Landscape The expression profile of [NIP7](/details-gene/51388) highlights its role as a key facilitator of protein synthesis in a wide array of physiologically active cells. **Overall**, the gene shows the highest significance in cell types with substantial requirements for ribosome production. This is particularly evident in the nervous system, where it is a top marker in both mature [GABAergic neuron](/details-cell/CL0000617) (CSI: 9.54) and developing [neural progenitor cell](/details-cell/CL0011020) (CSI: 8.48), suggesting its importance for both neuronal maintenance and neurogenesis. A similarly critical role is observed across the hematopoietic system. [NIP7](/details-gene/51388) is highly significant in terminally differentiated, protein-secreting immune cells like [effector CD8-positive, alpha-beta T cell](/details-cell/CL0001050) (CSI: 6.81) and [plasmablast](/details-cell/CL0000980) (CSI: 5.23), which must synthesize vast quantities of cytokines and antibodies, respectively. Furthermore, its high significance extends to various progenitor and precursor populations, including [precursor B cell](/details-cell/CL0000817), [small pre-B-II cell](/details-cell/CL0000954), [pro-B cell](/details-cell/CL0000826), and [common myeloid progenitor](/details-cell/CL0000049), which is consistent with the high demand for new ribosomes during cell division and lineage commitment. This is further supported by research identifying its expression in CD34+ hematopoietic stem/progenitor cells ([Link](https://doi.org/10.1101/gr.140200)). The broad significance of [NIP7](/details-gene/51388) in other proliferative or metabolically active cells, such as [placental villous trophoblast](/details-cell/CL2000060) and [stem cell](/details-cell/CL0000034), reinforces its identity as a fundamental "workhorse" gene essential for cellular growth and maintenance. ## Pathways and Molecular Function Functionally, [NIP7](/details-gene/51388) is intrinsically linked to ribosome biogenesis, a process localized primarily within the nucleolus. Its annotation as a component of the [preribosome, large subunit precursor (GO:0030687)](https://www.ebi.ac.uk/QuickGO/term/GO:0030687) and its localization to the [nucleolus (GO:0005730)](https://www.ebi.ac.uk/QuickGO/term/GO:0005730) are well-supported by proteomic analyses of this organelle ([Link](https://doi.org/10.1091/mbc.e02-05-0271)). The gene's primary biological process is [ribosomal large subunit biogenesis (GO:0042273)](https://www.ebi.ac.uk/QuickGO/term/GO:0042273), a critical step in the broader pathway of [ribosome assembly (GO:0042255)](https://www.ebi.ac.uk/QuickGO/term/GO:0042255). Reactome pathway analysis corroborates this, placing [NIP7](/details-gene/51388) centrally in the [major pathway of rRNA processing in the nucleolus and cytosol (R-HSA-6791226)](https://reactome.org/content/detail/R-HSA-6791226). Studies have shown that [NIP7](/details-gene/51388) interacts with other key processing factors, such as FTSJ3, to facilitate pre-rRNA maturation ([Link](https://doi.org/10.1371/journal.pone.0029174)). Additionally, its molecular functions include [RNA binding (GO:0003723)](https://www.ebi.ac.uk/QuickGO/term/GO:0003723) and [protein binding (GO:0005515)](https://www.ebi.ac.uk/QuickGO/term/GO:0005515), which enable it to associate with both the rRNA substrate and other proteins in the preribosomal complex. ## Research Directions The ubiquitous yet vital role of [NIP7](/details-gene/51388) in ribosome biogenesis makes it a critical node for controlling cell growth, proliferation, and function. Its potential role in human disease, particularly in conditions characterized by aberrant protein synthesis like cancer or ribosomopathies, warrants further investigation. **Proposed Hypotheses:** 1. Given the high significance of [NIP7](/details-gene/51388) in hematopoietic progenitors and its known interaction with the protein associated with Shwachman-Bodian-Diamond syndrome (a bone marrow failure disorder), it is hypothesized that haploinsufficiency or dysregulation of [NIP7](/details-gene/51388) is a contributing factor in undiagnosed ribosomopathies, leading to impaired hematopoiesis and specific cytopenias ([Link](https://doi.org/10.1016/j.yexcr.2007.06.024)). 2. Based on its high expression in effector lymphocytes, it is hypothesized that the rate of [NIP7](/details-gene/51388)-mediated ribosome production is a critical bottleneck that determines the magnitude and sustainability of an adaptive immune response. Cells unable to upregulate [NIP7](/details-gene/51388) may fail to achieve full effector function or undergo premature exhaustion. **Experimental Approach:** To test the second hypothesis regarding the role of [NIP7](/details-gene/51388) in T cell function, a conditional knockout mouse model could be employed (e.g., *Nip7fl/fl* x *Cd4-Cre*). Following an acute viral infection (e.g., LCMV), antigen-specific CD8+ T cells from knockout and control mice would be analyzed. Key readouts would include T cell expansion and contraction kinetics via flow cytometry, effector function via intracellular cytokine staining for IFN-gamma and TNF-alpha, and cytotoxic potential using in vitro killing assays. Concurrently, polysome profiling of these T cells would directly assess the impact of [NIP7](/details-gene/51388) loss on translational capacity. **Therapeutic Potential:** As a fundamental component of ribosome biogenesis, [NIP7](/details-gene/51388) is a challenging therapeutic target due to the risk of toxicity in healthy, proliferating tissues. However, many cancers exhibit a strong dependency on elevated ribosome production to sustain rapid growth. This "ribosome biogenesis addiction" suggests that tumors may be disproportionately sensitive to its disruption. Therefore, **inhibition** of [NIP7](/details-gene/51388) activity could represent a viable anti-cancer strategy, particularly in hematological malignancies or other cancers known to be sensitive to translational inhibitors. The therapeutic window would depend on the differential requirement for ribosome synthesis between malignant and normal cells.

Genular Protein ID: 28701651

Symbol: NIP7_HUMAN

Name: 60S ribosome subunit biogenesis protein NIP7 homolog

UniProtKB Accession Codes:

Q9Y221 B2RD04 Q9NZZ0

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CDD 2 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 9 EMDB 6 Ensembl 2 EvolutionaryTrace 1 ExpressionAtlas 1 GO 7 Gene3D 2 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 6 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 MetOSite 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PDB 8 PDBsum 8 PIRSF 1 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 Pumba 1 RNAct 1 Reactome 1 RefSeq 2 SMART 1 SMR 1 STRING 1 SUPFAM 2 SignaLink 1 SwissPalm 1 TopDownProteomics 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 10810093

Title: Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics.

PubMed ID: 10810093

DOI: 10.1101/gr.10.5.703

PubMed ID: 11042152

Title: Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells.

PubMed ID: 11042152

DOI: 10.1101/gr.140200

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 12429849

Title: Functional proteomic analysis of human nucleolus.

PubMed ID: 12429849

DOI: 10.1091/mbc.e02-05-0271

PubMed ID: 14660641

Title: A novel human nucleolar protein, Nop132, binds to the G proteins, RRAG A/C/D.

PubMed ID: 14660641

DOI: 10.1074/jbc.m305935200

PubMed ID: 17643419

Title: The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels.

PubMed ID: 17643419

DOI: 10.1016/j.yexcr.2007.06.024

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 22195017

Title: The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing.

PubMed ID: 22195017

DOI: 10.1371/journal.pone.0029174

PubMed ID: 15522784

Title: Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells.

PubMed ID: 15522784

DOI: 10.1016/j.jsb.2004.06.010

PubMed ID: 16959974

Title: The consensus coding sequences of human breast and colorectal cancers.

PubMed ID: 16959974

DOI: 10.1126/science.1133427

Sequence Information:

  • Length: 180
  • Mass: 20463
  • Checksum: FC6CFB2250AA4FC9
  • Sequence:
    • MRPLTEEETR VMFEKIAKYI GENLQLLVDR PDGTYCFRLH NDRVYYVSEK IMKLAANISG 
DKLVSLGTCF GKFTKTHKFR LHVTALDYLA PYAKYKVWIK PGAEQSFLYG NHVLKSGLGR 
ITENTSQYQG VVVYSMADIP LGFGVAAKST QDCRKVDPMA IVVFHQADIG EYVRHEETLT