Details for: NPIPB6

Gene ID: 728741

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: NPIPB6

Ensembl ID: ENSG00000198156

Description: nuclear pore complex interacting protein family member B6

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • plasmablast CL0000980
    CSI 4.31
    rCSI 3.39%
    PRS 99.84
  • basal cell of epidermis CL0002187
    CSI 2.11
    rCSI 3.74%
    PRS 96.91

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

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  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
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    • 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 Analyzed for its specificity (CSI Z-SCORE), `NPIPB6` (nuclear pore complex interacting protein family member B6) is a protein-coding gene located on chromosome 16p12.1. Despite being highly expressed in certain cell types, the available single-cell data suggests it lacks cell-type specificity, indicating a potential role in a more general or housekeeping cellular function rather than acting as a distinguishing cell marker. Its name suggests involvement in nucleocytoplasmic transport, a fundamental process for eukaryotic cells. The gene was identified and sequenced as part of large-scale genome characterization efforts (PubMed: [15616553](https://pubmed.ncbi.nlm.nih.gov/15616553), [11237011](https://pubmed.ncbi.nlm.nih.gov/11237011)). ## Cellular Roles and Expression Landscape The expression profile of `NPIPB6`, when evaluated for cell-type specificity, indicates it is not a defining marker for any particular cell population. In the **Overall** tissue context, its CSI (Z-SCORE) is 0.00 in top-expressing cells such as [plasmablast](/details-cell/CL0000980) and [basal cell of epidermis](/details-cell/CL0002187). A Z-score of zero, combined with statistically non-significant p-values (p > 0.65), demonstrates that its expression level in these cells is not significantly different from its average expression across all cell types. This lack of specificity suggests that `NPIPB6` is not uniquely responsible for the specialized identity of these cells. However, a high Percentile Rank Score (PRS) of over 96% in these cell types indicates that `NPIPB6` is, nonetheless, an abundantly expressed gene *within* those cells, ranking among the top few percent of all transcribed genes. This combination of high abundance but low specificity is characteristic of genes involved in essential, ubiquitous cellular processes. The high expression in [plasmablast](/details-cell/CL0000980)s, which are terminally differentiated B cells responsible for massive antibody production, and in proliferative [basal cell of epidermis](/details-cell/CL0002187), is consistent with a role in supporting high rates of transcription, translation, and cell division. The observed Effect Size of 1.00 is notable but appears inconsistent with the primary specificity metrics (Z-score and p-value), suggesting it may reflect high prevalence within a cell type rather than exclusive expression. ## Pathways and Molecular Function While specific pathway annotations are not provided, the gene's name, nuclear pore complex interacting protein family member B6, strongly implies a function related to the nuclear pore complex (NPC). The NPC is a critical cellular structure that mediates the transport of all macromolecules between the nucleus and the cytoplasm. Proteins with this designation are often involved in regulating the import and export of proteins, RNA, and ribosomal subunits. The expression pattern of `NPIPB6` supports this inferred function. Its high abundance in metabolically active and proliferative cells like [plasmablast](/details-cell/CL0000980)s and [basal cell of epidermis](/details-cell/CL0002187) is consistent with an elevated demand for nucleocytoplasmic transport to support robust protein synthesis and cell cycle progression. Therefore, `NPIPB6` may function as a facilitator or regulator of molecular transport through the nuclear pore, a fundamental process required by nearly all cells but particularly crucial for those with high biosynthetic or proliferative loads. ## Research Directions The current data highlights `NPIPB6` as an abundantly expressed but poorly characterized gene. Its specific molecular function and the reasons for its high expression in certain cellular contexts remain unclear. Future research should focus on elucidating its precise role within the cell. ### Proposed Testable Hypotheses: 1. **Hypothesis:** `NPIPB6` is a constituent of the nuclear pore basket or interacts with specific nucleoporins (Nups) to regulate the export of a subset of messenger RNAs (mRNAs) required for high-rate protein synthesis. * **Experimental Approach:** Utilize co-immunoprecipitation coupled with mass spectrometry (Co-IP-MS) in a plasmablast-like cell line (e.g., U266) to identify `NPIPB6`-interacting proteins within the NPC. Subsequently, perform RNA-immunoprecipitation followed by sequencing (RIP-seq) to identify RNAs that are specifically bound by `NPIPB6`. 2. **Hypothesis:** The expression of `NPIPB6` is not tied to cell lineage but is instead directly regulated by the cellular proliferation state. Its high level in basal epidermal cells and plasmablasts is a consequence of their proliferative or hyperactive metabolic status, respectively. * **Experimental Approach:** In a culture of primary human keratinocytes, compare `NPIPB6` mRNA and protein levels between quiescent cells (induced by contact inhibition or serum starvation) and proliferating cells (stimulated with growth factors). Correlate its expression levels with cell cycle markers like Ki-67 and PCNA using immunofluorescence and qPCR. 3. **Hypothesis:** The lack of a strong specificity signal for `NPIPB6` is a result of functional redundancy with other NPIPB family members (`NPIPB1-12`). These family members may have overlapping functions in nucleocytoplasmic transport, masking the effect of any single member in broad single-cell analyses. * **Experimental Approach:** Systematically knock down `NPIPB6` and other highly expressed NPIPB family members, both individually and in combination, using CRISPRi in a relevant cell line. Assess for defects in nucleocytoplasmic transport using a fluorescent reporter assay (e.g., tracking the localization of a GFP-tagged protein with a nuclear localization or export signal). ### Therapeutic Potential: Given its likely role in a fundamental cellular process, direct inhibition of `NPIPB6` could carry a high risk of toxicity. However, if `NPIPB6` is found to be a rate-limiting factor for the hyper-proliferative or hyper-secretory states of certain cancer cells, such as those in multiple myeloma (derived from plasmablasts) or basal cell carcinoma, it could represent a potential therapeutic target. Further investigation into its specific dependencies and functional role in pathological contexts is required to assess this possibility.

Genular Protein ID: 33529665

Symbol: NPIB6_HUMAN

Name: Nuclear pore complex-interacting protein family member B6

UniProtKB Accession Codes:

E9PJ23

Database IDs:

AGR 1 AlphaFoldDB 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 ChiTaRS 1 DNASU 1 EMBL 2 Ensembl 2 ExpressionAtlas 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MANE-Select 1 MassIVE 1 NCBI Taxonomy 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 Pharos 1 PhylomeDB 1 Proteomes 1 RNAct 1 RefSeq 2 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 neXtProt 1

Citations:

PubMed ID: 15616553

Title: The sequence and analysis of duplication-rich human chromosome 16.

PubMed ID: 15616553

DOI: 10.1038/nature03187

Sequence Information:

  • Length: 425
  • Mass: 49162
  • Checksum: 6FF21B299D4F7E29
  • Sequence:
    • MVKLSIVLTP QFLSHDQSQL TKELQQHVKS VTCPCEYLRK VINSLAVYRH RETDFGVGVR 
DHPGQHGKTP SPQKLDNLII IIIGFLRRYT FNILFCTSCL CVSFLKTIFW SRNGHDGSMD 
VQQRAWRSNR SRQKGLRSIC MHTKKRVSSF RGNKIGLKDV ITLRRHVETK VRAKIRKRKV 
TTKINRHDKI NGKRKTARKQ KMFQRAQELR RRAEDYHKCK IPPSARKPLC NWVRMVAAEH 
RHSSGLPYWP YLTAETLKNR MGRQPPPPTQ QHSITDNSLS LKTPTECLLT PLPPSVDDNI 
KECPLAPLPP SPLPPSVDDN LKECLFVPLP PSPLPPSVDD NLKTPPLATQ EAEVEKPPKP 
KRWRVDEVEQ SPKPKRRRVD EVEQSPKPKR QREAEAQQLP KPKRRRLSKL RTRHCTQAWA 
IRINP

Genular Protein ID: 4136002256

Symbol: B2RXF8_HUMAN

Name: N/A

UniProtKB Accession Codes:

B2RXF8

Database IDs:

ARBA 1 AlphaFoldDB 1 BioGRID-ORCS 1 CTD 1 DNASU 1 EMBL 2 InterPro 1 KEGG 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PeptideAtlas 1 Pfam 1 RefSeq 1 SAM 2

Citations:

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

Sequence Information:

  • Length: 455
  • Mass: 52491
  • Checksum: 781318160338E884
  • Sequence:
    • MMSRCLILQM VKLSIVLTPQ FLSHDQSQLT KELQQHVKSV TCPCEYLRKV INSLAVYRHR 
ETDFGVGVRD HPGQHGKTPS PQKLDNLIII IIGFLRRYTF NILFCTSCLC VSFLKTIFWS 
RNGHDGSMDV QQRAWRSNHS RQKGLRSICM HTKKRVSSFR GNKIGLKDVI TLRRHVETKV 
RAKIRKRKVT TKINRHDKIN GKRKTARKQK MFQRAQELRR RAEDYHKCKI PPSARKPLCN 
WVRMVAAEHR HSSGLPYWLY LTAETLKNRM GRQPPPPTQQ HSITDNSLSL KTPPECLLTP 
LPPSVDDNIK ECPLAPLPPS PLPPSVDDNL KECLFVPLPP SPLPPSVDDN LKECLFVPLP 
PSPLPPSVDD NLKTPPLATQ EAEVEKPPKP KRWRVDEVEQ SPKPKRRRVD EVEQSPKPKR 
QREAEAQQLP KPKRRRLSKL RTRHCTQAWA IRINP

Genular Protein ID: 3703055968

Symbol: E9PS57_HUMAN

Name: N/A

UniProtKB Accession Codes:

E9PS57

Database IDs:

ARBA 1 AlphaFoldDB 1 Bgee 1 BioGRID-ORCS 1 CTD 1 ChiTaRS 1 DNASU 1 EMBL 2 Ensembl 2 ExpressionAtlas 1 GeneTree 1 HGNC 1 InterPro 1 MassIVE 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PeptideAtlas 2 Pfam 1 Proteomes 2 ProteomicsDB 1 RefSeq 2 SAM 2 UCSC 1 VEuPathDB 1

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

PubMed ID: 15616553

Title: The sequence and analysis of duplication-rich human chromosome 16.

PubMed ID: 15616553

DOI: 10.1038/nature03187

Sequence Information:

  • Length: 407
  • Mass: 47243
  • Checksum: 25DE708CEC922927
  • Sequence:
    • MRLRFWLLIW LLLGFISHQP TPVINSLAVY RHRETDFGVG VRDHPGQHGK TPSPQKLDNL 
IIIIIGFLRR YTFNILFCTS CLCVSFLKTI FWSRNGHDGS MDVQQRAWRS NRSRQKGLRS 
ICMHTKKRVS SFRGNKIGLK DVITLRRHVE TKVRAKIRKR KVTTKINRHD KINGKRKTAR 
KQKMFQRAQE LRRRAEDYHK CKIPPSARKP LCNWVRMVAA EHRHSSGLPY WPYLTAETLK 
NRMGRQPPPP TQQHSITDNS LSLKTPTECL LTPLPPSVDD NIKECPLAPL PPSPLPPSVD 
DNLKECLFVP LPPSPLPPSV DDNLKTPPLA TQEAEVEKPP KPKRWRVDEV EQSPKPKRRR 
VDEVEQSPKP KRQREAEAQQ LPKPKRRRLS KLRTRHCTQA WAIRINP