Details for: SNAPC5

Gene ID: 10302

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: SNAPC5

Ensembl ID: ENSG00000174446

Description: small nuclear RNA activating complex polypeptide 5

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • plasmacytoid dendritic cell, human CL0001058
    CSI 6.23
    rCSI 4.35%
    PRS 89.49
  • mature alpha-beta T cell CL0000791
    CSI 4.67
    rCSI 16.92%
    PRS 96.95
  • effector CD8-positive, alpha-beta T cell CL0001050
    CSI 4.54
    rCSI 3.46%
    PRS 95.67
  • double negative thymocyte CL0002489
    CSI 3.82
    rCSI 2.65%
    PRS 94.9
  • naive T cell CL0000898
    CSI 3.56
    rCSI 2.47%
    PRS 96.09
  • activated type II NK T cell CL0000931
    CSI 3.46
    rCSI 3.9%
    PRS 95.23
  • epithelial cell of lung CL0000082
    CSI 3.43
    rCSI 2.84%
    PRS 87.09
  • hematopoietic stem cell CL0000037
    CSI 3.02
    rCSI 2%
    PRS 88
  • effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL0001062
    CSI 2.97
    rCSI 14.89%
    PRS 94.87
  • group 3 innate lymphoid cell CL0001071
    CSI 2.93
    rCSI 2.2%
    PRS 90.45
  • epithelial cell of lower respiratory tract CL0002632
    CSI 2.9
    rCSI 2.25%
    PRS 89.29
  • skin fibroblast CL0002620
    CSI 2.88
    rCSI 2.49%
    PRS 85.78
  • immature B cell CL0000816
    CSI 2.76
    rCSI 2.05%
    PRS 93.8
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 2.74
    rCSI 2.79%
    PRS 92.94
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 2.64
    rCSI 2.38%
    PRS 84.62
  • T follicular helper cell CL0002038
    CSI 2.62
    rCSI 1.96%
    PRS 95.11
  • CD4-positive, CD25-positive, alpha-beta regulatory T cell CL0000792
    CSI 2.6
    rCSI 2.55%
    PRS 95.55
  • rod bipolar cell CL0000751
    CSI 2.55
    rCSI 4.58%
    PRS 80.37
  • ON-bipolar cell CL0000749
    CSI 2.55
    rCSI 3.79%
    PRS 85.57
  • ciliated epithelial cell CL0000067
    CSI 2.49
    rCSI 2.19%
    PRS 76.46
  • fallopian tube secretory epithelial cell CL4030006
    CSI 2.46
    rCSI 2.37%
    PRS 85.14
  • CD8-positive, alpha-beta thymocyte CL0000811
    CSI 2.46
    rCSI 3.83%
    PRS 95.79
  • multi-ciliated epithelial cell CL0005012
    CSI 2.22
    rCSI 2.22%
    PRS 80.34
  • intestinal epithelial cell CL0002563
    CSI 2.22
    rCSI 2.32%
    PRS 83.54
  • common myeloid progenitor CL0000049
    CSI 2.16
    rCSI 1.74%
    PRS 87.86
  • bronchus fibroblast of lung CL2000093
    CSI 2.14
    rCSI 1.74%
    PRS 85.47
  • alternatively activated macrophage CL0000890
    CSI 2.13
    rCSI 2.68%
    PRS 92.88
  • neural crest cell CL0011012
    CSI 2.13
    rCSI 1.68%
    PRS 77.02
  • stem cell CL0000034
    CSI 2.06
    rCSI 1.99%
    PRS 80.87
  • granulocyte monocyte progenitor cell CL0000557
    CSI 2.04
    rCSI 1.76%
    PRS 89.06
  • retinal blood vessel endothelial cell CL0002585
    CSI 1.98
    rCSI 3.16%
    PRS 89.24
  • ciliated cell CL0000064
    CSI 1.97
    rCSI 3.19%
    PRS 80.7
  • sst GABAergic cortical interneuron CL4023017
    CSI 1.84
    rCSI 2.37%
    PRS 71.6
  • acinar cell CL0000622
    CSI 1.83
    rCSI 2.69%
    PRS 93.08
  • mesodermal cell CL0000222
    CSI 1.8
    rCSI 2.16%
    PRS 84.35
  • plasmablast CL0000980
    CSI 1.79
    rCSI 1.41%
    PRS 89.63
  • lung ciliated cell CL1000271
    CSI 1.75
    rCSI 2.02%
    PRS 79.6
  • common dendritic progenitor CL0001029
    CSI 1.7
    rCSI 2.14%
    PRS 92.34
  • intermediate monocyte CL0002393
    CSI 1.61
    rCSI 2.43%
    PRS 90.57
  • retina horizontal cell CL0000745
    CSI 1.58
    rCSI 2.4%
    PRS 83.17
  • club cell CL0000158
    CSI 1.55
    rCSI 2.27%
    PRS 81.03
  • astrocyte of the cerebral cortex CL0002605
    CSI 1.54
    rCSI 3.44%
    PRS 71.28
  • mesenchymal cell CL0008019
    CSI 1.47
    rCSI 3.74%
    PRS 80.02
  • glioblast CL0000030
    CSI 1.42
    rCSI 2.27%
    PRS 78.11
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 0.99
    rCSI 1.67%
    PRS 70.41
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 0.91
    rCSI 2.22%
    PRS 68.26
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.66
    rCSI 2.08%
    PRS 71.92
  • erythroid progenitor cell CL0000038
    CSI 0.63
    rCSI 3.6%
    PRS 89.4
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 0.63
    rCSI 1.96%
    PRS 74.07
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.43
    rCSI 1.56%
    PRS 68.39

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.

Comma-separated if multiple.
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 [SNAPC5](/details-gene/10302), or Small Nuclear RNA Activating Complex Polypeptide 5, is a protein-coding gene located on chromosome 15q22.31. It encodes a crucial subunit of the Small Nuclear RNA Activating Protein Complex (SNAPc). This complex functions as a general transcription initiation factor for both RNA polymerase II and III, playing a fundamental role in the transcription of small nuclear RNAs (snRNAs) ([Link](https://doi.org/10.1101/gad.12.17.2664)). Consistent with this essential housekeeping function, expression data indicates that [SNAPC5](/details-gene/10302) is significantly active in a wide range of cell types, particularly those with high transcriptional demands such as immune cells. It shows the highest significance in [plasmacytoid dendritic cell, human](/details-cell/CL0001058), as well as various T-lymphocyte subsets including [mature alpha-beta T cell](/details-cell/CL0000791) and [effector CD8-positive, alpha-beta T cell](/details-cell/CL0001050), highlighting its importance in immune cell development, activation, and function. ## Cellular Roles and Expression Landscape The expression profile of [SNAPC5](/details-gene/10302) underscores its role as a key component of the core transcriptional machinery, with particular prominence in the hematopoietic system. **Overall**, the gene exhibits its highest cell significance index in [plasmacytoid dendritic cell, human](/details-cell/CL0001058) (CSI: 6.23), a cell type renowned for its capacity for massive and rapid production of type I interferons upon pathogen detection. A strong theme of lymphoid cell activity is evident, with high significance scores across the T-cell lineage, from early developmental stages like [double negative thymocyte](/details-cell/CL0002489) (CSI: 3.82) to mature and activated states such as [mature alpha-beta T cell](/details-cell/CL0000791) (CSI: 4.67), [naive T cell](/details-cell/CL0000898) (CSI: 3.56), and terminally differentiated [effector memory CD8-positive, alpha-beta T cell, terminally differentiated](/details-cell/CL0001062) (CSI: 2.97). This pattern suggests that [SNAPC5](/details-gene/10302) is indispensable for the transcriptional programs that govern T-cell development, differentiation, and effector function. Its significance is also noted in [hematopoietic stem cell](/details-cell/CL0000037), [immature B cell](/details-cell/CL0000816), and [group 3 innate lymphoid cell](/details-cell/CL0001071), further cementing its importance in the broader immune system. Beyond the immune compartment, [SNAPC5](/details-gene/10302) shows significant expression in other transcriptionally active cells, including [epithelial cell of lung](/details-cell/CL0000082) and [skin fibroblast](/details-cell/CL0002620), which is consistent with its fundamental role in gene expression essential for cellular maintenance and function. ## Pathways and Molecular Function The functional annotations for [SNAPC5](/details-gene/10302) confirm its central role in transcription. According to Gene Ontology (GO), the protein is localized to the [nucleus](/details-go/GO:0005634), including the [nucleoplasm](/details-go/GO:0005654) and [nucleolus](/details-go/GO:0005730), where it participates in core molecular functions such as [RNA polymerase II general transcription initiation factor activity](/details-go/GO:0016251) and [RNA polymerase III general transcription initiation factor activity](/details-go/GO:0000995). Reactome pathways further detail its involvement in the overarching process of [Gene expression (transcription)](https://reactome.org/content/detail/R-HSA-74160). Specifically, [SNAPC5](/details-gene/10302) is a component of the machinery for [RNA polymerase II transcription](https://reactome.org/content/detail/R-HSA-73857) and [RNA polymerase III transcription](https://reactome.org/content/detail/R-HSA-74158). Its function is critical for the transcription of snRNA genes by both polymerase II ([R-HSA-6807505](https://reactome.org/content/detail/R-HSA-6807505)) and the initiation of transcription by polymerase III at type 3 promoters ([R-HSA-76071](https://reactome.org/content/detail/R-HSA-76071)). This dual role in Pol II and Pol III-mediated transcription of non-coding RNAs is fundamental for splicing and other essential cellular processes, explaining its widespread importance across diverse and active cell types. ## Research Directions The ubiquitous and fundamental nature of [SNAPC5](/details-gene/10302) presents a challenge for targeted research, yet its elevated expression in specific immune cell types offers avenues for investigation into the regulation of high-demand transcriptional programs. **Proposed Hypotheses:** 1. Given its top significance score in [plasmacytoid dendritic cell, human](/details-cell/CL0001058), [SNAPC5](/details-gene/10302) may be a rate-limiting factor for the massive and rapid transcriptional upregulation of type I interferons and other antiviral genes following TLR stimulation. Its availability could be a key determinant of the potency of the pDC antiviral response. 2. The consistently high CSI values for [SNAPC5](/details-gene/10302) across T-cell maturation stages suggest it is critical for executing the complex, stage-specific gene expression programs during thymopoiesis. Conditional depletion of [SNAPC5](/details-gene/10302) within the T-cell lineage may lead to specific developmental blocks, for instance, at the double-negative to double-positive transition, due to failed transcription of essential developmental regulators. **Experimental Approach:** To test the first hypothesis regarding the role of [SNAPC5](/details-gene/10302) in pDC function, one could utilize an shRNA- or CRISPR/Cas9-based approach to knock down its expression in a human pDC cell line (e.g., GEN2.2) or in primary pDCs isolated from peripheral blood. Control and knockdown cells would then be stimulated with a TLR9 agonist (e.g., CpG-A). The functional consequences could be assessed by measuring the secretion of IFN-alpha and other cytokines via ELISA, while the global impact on the antiviral transcriptional program could be profiled using RNA-sequencing. This would directly test whether [SNAPC5](/details-gene/10302) levels are critical for the scale and kinetics of the pDC response. **Therapeutic Potential:** As a core component of the general transcription machinery essential for the viability of most cells, [SNAPC5](/details-gene/10302) is considered a poor direct therapeutic target. Systemic inhibition would likely result in profound, widespread toxicity. Its function is not specific to a disease state but rather a fundamental requirement for cellular life. Therefore, therapeutic strategies involving the direct inhibition of [SNAPC5](/details-gene/10302) are unlikely to be viable.

Genular Protein ID: 790289121

Symbol: SNPC5_HUMAN

Name: snRNA-activating protein complex subunit 5

UniProtKB Accession Codes:

O75971 A8K7N6 Q96CF3

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CORUM 1 CTD 1 ChiTaRS 1 ComplexPortal 1 DNASU 1 DisGeNET 1 EMBL 4 EMDB 5 Ensembl 5 ExpressionAtlas 1 GO 9 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MalaCards 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PDB 5 PDBsum 5 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 Pumba 1 RNAct 1 Reactome 3 RefSeq 3 SMR 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 9732265

Title: SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III.

PubMed ID: 9732265

DOI: 10.1101/gad.12.17.2664

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: 11056176

Title: A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc.

PubMed ID: 11056176

DOI: 10.1074/jbc.m009301200

PubMed ID: 17081983

Title: Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

PubMed ID: 17081983

DOI: 10.1016/j.cell.2006.09.026

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

Sequence Information:

  • Length: 98
  • Mass: 11328
  • Checksum: 4D797E35AF2D1485
  • Sequence:
    • MLSRLQELRK EEETLLRLKA ALHDQLNRLK VEELALQSMI SSRRGDEMLS SHTVPEQSHD 
MLVHVDNEAS INQTTLELST KSHVTEEEEE EEEEESDS