Details for: FAM153CP

Gene ID: 653316

Gene Type:  Pseudogene  - A non-functional segment of DNA that resembles a functional gene but has lost its protein-coding ability or is otherwise no longer expressed.

Symbol: FAM153CP

Ensembl ID: ENSG00000204677

Description: protein FAM153C

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 8.58
    rCSI 20.86%
    PRS 90.48
  • L6b glutamatergic cortical neuron CL4023038
    CSI 7.34
    rCSI 22.95%
    PRS 92.47
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 6.68
    rCSI 24.06%
    PRS 90.66
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 6.06
    rCSI 22.89%
    PRS 91.74
  • naive thymus-derived CD4-positive, alpha-beta T cell CL0000895
    CSI 5.68
    rCSI 7.14%
    PRS 99.27
  • VIP GABAergic cortical interneuron CL4023016
    CSI 5.13
    rCSI 6.12%
    PRS 91.88
  • sst GABAergic cortical interneuron CL4023017
    CSI 5.11
    rCSI 6.58%
    PRS 92.44
  • naive thymus-derived CD8-positive, alpha-beta T cell CL0000900
    CSI 4.75
    rCSI 3.33%
    PRS 99.24
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 4.72
    rCSI 5.87%
    PRS 90.47
  • ciliated epithelial cell CL0000067
    CSI 4.69
    rCSI 4.12%
    PRS 92.88
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 4.39
    rCSI 7.75%
    PRS 91.76
  • pancreatic acinar cell CL0002064
    CSI 4.12
    rCSI 5.48%
    PRS 97.87
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 4.01
    rCSI 23.59%
    PRS 91.93
  • inhibitory interneuron CL0000498
    CSI 3.91
    rCSI 9.04%
    PRS 92.86
  • cerebellar granule cell CL0001031
    CSI 3.81
    rCSI 5.6%
    PRS 94.57
  • lung neuroendocrine cell CL1000223
    CSI 3.52
    rCSI 5.21%
    PRS 97.14
  • ionocyte CL0005006
    CSI 3.44
    rCSI 3.69%
    PRS 97.71
  • glutamatergic neuron CL0000679
    CSI 3.32
    rCSI 6.83%
    PRS 90.14
  • sncg GABAergic cortical interneuron CL4023015
    CSI 3.28
    rCSI 5.27%
    PRS 92.25
  • pancreatic D cell CL0000173
    CSI 3.21
    rCSI 3.16%
    PRS 97.4
  • GABAergic neuron CL0000617
    CSI 2.78
    rCSI 9.3%
    PRS 89.65
  • neuron CL0000540
    CSI 2.64
    rCSI 7.02%
    PRS 89.5
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 2.63
    rCSI 4.42%
    PRS 92.03
  • mesothelial cell CL0000077
    CSI 2.43
    rCSI 9.51%
    PRS 89.84
  • regulatory T cell CL0000815
    CSI 2.42
    rCSI 2.8%
    PRS 92.21
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 2.25
    rCSI 5.37%
    PRS 91.58
  • L5/6 near-projecting glutamatergic neuron CL4030067
    CSI 2.2
    rCSI 7.24%
    PRS 90.6
  • retinal ganglion cell CL0000740
    CSI 1.97
    rCSI 4.35%
    PRS 92.13
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 1.54
    rCSI 4.81%
    PRS 93.31
  • smooth muscle cell of prostate CL1000487
    CSI 1.46
    rCSI 8.59%
    PRS 98.22
  • type B pancreatic cell CL0000169
    CSI 1.38
    rCSI 3.06%
    PRS 96.96
  • direct pathway medium spiny neuron CL4023026
    CSI 1.2
    rCSI 28.79%
    PRS 89.74
  • GABAergic amacrine cell CL4030027
    CSI 1.15
    rCSI 3.95%
    PRS 89.95
  • OFF midget ganglion cell CL4033047
    CSI 1.14
    rCSI 23.25%
    PRS 92.39
  • ON parasol ganglion cell CL4033052
    CSI 1.1
    rCSI 15.67%
    PRS 92.58
  • indirect pathway medium spiny neuron CL4023029
    CSI 1.1
    rCSI 26.45%
    PRS 89.48
  • ON midget ganglion cell CL4033046
    CSI 0.9
    rCSI 18.4%
    PRS 92.23

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 **[FAM153CP](/details-gene/653316)** is a pseudogene located on human chromosome 5q35.3. Expression data indicates that this gene has a remarkably high significance score in a wide array of neuronal subtypes within the central nervous system. It is particularly prominent in various glutamatergic and GABAergic cortical neurons, suggesting a potential role in the complex circuitry of the cerebral cortex. Interestingly, **[FAM153CP](/details-gene/653316)** also shows notable significance in naive T-lymphocytes, hinting at a possible, yet uncharacterized, function within the immune system. As a pseudogene, its product may not be a functional protein, but its transcript could potentially exert regulatory functions. ## Cellular Roles and Expression Landscape The expression profile of **[FAM153CP](/details-gene/653316)** is strongly dominated by cells of the central nervous system. **Overall**, it demonstrates the highest significance in diverse classes of cortical neurons. The top-ranked cell type is the [L2/3-6 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4023040) (CSI: 8.58), followed by other excitatory neurons such as the [L6b glutamatergic cortical neuron](/details-cell/CL4023038) (CSI: 7.34) and [L5 extratelencephalic projecting glutamatergic cortical neuron](/details-cell/CL4023041) (CSI: 6.68). Concurrently, it is also highly significant in various inhibitory interneurons, including [VIP GABAergic cortical interneuron](/details-cell/CL4023016) (CSI: 5.13) and [sst GABAergic cortical interneuron](/details-cell/CL4023017) (CSI: 5.11). This broad expression across both excitatory and inhibitory neuronal subtypes suggests a potentially fundamental role in maintaining cortical neuron identity or function. Beyond the nervous system, **[FAM153CP](/details-gene/653316)** shows a distinct signature in the adaptive immune system, with high significance in both [naive thymus-derived CD4-positive, alpha-beta T cell](/details-cell/CL0000895) (CSI: 5.68) and [naive thymus-derived CD8-positive, alpha-beta T cell](/details-cell/CL0000900) (CSI: 4.75). This dual expression pattern in the brain and naive T cells is noteworthy and may point to shared regulatory networks. Lower but still significant expression is observed in other cell types, such as [ciliated epithelial cell](/details-cell/CL0000067) (CSI: 4.69) and [pancreatic acinar cell](/details-cell/CL0002064) (CSI: 4.12), indicating a broader, albeit highly cell-specific, expression landscape. ## Pathways and Molecular Function Detailed functional annotation for **[FAM153CP](/details-gene/653316)** is not available in the provided dataset. As a pseudogene, it is not predicted to be translated into a functional protein. However, transcripts from pseudogenes can play significant regulatory roles, for example, by acting as long non-coding RNAs (lncRNAs) or as competing endogenous RNAs (ceRNAs) that sequester microRNAs, thereby influencing the expression of other genes. Given its high and specific expression pattern, the **[FAM153CP](/details-gene/653316)** transcript may be involved in biological processes essential to the cell types in which it is found. Its prevalence in numerous mature neuronal subtypes could suggest a role in maintaining neuronal identity, synaptic function, or metabolic homeostasis. Similarly, its expression specifically in naive T cells might indicate a function in maintaining a state of quiescence or readiness, a role that may be lost upon T cell activation and differentiation. ## Research Directions The unique expression profile of **[FAM1S3CP](/details-gene/653316)**, particularly its high significance in both cortical neurons and naive T cells, warrants further investigation into its potential regulatory functions. ### Proposed Hypotheses 1. **[FAM153CP](/details-gene/653316)** functions as a non-coding RNA that helps maintain the quiescent state of naive T lymphocytes. Its expression is predicted to be rapidly downregulated upon T cell receptor (TCR) stimulation, allowing for cellular activation and differentiation. 2. In the cerebral cortex, the **[FAM153CP](/details-gene/653316)** transcript acts as a ceRNA, titrating specific microRNAs that would otherwise repress a suite of genes essential for mature neuronal function and identity. Dysregulation of its expression could therefore contribute to the loss of neuronal stability in neurodegenerative conditions. ### Suggested Key Experiment To test the hypothesis that **[FAM153CP](/details-gene/653316)** is involved in maintaining T cell quiescence (Hypothesis 1), a straightforward experiment would be to measure its expression dynamics during T cell activation. Primary naive [CD4-positive, alpha-beta T cells](/details-cell/CL0000895) could be isolated from healthy human donors and stimulated *in vitro* using anti-CD3/CD28 antibodies. RNA would be extracted at multiple time points (e.g., 0, 6, 24, 48, and 72 hours) post-stimulation. The relative expression of the **[FAM153CP](/details-gene/653316)** transcript would be quantified using RT-qPCR. A significant and rapid decrease in its expression following activation would provide strong correlational evidence for its role as a regulator of T cell quiescence. ### Therapeutic Potential As a pseudogene, **[FAM153CP](/details-gene/653316)** is not a conventional drug target for small molecule inhibitors. However, if its RNA transcript is found to have a critical regulatory function in disease, it could be a target for nucleic acid-based therapies. For instance, if its overexpression in a specific context (e.g., an autoimmune disease characterized by T cell anergy) is pathogenic, antisense oligonucleotides (ASOs) could be designed to promote its degradation. Conversely, if its loss contributes to neurodegeneration, strategies to stabilize or re-express the transcript might be considered. The high expression in many essential neuronal subtypes raises a significant concern for off-target effects, suggesting that any therapeutic approach would likely require a highly targeted cell-type-specific delivery system.