Details for: TNRC18P2

Gene ID: 27320

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: TNRC18P2

Ensembl ID: ENSG00000223566

Description: trinucleotide repeat containing 18 pseudogene 2

Cell Significance Landscape

Significant Cells

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

  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.61
    rCSI 3.92%
    PRS 99.88

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):
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    • High
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    • 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), [TNRC18P2](/details-gene/27320) is a pseudogene located on chromosome 7. Current single-cell data suggests its expression, while appearing highly restricted, lacks statistical significance as a specific marker for any cell type. Its detection is confined to a subset of glutamatergic neurons, but the low confidence of this observation suggests it may represent transcriptional noise or a very low-abundance transcript whose biological role, if any, remains to be determined. ## Cellular Roles and Expression Landscape The expression profile of [TNRC18P2](/details-gene/27320) is characterized by a notable lack of statistically significant cell-type specificity. In the **Overall** context, the gene is detected exclusively in [L2/3-6 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4023040), a finding supported by a perfect Effect Size of 1.00. This suggests that within the detected dataset, its transcripts were found only in this cell population. However, this apparent specificity is not statistically robust. The CSI (Z-SCORE) is 0.00 with a corresponding non-significant p-value of 0.639. This combination indicates that while the expression pattern is restricted, the level of expression is too low or infrequent to confidently distinguish these neurons from other cells. The high Percentile Rank Score (PRS: 99.88%) is likely an artifact of the binary expression pattern (present in one cell type, absent in all others) rather than a reflection of biologically meaningful, high-confidence specificity. As a pseudogene, [TNRC18P2](/details-gene/27320) is not expected to be translated into a functional protein, and its transcript levels are often very low, which is consistent with these findings. ## Pathways and Molecular Function As a designated pseudogene, [TNRC18P2](/details-gene/27320) is not annotated with protein-coding functions or associated with established signaling or metabolic pathways. The primary question regarding its molecular function is whether its transcript serves a regulatory role, for instance as a long non-coding RNA (lncRNA), or if its detection represents spurious transcriptional activity from a dormant genomic region. The current data, showing low-confidence expression in a specific neuronal subtype, is insufficient to assign any definitive function but opens avenues for investigating potential non-coding roles within the cerebral cortex. ## Research Directions The central ambiguity surrounding [TNRC18P2](/details-gene/27320) is whether its statistically non-significant but highly localized expression in L2/3-6 glutamatergic neurons has any biological relevance. Future research should focus on validating this expression pattern with higher-sensitivity methods and exploring potential non-coding functions. ### Proposed Testable Hypotheses: 1. **Hypothesis 1:** The observed expression of [TNRC18P2](/details-gene/27320) is transcriptional noise and lacks a functional role in glutamatergic neurons. * **Experimental Approach:** Utilize highly sensitive single-molecule Fluorescence In Situ Hybridization (smFISH) on human cortical tissue sections. If transcripts are detected at extremely low copy numbers (e.g., 1-2 per cell) and show a sporadic, non-localized pattern within the cytoplasm or nucleus of [L2/3-6 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4023040), it would support the hypothesis of transcriptional noise rather than active function. 2. **Hypothesis 2:** [TNRC18P2](/details-gene/27320) functions as a lncRNA that regulates gene expression in *cis* or *trans* within L2/3-6 glutamatergic neurons. * **Experimental Approach:** In an iPSC-derived model of human cortical neurons, perform a targeted knockdown of [TNRC18P2](/details-gene/27320) using CRISPR interference (CRISPRi). Subsequent single-cell RNA sequencing could then identify downstream transcriptional changes specifically within the targeted neuronal population, revealing potential regulatory networks. 3. **Hypothesis 3:** The [TNRC18P2](/details-gene/27320) transcript acts as a competitive endogenous RNA (ceRNA), sequestering specific microRNAs in glutamatergic neurons. * **Experimental Approach:** Perform an RNA immunoprecipitation (RIP) assay using an antibody against the AGO2 protein (a core component of the RNA-induced silencing complex) on lysates from human cortical organoids. If quantitative PCR or sequencing of the co-precipitated RNA reveals an enrichment of the [TNRC18P2](/details-gene/27320) transcript, it would provide strong evidence of its interaction with the miRNA machinery. ### Therapeutic Potential: Given its pseudogene status and the lack of statistically significant expression, the direct therapeutic potential of targeting [TNRC18P2](/details-gene/27320) is likely negligible. However, if future research validates its role as a functional lncRNA with a highly specific expression pattern in a key neuronal subtype, it could potentially serve as a diagnostic biomarker for conditions affecting L2/3-6 glutamatergic neurons or as a novel, highly specific target for RNA-based therapeutics designed to modulate cortical circuit function.