Details for: LOC100506274

Gene ID: 100506274

Gene Type:  ncRNA (Non-coding RNA)  - A functional RNA molecule that is transcribed from DNA but not translated into a protein. Includes classes like miRNA and lncRNA.

Symbol: LOC100506274

Ensembl ID: ENSG00000229727

Description: uncharacterized LOC100506274

Cell Significance Landscape

Significant Cells

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

  • direct pathway medium spiny neuron CL4023026
    CSI 0.48
    rCSI 11.38%
    PRS 99.81
  • indirect pathway medium spiny neuron CL4023029
    CSI 0.47
    rCSI 11.34%
    PRS 99.75

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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  • 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 Analyzed for its expression specificity (CSI Z-SCORE), **LOC100506274** is an uncharacterized non-coding RNA (ncRNA) that displays a remarkably restricted expression pattern. The available data strongly suggest it is exclusively expressed in [direct pathway medium spiny neuron](/details-cell/CL4023026) and [indirect pathway medium spiny neuron](/details-cell/CL4023029). While its perfect Effect Size of 1.00 points to it being an ideal cell-type marker, the lack of statistical significance in the current dataset suggests its expression may be at low levels or confined to a small subset of these cells, warranting further investigation into its potential role in striatal neuron identity and function. ## Cellular Roles and Expression Landscape The primary significance of [LOC100506274](/gene-details/100506274) lies in its exquisite cell-type specificity. Within the **Overall** context, its expression is tightly confined to two critical neuronal populations of the striatum: [direct pathway medium spiny neuron](/details-cell/CL4023026) and [indirect pathway medium spiny neuron](/details-cell/CL4023029). This specificity is highlighted by a perfect Effect Size (deltaVal: 1.00) in both cell types, which indicates that transcripts of this gene are detected almost exclusively within these populations compared to all other profiled cells. However, a notable discrepancy exists in the statistical metrics. Despite the perfect effect size, the expression does not reach statistical significance (p-value: 0.622), resulting in a CSI (Z-SCORE) of 0.00. This combination suggests that while [LOC100506274](/gene-details/100506274) may be an absolute marker, its transcript abundance is likely very low, or its expression is limited to a small, specialized fraction of these neurons, thereby limiting the statistical power of the analysis. Nonetheless, its high Percentile Rank Score (PRS: >99.7%) confirms that its specificity profile, even if not statistically significant in this dataset, ranks it among the most uniquely expressed genes in the entire transcriptome. This positions [LOC100506274](/gene-details/100506274) as a high-potential, albeit low-abundance, marker for delineating the two major outputs of the basal ganglia. ## Pathways and Molecular Function The function of [LOC100506274](/gene-details/100506274) is currently unknown. As an uncharacterized non-coding RNA, it is not annotated in major functional databases such as Gene Ontology or Reactome. However, its exclusive expression in medium spiny neurons (MSNs) strongly implies a role in the unique biology of these cells. MSNs are central to motor control, reward-based learning, and goal-directed behavior. As an ncRNA, [LOC100506274](/gene-details/100506274) could exert its function through several mechanisms. It might act in *cis* to regulate the expression of neighboring genes critical for MSN development or synaptic plasticity. Alternatively, it could function in *trans* as a molecular scaffold for protein complexes or as a competing endogenous RNA (ceRNA), sequestering microRNAs to fine-tune the expression of key neuronal proteins. Its presence in both direct (D1-receptor expressing) and indirect (D2-receptor expressing) pathway MSNs suggests it may be involved in a shared fundamental process rather than pathway differentiation. ## Research Directions The highly specific expression pattern of [LOC100506274](/gene-details/100506274) in MSNs, coupled with its uncharacterized nature, makes it a compelling target for future research, particularly in the context of neurological and psychiatric disorders involving the basal ganglia, such as Parkinson's disease, Huntington's disease, and addiction. ### Testable Hypotheses 1. **Hypothesis:** [LOC100506274](/gene-details/100506274) is an activity-dependent ncRNA whose expression is induced in a small subset of MSNs upon robust synaptic stimulation, explaining its low overall abundance but high specificity. * **Experimental Approach:** Utilize primary rodent striatal cultures or human iPSC-derived MSN models. Induce neuronal activity using chemical long-term potentiation (cLTP) protocols and perform single-molecule fluorescence in situ hybridization (smFISH) for [LOC100506274](/gene-details/100506274) alongside immunofluorescence for activity markers like FOS. This would reveal if its expression is restricted to and correlated with recently active neurons. 2. **Hypothesis:** [LOC100506274](/gene-details/100506274) functions as a key regulator of MSN dendritic spine morphology or synaptic function. * **Experimental Approach:** Design and deliver an antisense oligonucleotide (ASO) or shRNA targeting [LOC100506274](/gene-details/100506274) to iPSC-derived MSNs. Following knockdown, assess changes in dendritic spine density and morphology using high-resolution microscopy and evaluate synaptic function through patch-clamp electrophysiology to measure miniature excitatory postsynaptic currents (mEPSCs). 3. **Hypothesis:** The genomic locus of [LOC100506274](/gene-details/100506274) acts as a *cis*-regulatory enhancer element essential for maintaining MSN-specific gene expression programs. * **Experimental Approach:** Employ CRISPR-Cas9 to delete the [LOC100506274](/gene-details/100506274) gene locus in an MSN cell line or iPSC model. Perform RNA-sequencing and ATAC-sequencing to identify downstream changes in the expression and chromatin accessibility of neighboring genes and other MSN identity markers. ### Therapeutic Potential The exquisite specificity of [LOC100506274](/gene-details/100506274) for MSNs presents significant therapeutic potential. Its promoter could be harnessed to drive MSN-specific expression of therapeutic transgenes in gene therapy approaches for disorders like Huntington's disease. Furthermore, if its function is linked to MSN dysfunction, ASOs targeting this ncRNA could offer a highly specific means to modulate striatal circuit activity with minimal risk of off-target effects in other cell types in the brain.