Details for: LOC124909401

Gene ID: 124909401

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: LOC124909401

Ensembl ID: ENSG00000243089

Description: uncharacterized LOC124909401

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • retinal pigment epithelial cell CL0002586
    CSI 13.84
    rCSI 27.48%
    PRS 99.85
  • basal cell of epidermis CL0002187
    CSI 4.66
    rCSI 8.26%
    PRS 97.64
  • melanocyte of skin CL1000458
    CSI 1.87
    rCSI 2.55%
    PRS 98.38

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)

Loading network (please wait)...

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), [LOC124909401](/details-gene/124909401) is an uncharacterized non-coding RNA (ncRNA) that exhibits a highly restricted expression pattern. The available data suggests it may function as a defining molecular marker for a select group of specialized, pigmented cell types derived from the ectoderm and neural crest, most notably the [retinal pigment epithelial cell](/details-cell/CL0002586). Its expression profile points towards a potential role in establishing or maintaining the unique identity of these cells. ## Cellular Roles and Expression Landscape The primary role of [LOC124909401](/details-gene/124909401), when viewed through the lens of expression specificity, appears to be as a highly selective cell identity marker. In the **Overall** tissue context, its expression is most uniquely associated with the [retinal pigment epithelial cell](/details-cell/CL0002586). This assertion is supported by its exceptional percentile rank (PRS: 99.85%) and a perfect effect size (deltaVal: 1.00), indicating that its expression is effectively exclusive to this cell type when compared to a composite background. While its Z-score and p-value are not statistically significant, potentially due to low cell counts or minimal expression variance in the dataset, the other metrics strongly support its role as a top-tier specificity marker. This pattern of high specificity extends to other related cell types, including the [basal cell of epidermis](/details-cell/CL0002187) (PRS: 97.64%) and the [melanocyte of skin](/details-cell/CL1000458) (PRS: 98.38%). Both cell types also show a perfect positive effect size (deltaVal: 1.00), reinforcing the gene's restricted expression profile. The common thread among these cell types is their origin from the ectoderm or neural crest and their involvement in forming pigmented, protective epithelial layers. The highly constrained expression of this ncRNA suggests it may be part of a core regulatory program governing the development or function of this specific cellular lineage. ## Pathways and Molecular Function As an uncharacterized ncRNA, the precise molecular functions of [LOC124909401](/details-gene/124909401) remain unknown. Functional annotations from databases such as Gene Ontology or Reactome are not currently available for this gene. However, its highly specific expression landscape provides critical clues to its potential biological roles. Its exclusivity to [retinal pigment epithelial cell](/details-cell/CL0002586), [basal cell of epidermis](/details-cell/CL0002187), and [melanocyte of skin](/details-cell/CL1000458) suggests involvement in processes central to the identity of these cells. These could include the regulation of melanin synthesis, maintenance of an undifferentiated progenitor state in the epidermis, or establishment of epithelial barrier integrity. Given its classification as an ncRNA, it likely functions through a regulatory mechanism, such as guiding chromatin-modifying complexes, acting as a scaffold for protein assembly, or modulating the transcription of adjacent protein-coding genes critical for these specialized cell fates. ## Research Directions The provided data is limited to a single **Overall** context, which prevents a comparative analysis of [LOC124909401](/details-gene/124909401) expression across different biological conditions, such as healthy versus diseased states. Future studies focusing on disease-specific contexts, particularly those involving the retina, skin, or melanocytes, would be highly informative. ### Testable Hypotheses 1. **[LOC124909401](/details-gene/124909401) is essential for the functional maturation and identity of retinal pigment epithelial cells.** Its specific expression suggests a role in regulating key RPE functions, such as phagocytosis of photoreceptor outer segments or melanin production. * **Experimental Approach:** Utilize CRISPR interference (CRISPRi) to achieve targeted knockdown of [LOC124909401](/details-gene/124909401) in human induced pluripotent stem cell (iPSC)-derived RPE cultures. The functional consequences could be assessed by measuring changes in the expression of canonical RPE markers (e.g., RPE65, BEST1), quantifying melanin content, and performing phagocytosis assays using fluorescently-labeled photoreceptor outer segments. 2. **[LOC124909401](/details-gene/124909401) functions to maintain the progenitor state of epidermal basal cells.** The gene's expression in [basal cell of epidermis](/details-cell/CL0002187) may indicate a role in suppressing differentiation and promoting self-renewal, a critical aspect of skin homeostasis. * **Experimental Approach:** Employ single-molecule fluorescence in situ hybridization (smFISH) on human skin cross-sections to precisely map the subcellular localization of [LOC124909401](/details-gene/124909401) within the basal layer. Subsequently, use antisense oligonucleotides (ASOs) to deplete the ncRNA in 3D organotypic skin models and analyze the effects on epidermal stratification and the expression of basal (KRT14, TP63) versus differentiation (KRT10, Involucrin) markers via immunofluorescence and RNA-sequencing. 3. **The expression of [LOC124909401](/details-gene/124909401) is controlled by the master transcriptional regulator MITF, integrating it into the core network governing melanocytic and RPE cell identity.** The shared expression between melanocytes and RPE cells, both of which depend on the transcription factor MITF, suggests [LOC124909401](/details-gene/124909401) may be a downstream target in this pathway. * **Experimental Approach:** Perform Cleavage Under Targets and Release Using Nuclease (CUT&RUN) or ChIP-seq for MITF in primary human melanocytes and iPSC-derived RPE cells to identify potential binding sites in the promoter region of [LOC124909401](/details-gene/124909401). Validate this regulatory link by knocking down MITF using siRNA and measuring the corresponding change in [LOC124909401](/details-gene/124909401) expression via qRT-PCR. ### Therapeutic Potential The extreme cell-type specificity of [LOC124909401](/details-gene/124909401) makes it an attractive candidate as a diagnostic biomarker. Its levels could potentially be monitored in liquid biopsies or tissue samples to assess the health or disease state of RPE (e.g., in age-related macular degeneration) or melanocytes (e.g., in melanoma). Furthermore, if this ncRNA is found to be a driver of pathology, its restricted expression profile would make it an ideal target for RNA-based therapeutics like ASOs, which could modulate its function with a reduced risk of off-target effects in other cell types.