Details for: LINC01239

Gene ID: 441389

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: LINC01239

Ensembl ID: ENSG00000234840

Description: long intergenic non-protein coding RNA 1239

Cell Significance Landscape

Significant Cells

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

  • retinal pigment epithelial cell CL0002586
    CSI 7.77
    rCSI 15.43%
    PRS 95.34
  • epithelial cell of proximal tubule CL0002306
    CSI 5.75
    rCSI 14.05%
    PRS 93.44
  • fibroblast of lung CL0002553
    CSI 5.72
    rCSI 5.32%
    PRS 98.18
  • mesothelial cell CL0000077
    CSI 5.2
    rCSI 20.35%
    PRS 89.72
  • adipocyte CL0000136
    CSI 4.94
    rCSI 6.34%
    PRS 93.11
  • subcutaneous adipocyte CL0002521
    CSI 4.7
    rCSI 24.08%
    PRS 98.23
  • keratocyte CL0002363
    CSI 3.92
    rCSI 9.43%
    PRS 97.31
  • melanocyte of skin CL1000458
    CSI 3.91
    rCSI 5.33%
    PRS 78.49
  • alveolar type 1 fibroblast cell CL4028004
    CSI 3.46
    rCSI 3.79%
    PRS 98.03
  • conjunctival epithelial cell CL1000432
    CSI 3.13
    rCSI 4.79%
    PRS 96.46
  • choroid plexus epithelial cell CL0000706
    CSI 3.06
    rCSI 5.01%
    PRS 94.38
  • hepatocyte CL0000182
    CSI 2.89
    rCSI 5.17%
    PRS 95.75
  • Bergmann glial cell CL0000644
    CSI 2.85
    rCSI 3.9%
    PRS 93.41
  • L6b glutamatergic cortical neuron CL4023038
    CSI 2.81
    rCSI 8.78%
    PRS 92.41
  • adventitial cell CL0002503
    CSI 2.52
    rCSI 6.03%
    PRS 98.24
  • alveolar adventitial fibroblast CL4028006
    CSI 2.3
    rCSI 3.63%
    PRS 97.92
  • astrocyte of the cerebral cortex CL0002605
    CSI 2.2
    rCSI 4.94%
    PRS 92.07
  • kidney connecting tubule epithelial cell CL1000768
    CSI 1.66
    rCSI 4.2%
    PRS 94.86
  • epicardial adipocyte CL1000309
    CSI 1.54
    rCSI 5%
    PRS 95.67

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 [LINC01239](/details-gene/441389) is a long intergenic non-protein coding RNA (lncRNA) located on chromosome 9p21.3. Expression data indicates that this gene is a highly significant marker for a diverse set of specialized cell types, particularly those with epithelial and mesenchymal origins. It shows its most pronounced and specific expression in the [retinal pigment epithelial cell](/details-cell/CL0002586), suggesting a crucial role in retinal biology. Its significant expression is also noted in other barrier and metabolic tissues, including the [epithelial cell of proximal tubule](/details-cell/CL0002306) and various stromal cells like the [fibroblast of lung](/details-cell/CL0002553), pointing towards potential regulatory functions in tissue homeostasis, metabolism, and structural integrity. ## Cellular Roles and Expression Landscape The **Overall** expression profile of [LINC01239](/details-gene/441389) highlights its role as a key identifier for several distinct cell lineages, primarily outside of the hematopoietic system. * **Dominance in Retinal Epithelium:** The gene's highest significance score (CSI: 7.77) is observed in the [retinal pigment epithelial cell](/details-cell/CL0002586), establishing it as a premier marker for this cell type. This strong association suggests a fundamental role in the highly specialized functions of the RPE, which supports photoreceptor health. * **Broad Epithelial and Secretory Expression:** Beyond the retina, [LINC01239](/details-gene/441389) is significantly expressed in a variety of epithelial cells that form critical functional barriers or have high metabolic activity. These include the [epithelial cell of proximal tubule](/details-cell/CL0002306) in the kidney, [mesothelial cell](/details-cell/CL0000077) lining body cavities, [conjunctival epithelial cell](/details-cell/CL1000432) of the eye, [choroid plexus epithelial cell](/details-cell/CL0000706) responsible for cerebrospinal fluid production, and the [hepatocyte](/details-cell/CL0000182) in the liver. * **Mesenchymal and Stromal Significance:** The gene is also a prominent marker in several mesenchymal-derived cells. Its high significance in [fibroblast of lung](/details-cell/CL0002553), [adipocyte](/details-cell/CL0000136), and [keratocyte](/details-cell/CL0002363) (corneal fibroblasts) suggests involvement in connective tissue maintenance, extracellular matrix regulation, and lipid metabolism. * **Other Specialized Cells:** Lower but still notable significance is seen in specialized cell types such as the [melanocyte of skin](/details-cell/CL1000458), as well as certain neural populations like the [Bergmann glial cell](/details-cell/CL0000644) and [L6b glutamatergic cortical neuron](/details-cell/CL4023038), indicating a widespread, yet cell-type specific, regulatory function. ## Pathways and Molecular Function Specific functional annotations from Gene Ontology (GO) or Reactome were not available in the provided dataset. However, based on the cell types where [LINC01239](/details-gene/441389) is most significantly expressed, its function can be inferred to be regulatory. As a long non-coding RNA, it likely modulates gene expression epigenetically, acts as a scaffold for protein complexes, or functions as a competing endogenous RNA (ceRNA) by sequestering microRNAs. The strong expression in [retinal pigment epithelial cell](/details-cell/CL0002586) suggests a potential role in processes vital for vision, such as the visual cycle, phagocytosis of photoreceptor outer segments, or maintaining the blood-retina barrier. Its enrichment in kidney tubule cells and hepatocytes points towards a possible involvement in regulating metabolic pathways or transmembrane transport, which are hallmark functions of these tissues. ## Research Directions The specific and high-level expression of [LINC01239](/details-gene/441389) in functionally critical cell types presents several avenues for future investigation. **Proposed Hypotheses:** 1. [LINC01239](/details-gene/441389) is a key regulator of cellular identity and function in the [retinal pigment epithelial cell](/details-cell/CL0002586). Its dysregulation may contribute to the pathophysiology of retinal degenerative diseases, such as age-related macular degeneration (AMD), where RPE health is compromised. 2. Given its consistent expression across diverse metabolic and barrier epithelia (kidney, liver, choroid plexus), [LINC01239](/details-gene/441389) may act as a common regulatory node governing pathways related to solute transport, detoxification, or cellular polarity. 3. In mesenchymal cells like fibroblasts and adipocytes, [LINC01239](/details-gene/441389) may modulate cellular plasticity, differentiation, or response to stress, potentially playing a role in tissue fibrosis or metabolic disorders. **Experimental Approach:** To test the hypothesis that [LINC01239](/details-gene/441389) is critical for RPE function (Hypothesis 1), a loss-of-function study could be performed. Expression of [LINC01239](/details-gene/441389) could be knocked down in human iPSC-derived RPE monolayers using targeted antisense oligonucleotides (ASOs). The functional consequences would be evaluated by assessing key RPE functions, including transepithelial electrical resistance (to measure barrier integrity), quantifying the phagocytosis of fluorescently labeled photoreceptor outer segments, and performing RNA-sequencing to identify downstream gene expression changes that could reveal its molecular mechanism. **Therapeutic Potential:** As a long non-coding RNA with a highly cell-type-specific expression pattern, [LINC01239](/details-gene/441389) represents a novel, albeit challenging, therapeutic target. Its specificity for cells like the RPE could allow for targeted therapies with minimal off-target effects. Therapeutic intervention would likely rely on nucleic acid-based drugs. If loss of [LINC01239](/details-gene/441389) is implicated in retinal disease, a therapeutic strategy could involve RNA-based **activation** or stabilization. Conversely, if its overexpression is linked to pathology (e.g., in fibrosis), ASO-mediated **inhibition** could be a viable approach.