Details for: LINC01411

Gene ID: 101928176

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: LINC01411

Ensembl ID: ENSG00000249306

Description: long intergenic non-protein coding RNA 1411

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • cardiac muscle cell CL0000746
    CSI 6.87
    rCSI 9.86%
    PRS 97.7
  • regular atrial cardiac myocyte CL0002129
    CSI 5.71
    rCSI 18.37%
    PRS 98.34
  • Bergmann glial cell CL0000644
    CSI 4.05
    rCSI 5.55%
    PRS 97.89
  • VIP GABAergic cortical interneuron CL4023016
    CSI 3.75
    rCSI 4.48%
    PRS 97.47
  • retinal pigment epithelial cell CL0002586
    CSI 3.47
    rCSI 6.89%
    PRS 98.53
  • astrocyte of the cerebral cortex CL0002605
    CSI 3.04
    rCSI 6.82%
    PRS 97.64
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 2.35
    rCSI 8.9%
    PRS 97.02
  • indirect pathway medium spiny neuron CL4023029
    CSI 0.49
    rCSI 11.84%
    PRS 95.9
  • direct pathway medium spiny neuron CL4023026
    CSI 0.39
    rCSI 9.26%
    PRS 95.97

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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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 [LINC01411](/details-gene/101928176) is a long intergenic non-protein coding RNA (lncRNA) located on chromosome 5q35.2. Expression data indicates a highly specific role for this gene, with its most significant expression observed in [cardiac muscle cell](/details-cell/CL0000746)s. Additionally, [LINC01411](/details-gene/101928176) shows a distinct expression pattern across various cell types of the central nervous system, including glial cells and specific neuronal subtypes. This profile suggests that [LINC01411](/details-gene/101928176) may function as a key regulatory molecule involved in the unique biology of cardiac and neural tissues. ## Cellular Roles and Expression Landscape The expression profile of [LINC01411](/details-gene/101928176) points to a specialized function primarily within two major organ systems: the heart and the central nervous system. **Overall**, the most significant expression is found in cardiac tissue, with the highest Cell Significance Index (CSI) in [cardiac muscle cell](/details-cell/CL0000746) (CSI: 6.87) and [regular atrial cardiac myocyte](/details-cell/CL0002129) (CSI: 5.71). This strong and specific signal suggests a fundamental role in establishing or maintaining the cardiomyocyte phenotype and function. A secondary, but also prominent, expression cluster is observed in the central nervous system. The gene is significantly expressed in both glial and neuronal populations. Notable glial expression is seen in [Bergmann glial cell](/details-cell/CL0000644) (CSI: 4.05) and [astrocyte of the cerebral cortex](/details-cell/CL0002605) (CSI: 3.04). Among neurons, its expression is significant in specialized subtypes such as [VIP GABAergic cortical interneuron](/details-cell/CL4023016) (CSI: 3.75) and [near-projecting glutamatergic cortical neuron](/details-cell/CL4023012) (CSI: 2.35), while being less pronounced in [indirect pathway medium spiny neuron](/details-cell/CL4023029) and [direct pathway medium spiny neuron](/details-cell/CL4023026). Furthermore, its specific expression in [retinal pigment epithelial cell](/details-cell/CL0002586) (CSI: 3.47) highlights a potential role in the specialized environment of the retina. The highly selective nature of its expression across these diverse cell types is consistent with a regulatory function tailored to specific cellular contexts. ## Pathways and Molecular Function As a long non-coding RNA, [LINC01411](/details-gene/101928176) does not code for a protein. Instead, it is presumed to function at the RNA level to regulate gene expression. LncRNAs can exert their effects through various mechanisms, including acting as molecular scaffolds to assemble protein complexes, modulating chromatin structure to control transcription, or serving as "sponges" to sequester microRNAs. The provided dataset does not contain specific Gene Ontology (GO) or Reactome pathway annotations for [LINC01411](/details-gene/101928176), which is common for less-characterized lncRNAs. However, its distinct expression pattern strongly implies involvement in biological processes central to the cell types in which it is active. Its high significance in cardiomyocytes suggests a potential role in regulating genes related to muscle contraction, calcium handling, or metabolic homeostasis in the heart. Similarly, its presence in specific glial and neuronal cells suggests a function in neural development, synaptic transmission, or metabolic support within the brain. ## Research Directions The specific expression pattern of [LINC01411](/details-gene/101928176) in terminally differentiated cardiac and neural cells makes it a compelling subject for further investigation into tissue-specific gene regulation. **Testable Hypotheses:** 1. [LINC01411](/details-gene/101928176) is a critical post-transcriptional regulator in cardiomyocytes, essential for maintaining the mature contractile phenotype. Its downregulation may lead to cellular dysfunction characteristic of heart failure or cardiomyopathy. 2. In the central nervous system, [LINC01411](/details-gene/101928176) functions as a key determinant of cell identity or function in specialized glial populations like Bergmann glia, potentially by regulating the expression of genes involved in glutamate transport or synaptic support. **Proposed Key Experiment:** To test the hypothesis of its role in cardiomyocyte function, a loss-of-function study in a human cell model would be highly informative. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) could be treated with antisense oligonucleotides (ASOs) designed to specifically degrade [LINC01411](/details-gene/101928176) transcripts. The functional consequences of this knockdown could be assessed by measuring changes in contractility, calcium transient dynamics, and electrophysiological properties. Concurrently, RNA-sequencing of the knockdown hiPSC-CMs would reveal the downstream transcriptional network regulated by [LINC01411](/details-gene/101928176), providing mechanistic insight into its molecular function. **Therapeutic Potential:** Given its nature as a non-coding RNA, [LINC01411](/details-gene/101928176) is a non-traditional drug target. However, its high tissue-specificity in cardiac and neural cells makes it an attractive candidate for RNA-targeted therapies, such as ASOs. If [LINC01411](/details-gene/101928176) is found to be aberrantly upregulated in a disease state (e.g., cardiac fibrosis or a neurological disorder), a strategy of therapeutic **inhibition** could be pursued. Its limited expression profile suggests that such an approach might have a favorable safety profile with minimal off-target effects in other tissues.