Details for: LINC01250

Gene ID: 101927554

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: LINC01250

Ensembl ID: ENSG00000234423

Description: long intergenic non-protein coding RNA 1250

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • L2/3 intratelencephalic projecting glutamatergic neuron CL4030059
    CSI 34.86
    rCSI 75.61%
    PRS 98.85
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 25.61
    rCSI 62.25%
    PRS 98.68
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 22.1
    rCSI 52.84%
    PRS 99.01
  • L5/6 near-projecting glutamatergic neuron CL4030067
    CSI 20.6
    rCSI 67.69%
    PRS 98.77
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 20.44
    rCSI 25.42%
    PRS 99.05
  • L6b glutamatergic cortical neuron CL4023038
    CSI 19.66
    rCSI 61.45%
    PRS 99.1
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 19.1
    rCSI 33.73%
    PRS 99.14
  • sncg GABAergic cortical interneuron CL4023015
    CSI 18.58
    rCSI 29.87%
    PRS 99.02
  • inhibitory interneuron CL0000498
    CSI 18.45
    rCSI 42.59%
    PRS 99.28
  • sst GABAergic cortical interneuron CL4023017
    CSI 17.97
    rCSI 23.17%
    PRS 99.37
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 16.72
    rCSI 60.17%
    PRS 98.9
  • VIP GABAergic cortical interneuron CL4023016
    CSI 15.37
    rCSI 18.36%
    PRS 99.14
  • neuron CL0000540
    CSI 15.19
    rCSI 40.45%
    PRS 98.65
  • glutamatergic neuron CL0000679
    CSI 13.09
    rCSI 26.9%
    PRS 98.03
  • GABAergic neuron CL0000617
    CSI 12.3
    rCSI 41.22%
    PRS 97.85
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 11.79
    rCSI 19.79%
    PRS 99.17
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 11.54
    rCSI 43.61%
    PRS 98.81
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 11.36
    rCSI 66.9%
    PRS 98.95
  • basal cell of epidermis CL0002187
    CSI 8.65
    rCSI 15.33%
    PRS 93.34
  • retinal ganglion cell CL0000740
    CSI 8.15
    rCSI 18.01%
    PRS 99.13
  • renal beta-intercalated cell CL0002201
    CSI 7.38
    rCSI 17.59%
    PRS 99.78
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 6.69
    rCSI 20.92%
    PRS 99.29
  • ON parasol ganglion cell CL4033052
    CSI 5.43
    rCSI 77.1%
    PRS 99.21
  • melanocyte of skin CL1000458
    CSI 4.37
    rCSI 5.95%
    PRS 94.9
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 4
    rCSI 4.84%
    PRS 95.14
  • suprabasal keratinocyte CL4033013
    CSI 3.72
    rCSI 6.07%
    PRS 95.07
  • direct pathway medium spiny neuron CL4023026
    CSI 3.23
    rCSI 77.25%
    PRS 98.32
  • indirect pathway medium spiny neuron CL4023029
    CSI 3.19
    rCSI 77%
    PRS 98.3
  • helper T cell CL0000912
    CSI 2.21
    rCSI 3.12%
    PRS 98.38
  • ON midget ganglion cell CL4033046
    CSI 1.99
    rCSI 40.5%
    PRS 99.21
  • OFF midget ganglion cell CL4033047
    CSI 1.71
    rCSI 34.78%
    PRS 99.22

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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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 [LINC01250](/details-gene/101927554) is a long intergenic non-protein coding RNA (lncRNA) located on human chromosome 2. The expression profile of this gene indicates a highly specialized role within the central nervous system. **Overall**, it exhibits exceptionally strong and specific expression across a range of cortical [neuron](/details-cell/CL0000540) subtypes. Its significance is highest in excitatory neurons, particularly [L2/3 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4030059), as well as in various inhibitory [GABAergic neuron](/details-cell/CL0000617) populations. This distinct expression pattern suggests that [LINC01250](/details-gene/101927554), while functionally uncharacterized, is likely involved in fundamental processes of neuronal identity, circuit formation, or synaptic function within the cerebral cortex. ## Cellular Roles and Expression Landscape The expression landscape of [LINC01250](/details-gene/101927554) is remarkably restricted to the nervous system, positioning it as a key marker for specific neuronal populations. Analysis of its expression profile reveals its highest significance in cortical excitatory neurons, including [L2/3 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4030059) (CSI: 34.86), [L4 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4030063) (CSI: 22.10), and [L5/6 near-projecting glutamatergic neuron](/details-cell/CL4030067) (CSI: 20.60). Notably, [LINC01250](/details-gene/101927554) is also highly significant in diverse inhibitory interneuron populations. These include [pvalb GABAergic cortical interneuron](/details-cell/CL4023018) (CSI: 20.44), [sst GABAergic cortical interneuron](/details-cell/CL4023017) (CSI: 17.97), and [VIP GABAergic cortical interneuron](/details-cell/CL4023016) (CSI: 15.37). Its prominent expression across both major classes of cortical neurons—excitatory glutamatergic and inhibitory GABAergic—suggests a potentially broad role in establishing or maintaining the complex circuitry and excitatory/inhibitory balance essential for cortical function. The provided data strongly implies that its expression is highly specific to neural tissues. ## Pathways and Molecular Function The precise molecular function of [LINC01250](/details-gene/101927554) remains uncharacterized, as it is not currently associated with any specific pathways in functional annotation databases such as GO or Reactome. As a long non-coding RNA, it is predicted to function as a regulator of gene expression. LncRNAs can exert their effects through various mechanisms, including acting as molecular scaffolds for chromatin-modifying complexes, serving as decoys for microRNAs or transcription factors, or guiding proteins to specific genomic loci. Given its highly specific expression pattern in post-mitotic [neurons](/details-cell/CL0000540), it is plausible that [LINC01250](/details-gene/101927554) is involved in the transcriptional or post-transcriptional regulation of genes that define neuronal subtype identity, govern synaptic architecture, or modulate neuronal activity. Its role may be crucial for the long-term maintenance and functional integrity of cortical circuits. ## Research Directions The neuron-specific expression profile of [LINC01250](/details-gene/101927554) prompts several key questions regarding its role in neurobiology and its potential involvement in neurological disease. **Proposed Hypotheses:** 1. **Neuronal Identity and Maintenance:** [LINC01250](/details-gene/101927554) may function as a master regulator in the gene expression networks that establish and maintain the identity of specific cortical [neuron](/details-cell/CL0000540) subtypes, particularly the upper-layer excitatory neurons where its expression is most prominent. 2. **Synaptic Function Regulation:** [LINC01250](/details-gene/101927554) could be localized to synaptic compartments, where it may regulate the local translation of mRNAs critical for synaptic plasticity, thereby influencing learning and memory processes. 3. **Neurodevelopmental Role:** Expression of [LINC01250](/details-gene/101927554) may be dynamically regulated during corticogenesis, playing an essential role in the proper migration, lamination, and circuit integration of cortical neurons. **Suggested Experimental Approach:** To test the hypothesis that [LINC01250](/details-gene/101927554) is essential for neuronal identity, a loss-of-function study in a human-relevant model could be performed. Using CRISPR interference (CRISPRi) to achieve targeted knockdown of [LINC01250](/details-gene/101927554) in human induced pluripotent stem cells (iPSCs) differentiated into cortical organoids would be a powerful approach. Single-cell RNA sequencing (scRNA-seq) on these perturbed organoids could then be used to determine if the development or maturation of specific neuronal lineages, such as [L2/3 intratelencephalic projecting glutamatergic neuron](/details-cell/CL4030059), is compromised. This would provide direct evidence of its role in neurodevelopment and cell fate specification. **Therapeutic Potential:** The high neural specificity of [LINC01250](/details-gene/101927554) makes it an intriguing, though challenging, therapeutic target. If its dysregulation is linked to neurological or psychiatric disorders characterized by cortical dysfunction (e.g., epilepsy, certain forms of autism, or schizophrenia), it could be a candidate for targeted modulation. Given its nature as an RNA molecule, therapeutic intervention would likely involve antisense oligonucleotides (ASOs) delivered directly to the central nervous system. Depending on its pathogenic role, strategies could aim for either inhibition (if overexpressed) or stabilization/upregulation (if its loss contributes to disease). However, a thorough understanding of its fundamental biological function is a prerequisite for any therapeutic development.