Details for: LOC102724019

Gene ID: 102724019

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: LOC102724019

Ensembl ID: ENSG00000240086

Description: uncharacterized LOC102724019

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • sst GABAergic cortical interneuron CL4023017
    CSI 22.66
    rCSI 29.22%
    PRS 99.76
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 12.01
    rCSI 14.94%
    PRS 99.57
  • retinal cone cell CL0000573
    CSI 11.95
    rCSI 19.23%
    PRS 99.19
  • VIP GABAergic cortical interneuron CL4023016
    CSI 10.92
    rCSI 13.05%
    PRS 99.6
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 6.85
    rCSI 12.1%
    PRS 99.57
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 6.83
    rCSI 11.46%
    PRS 99.64
  • GABAergic neuron CL0000617
    CSI 6.58
    rCSI 22.05%
    PRS 98.69
  • amacrine cell CL0000561
    CSI 6.52
    rCSI 18.89%
    PRS 99.76
  • sncg GABAergic cortical interneuron CL4023015
    CSI 6.05
    rCSI 9.74%
    PRS 99.51
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 5.98
    rCSI 14.31%
    PRS 99.71
  • L6b glutamatergic cortical neuron CL4023038
    CSI 5.41
    rCSI 16.91%
    PRS 99.57
  • ON parasol ganglion cell CL4033052
    CSI 4.32
    rCSI 61.31%
    PRS 99.76
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 3.52
    rCSI 20.74%
    PRS 99.5
  • retinal ganglion cell CL0000740
    CSI 2.98
    rCSI 6.59%
    PRS 99.53
  • direct pathway medium spiny neuron CL4023026
    CSI 2.64
    rCSI 63.16%
    PRS 99.05
  • indirect pathway medium spiny neuron CL4023029
    CSI 2.61
    rCSI 62.95%
    PRS 98.98
  • ON midget ganglion cell CL4033046
    CSI 2.52
    rCSI 51.23%
    PRS 99.68
  • OFF midget ganglion cell CL4033047
    CSI 2.06
    rCSI 41.91%
    PRS 99.74
  • GABAergic amacrine cell CL4030027
    CSI 1.44
    rCSI 4.95%
    PRS 99.61
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 1.44
    rCSI 5.43%
    PRS 99.37

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 [LOC102724019](/details-gene/102724019) is an uncharacterized long non-coding RNA (lncRNA) located on chromosome 3q22.2. Expression data reveals a highly specific profile within the central nervous system, suggesting a specialized role in neuronal function. **Overall**, it is most significantly expressed in distinct subtypes of inhibitory cortical interneurons, particularly `sst GABAergic cortical interneuron`s ([CL4023017](/details-cell/CL4023017)), and also shows prominent expression in various cell types of the retina, including `retinal cone cell`s ([CL0000573](/details-cell/CL0000573)). This pattern suggests its potential involvement in regulating inhibitory circuits in the cortex and visual processing in the retina. ## Cellular Roles and Expression Landscape The expression landscape of [LOC102724019](/details-gene/102724019) is remarkably restricted to neuronal lineages, pointing towards a specialized function in the nervous system. Its highest significance is observed within diverse populations of cortical GABAergic neurons, which are critical for shaping cortical circuit activity. The gene is a top marker for `sst GABAergic cortical interneuron`s ([CL4023017](/details-cell/CL4023017)) (CSI: 22.66), `pvalb GABAergic cortical interneuron`s ([CL4023018](/details-cell/CL4023018)) (CSI: 12.01), and `VIP GABAergic cortical interneuron`s ([CL4023016](/details-cell/CL4023016)) (CSI: 10.92). This strong and subtype-specific expression suggests a potential role in establishing or maintaining the unique functional identities of these inhibitory neuron classes. A second major site of expression is the retina. [LOC102724019](/details-gene/102724019) is a significant marker for `retinal cone cell`s ([CL0000573](/details-cell/CL0000573)), `amacrine cell`s ([CL0000561](/details-cell/CL0000561)), and `retinal ganglion cell`s ([CL0000740](/details-cell/CL0000740)). Its presence across these functionally distinct retinal layers, involved in photoreception, signal integration, and output, respectively, indicates a potentially broad role in the visual processing pathway. While the gene's primary association is with inhibitory and sensory neurons, it also shows moderate significance in some glutamatergic excitatory neuron populations, such as `L4 intratelencephalic projecting glutamatergic neuron`s ([CL4030063](/details-cell/CL4030063)) and `L6b glutamatergic cortical neuron`s ([CL4023038](/details-cell/CL4023038)). This suggests its function, while concentrated in certain cell types, may extend to the broader regulation of neuronal homeostasis or function. ## Pathways and Molecular Function As an uncharacterized non-coding RNA, the precise molecular function of [LOC102724019](/details-gene/102724019) remains unknown, and it is not currently annotated in major pathway databases like Reactome or Gene Ontology. However, based on its highly specific expression pattern in mature neuronal subtypes, it is plausible that [LOC102724019](/details-gene/102724019) functions as a regulatory RNA. It may be involved in epigenetic modulation, transcriptional regulation of nearby genes, or post-transcriptional control of mRNA stability or translation, all of which are critical for defining and maintaining the specialized properties of neurons like `GABAergic neuron`s ([CL0000617](/details-cell/CL0000617)) and `retinal cone cell`s ([CL0000573](/details-cell/CL0000573)). ## Research Directions The highly specific expression of [LOC102724019](/details-gene/102724019) in distinct neuronal circuits presents several compelling avenues for future research, particularly in understanding the molecular basis of neuronal diversity and function. ### Proposed Hypotheses 1. **[LOC102724019](/details-gene/102724019) is a key determinant of cortical interneuron identity.** Given its exceptionally high and specific expression in `sst GABAergic cortical interneuron`s ([CL4023017](/details-cell/CL4023017)) and other interneuron subtypes, it may function as a master regulator that controls the gene expression programs essential for the terminal differentiation and functional maturation of these cells. 2. **[LOC102724019](/details-gene/102724019) regulates phototransduction or synaptic signaling in the retina.** Its significant presence in `retinal cone cell`s ([CL0000573](/details-cell/CL0000573)) suggests it could modulate the expression of opsins, ion channels, or other key components of the light-sensing and signal transmission machinery. ### Experimental Approach To test the hypothesis that [LOC102724019](/details-gene/102724019) is a key determinant of cortical interneuron identity (Hypothesis 1), a loss-of-function study in a model organism would be highly informative. One could use AAV-delivered CRISPR-Cas9 or antisense oligonucleotides (ASOs) to specifically knock down [LOC102724019](/details-gene/102724019) expression in the developing mouse cortex. Subsequent single-cell RNA sequencing (scRNA-seq) of cortical cells would reveal if its depletion leads to a failure of interneurons to acquire their specific molecular identity (e.g., loss of SST expression) or a shift towards an alternative cell fate. This could be complemented by electrophysiological recordings to assess whether the functional properties of the targeted interneurons are compromised. ### Therapeutic Potential The exquisite cell-type specificity of [LOC102724019](/details-gene/102724019) makes it an attractive potential therapeutic target. Neurological and psychiatric disorders such as epilepsy and schizophrenia are often linked to the dysfunction of cortical inhibitory circuits, particularly those involving `pvalb GABAergic cortical interneuron`s ([CL4023018](/details-cell/CL4023018)) and `sst GABAergic cortical interneuron`s ([CL4023017](/details-cell/CL4023017)). If dysregulation of [LOC102724019](/details-gene/102724019) is implicated in the pathology of such diseases, its nature as a non-coding RNA makes it a suitable candidate for ASO-based therapies designed to either inhibit (if overexpressed) or potentially stabilize/upregulate its expression. The ability to target specific neuronal populations while sparing others could offer a significant advantage over conventional small-molecule drugs with broader effects.