Details for: LOC729998

Gene ID: 729998

Gene Type:  Pseudogene  - A non-functional segment of DNA that resembles a functional gene but has lost its protein-coding ability or is otherwise no longer expressed.

Symbol: LOC729998

Ensembl ID: ENSG00000283041

Description: eukaryotic translation elongation factor 1 gamma pseudogene

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • CD4-positive, alpha-beta thymocyte CL0000810
    CSI 15.01
    rCSI 12.02%
    PRS 98.42
  • CD8-positive, alpha-beta thymocyte CL0000811
    CSI 10.75
    rCSI 16.77%
    PRS 99.57
  • conjunctival epithelial cell CL1000432
    CSI 8.55
    rCSI 13.07%
    PRS 99.87
  • retinal blood vessel endothelial cell CL0002585
    CSI 8.33
    rCSI 13.3%
    PRS 99.98
  • professional antigen presenting cell CL0000145
    CSI 7.27
    rCSI 25.02%
    PRS 98.76
  • chondrocyte CL0000138
    CSI 6.69
    rCSI 10.64%
    PRS 99.62
  • retinal rod cell CL0000604
    CSI 5.28
    rCSI 9.31%
    PRS 99.69

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 [LOC729998](/details-gene/729998) is a pseudogene located on chromosome 7q33 in *Homo sapiens*. It is identified as a pseudogene of the eukaryotic translation elongation factor 1 gamma (*EEF1G*), a key component in protein synthesis. While pseudogenes are typically considered non-functional relics of evolution, their transcripts can sometimes exert regulatory roles. Expression data indicates that [LOC729998](/details-gene/729998) shows significant expression in specific immune cell precursors, particularly [CD4-positive, alpha-beta thymocyte](/details-cell/CL0000810) and [CD8-positive, alpha-beta thymocyte](/details-cell/CL0000811), as well as in a diverse set of non-immune cells, including several ocular cell types and chondrocytes. ## Cellular Roles and Expression Landscape **Overall**, the expression profile of [LOC729998](/details-gene/729998) is characterized by high significance in developing T-lymphocytes within the thymus. The highest cell significance index (CSI) values are observed in [CD4-positive, alpha-beta thymocyte](/details-cell/CL0000810) (CSI: 15.01) and [CD8-positive, alpha-beta thymocyte](/details-cell/CL0000811) (CSI: 10.75), suggesting that its transcription is prominent during critical stages of T-cell maturation. Its relevance within the immune system is further supported by significant expression in [professional antigen presenting cell](/details-cell/CL0000145) (CSI: 7.27). Interestingly, the gene's expression is not restricted to the immune system. A notable pattern emerges in various cell types of the eye, including [conjunctival epithelial cell](/details-cell/CL1000432) (CSI: 8.55), [retinal blood vessel endothelial cell](/details-cell/CL0002585) (CSI: 8.33), and [retinal rod cell](/details-cell/CL0000604) (CSI: 5.28). Additionally, its expression in structural cells like the [chondrocyte](/details-cell/CL0000138) (CSI: 6.69) highlights a broad but specific expression landscape. This pattern across functionally distinct lineages may suggest that transcription of [LOC729998](/details-gene/729998) is linked to shared, fundamental cellular processes or is a byproduct of the chromatin state at this locus in these specific cells. ## Pathways and Molecular Function As a pseudogene, [LOC729998](/details-gene/729998) is not annotated to a canonical protein-coding pathway and does not produce a functional protein. Its sequence is derived from the gene encoding the gamma subunit of the eukaryotic translation elongation factor-1 (eEF-1), which is crucial for delivering aminoacyl-tRNAs to the ribosome during the elongation step of protein synthesis. Any potential function of [LOC729998](/details-gene/729998) would be regulatory in nature, likely at the RNA level. If transcribed, it could function as a long non-coding RNA (lncRNA). Such lncRNAs can influence gene expression through various mechanisms, including acting as a "sponge" or competitive endogenous RNA (ceRNA) to sequester microRNAs that would otherwise target its parent gene (*EEF1G*) or other transcripts. This could serve as a mechanism to fine-tune the rate of protein synthesis in cells with high metabolic or proliferative demands, such as developing thymocytes. ## Research Directions The specific expression pattern of [LOC729998](/details-gene/729998), particularly its high significance in thymocytes, presents several avenues for future research to determine if it is a functional regulatory element or simply transcriptional noise. **Testable Hypotheses:** 1. The [LOC729998](/details-gene/729998) transcript acts as a competitive endogenous RNA (ceRNA) in thymocytes, binding to microRNAs that target the parent *EEF1G* gene, thereby upregulating protein synthesis machinery to support T-cell proliferation and differentiation. 2. Transcription of [LOC729998](/details-gene/729998) serves as a marker for a specific chromatin state required for the regulation of nearby genes on chromosome 7q33 that are critical for T-cell development, but the transcript itself is non-functional. **Proposed Key Experiment:** To test the first hypothesis, one could employ a loss-of-function approach in a relevant cellular model. Specifically, CRISPR interference (CRISPRi) could be used to specifically silence the transcription of [LOC729998](/details-gene/729998) in primary human thymocytes or a T-cell precursor line. The functional consequences would be assessed by monitoring cell proliferation, differentiation via flow cytometry for CD4/CD8 markers, and changes in the overall rate of protein synthesis. RNA-sequencing would be performed to quantify the expression levels of the parent *EEF1G* gene and other potential mRNA targets of shared microRNAs to validate the ceRNA mechanism. **Therapeutic Potential:** At present, the therapeutic potential of [LOC729998](/details-gene/729998) is considered low due to its status as a pseudogene with unconfirmed function. However, should it be validated as a key regulator of T-cell development, it could emerge as a novel target. For instance, in T-cell acute lymphoblastic leukemia (T-ALL) or autoimmune diseases, RNA-based therapies like antisense oligonucleotides (ASOs) could be designed to modulate its expression and thereby influence T-cell fate. Its utility would most likely be as a highly specific modulator of cellular function in a therapeutic context rather than a target for direct protein inhibition.