Details for: SYCE1L

Gene ID: 100130958

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: SYCE1L

Ensembl ID: ENSG00000205078

Description: synaptonemal complex central element protein 1 like

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • retinal cone cell CL0000573
    CSI 3.85
    rCSI 6.19%
    PRS 90.76
  • mesodermal cell CL0000222
    CSI 3.21
    rCSI 3.85%
    PRS 96.07
  • neural crest cell CL0011012
    CSI 3.18
    rCSI 2.52%
    PRS 92.87
  • myofibroblast cell CL0000186
    CSI 3.13
    rCSI 4.33%
    PRS 94.27
  • epithelial cell of lower respiratory tract CL0002632
    CSI 3.12
    rCSI 2.42%
    PRS 97.45
  • retinal rod cell CL0000604
    CSI 3.07
    rCSI 5.41%
    PRS 93.15
  • duct epithelial cell CL0000068
    CSI 3.06
    rCSI 4.48%
    PRS 97.69
  • ionocyte CL0005006
    CSI 2.68
    rCSI 2.87%
    PRS 96.54
  • lung neuroendocrine cell CL1000223
    CSI 2.52
    rCSI 3.73%
    PRS 96.09
  • common myeloid progenitor CL0000049
    CSI 2.51
    rCSI 2.03%
    PRS 96.93
  • mucus secreting cell CL0000319
    CSI 2.45
    rCSI 3.89%
    PRS 97.96
  • intestine goblet cell CL0019031
    CSI 2.44
    rCSI 2.17%
    PRS 94.51
  • transit amplifying cell of colon CL0009011
    CSI 2.42
    rCSI 2.85%
    PRS 96.32
  • myoepithelial cell CL0000185
    CSI 2.34
    rCSI 5.93%
    PRS 97.2
  • intestinal epithelial cell CL0002563
    CSI 2.33
    rCSI 2.43%
    PRS 94.54
  • acinar cell CL0000622
    CSI 2.31
    rCSI 3.39%
    PRS 98
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 2.21
    rCSI 2.55%
    PRS 91.17
  • BEST4+ enteroycte CL4030026
    CSI 2.09
    rCSI 2.6%
    PRS 95.25
  • radial glial cell CL0000681
    CSI 2.04
    rCSI 2.84%
    PRS 95.21
  • tendon cell CL0000388
    CSI 2.04
    rCSI 5.29%
    PRS 97.26
  • ependymal cell CL0000065
    CSI 1.94
    rCSI 3.94%
    PRS 83.83
  • basal cell CL0000646
    CSI 1.76
    rCSI 2.35%
    PRS 94.11
  • colon goblet cell CL0009039
    CSI 1.63
    rCSI 3.89%
    PRS 96.4
  • amacrine cell CL0000561
    CSI 1.63
    rCSI 4.72%
    PRS 90.79
  • peripheral nervous system neuron CL2000032
    CSI 1.62
    rCSI 2.2%
    PRS 92.34
  • transit amplifying cell of small intestine CL0009012
    CSI 1.06
    rCSI 4.67%
    PRS 97.21
  • mesenchymal cell CL0008019
    CSI 0.96
    rCSI 2.45%
    PRS 93.96
  • luminal cell of prostate epithelium CL0002340
    CSI 0.94
    rCSI 5.05%
    PRS 97.49
  • enteroendocrine cell of colon CL0009042
    CSI 0.78
    rCSI 3.67%
    PRS 95.76
  • eye photoreceptor cell CL0000287
    CSI 0.75
    rCSI 8.45%
    PRS 95.85

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 [SYCE1L](/details-gene/100130958) is a protein-coding gene located on chromosome 16q23.1, first characterized as part of the human genome sequencing project ([Link](https://doi.org/10.1038/nature03187)). The gene is named "synaptonemal complex central element protein 1 like," and functional annotations link it to the [synaptonemal complex](/details-gene/GO:0000795), a structure critical for meiosis. However, expression data reveals a broader role, with significant expression observed in a diverse array of somatic cell types. These include sensory neurons like [retinal cone cell](/details-cell/CL0000573), developmental precursors such as [mesodermal cell](/details-cell/CL0000222) and [neural crest cell](/details-cell/CL0011012), and various structural cells including [myofibroblast cell](/details-cell/CL0000186) and multiple epithelial lineages. This pattern, combined with its association with the [intermediate filament cytoskeleton](/details-gene/GO:0045111), suggests that [SYCE1L](/details-gene/100130958) may possess functions beyond meiosis, potentially playing a role in maintaining cellular architecture and integrity in specialized somatic tissues. ## Cellular Roles and Expression Landscape The expression profile of [SYCE1L](/details-gene/100130958) indicates a multifaceted role across various cellular contexts. **Overall**, the gene's significance is highest in several distinct functional groups, suggesting it is not restricted to a single lineage. A primary role appears to be in specialized sensory neurons, evidenced by its high significance in [retinal cone cell](/details-cell/CL0000573) (CSI: 3.85) and [retinal rod cell](/details-cell/CL0000604) (CSI: 3.07). This suggests a potential function in establishing or maintaining the complex cytoarchitecture of photoreceptor cells. The gene also shows high significance in developmental progenitor populations, including [mesodermal cell](/details-cell/CL0000222) (CSI: 3.21) and [neural crest cell](/details-cell/CL0011012) (CSI: 3.18). This expression pattern points towards a possible involvement in cellular differentiation and morphogenesis during embryogenesis. Furthermore, [SYCE1L](/details-gene/100130958) is prominently expressed across a wide range of structural and secretory cell types. These include contractile [myofibroblast cell](/details-cell/CL0000186) (CSI: 3.13) and numerous epithelial cells, such as [epithelial cell of lower respiratory tract](/details-cell/CL0002632) (CSI: 3.12), [duct epithelial cell](/details-cell/CL0000068) (CSI: 3.06), and [intestine goblet cell](/details-cell/CL0019031) (CSI: 2.44). This widespread expression in tissues requiring robust structural integrity is consistent with its annotated association with the cytoskeleton. Finally, its relevance in [common myeloid progenitor](/details-cell/CL0000049) (CSI: 2.51) suggests a potential, though less defined, role in hematopoiesis. ## Pathways and Molecular Function Functional annotations for [SYCE1L](/details-gene/100130958) highlight a dual role related to both meiosis and general cellular structure. Its name and primary annotation are linked to [Synaptonemal complex assembly](/details-gene/GO:0007130), a process essential for synapsis of homologous chromosomes during prophase I of meiosis. This function is further supported by its localization to the [Synaptonemal complex](/details-gene/GO:0000795). While this suggests a role in germline cells, the observed high expression in somatic cells indicates this may be an ancestral function or one that is context-specific. Crucially, [SYCE1L](/details-gene/100130958) is also associated with the [Intermediate filament cytoskeleton](/details-gene/GO:0045111). This annotation provides a compelling molecular explanation for its high significance in structurally demanding cells like retinal photoreceptors, myofibroblasts, and various epithelial cells. It suggests [SYCE1L](/details-gene/100130958) may act as a linker or organizing protein within the cytoskeletal network, contributing to cellular stability, shape, and mechanical resilience. This cytoskeletal function likely represents its primary role in the somatic tissues where it is prominently expressed. ## Research Directions The discrepancy between the gene's name, which implies a meiotic function, and its observed expression predominantly in diverse somatic cells, presents key avenues for future research. **Proposed Hypotheses:** 1. [SYCE1L](/details-gene/100130958) functions as a novel structural component of the intermediate filament network in terminally differentiated cells. Its role is particularly critical in cells with complex morphologies and high mechanical stress, such as photoreceptors and secretory epithelial cells, where it contributes to cellular integrity. 2. The expression of [SYCE1L](/details-gene/100130958) in progenitor populations like [mesodermal cell](/details-cell/CL0000222) and [neural crest cell](/details-cell/CL0011012) indicates a transient role in organizing the cytoskeleton during cell migration, differentiation, and tissue morphogenesis, after which its expression may be downregulated in some lineages. 3. Despite its broad somatic expression, [SYCE1L](/details-gene/100130958) may retain a conserved, canonical role in [Synaptonemal complex assembly](/details-gene/GO:0007130) within germline cells, a context that may be underrepresented in the provided expression dataset. **Experimental Approach:** To test the hypothesis that [SYCE1L](/details-gene/100130958) is a critical structural component in photoreceptors, a powerful approach would involve using a human retinal organoid model system. CRISPR-Cas9 could be used to generate a knockout of [SYCE1L](/details-gene/100130958) in induced pluripotent stem cells (iPSCs), which would then be differentiated into retinal organoids. The effects of its absence would be assessed by comparing knockout and wild-type organoids using super-resolution microscopy to visualize the intermediate filament cytoskeleton and transmission electron microscopy to detect ultrastructural defects in photoreceptor outer segments or synaptic terminals. **Therapeutic Potential:** Given its widespread expression in many essential somatic cell types, [SYCE1L](/details-gene/100130958) is unlikely to be a suitable target for systemic inhibition, as this would risk significant off-target toxicity. However, if mutations leading to loss-of-function are linked to specific pathologies, such as retinal degeneration or epithelial barrier defects, it could become a candidate for gene replacement therapy. In such a scenario, a therapeutic strategy would focus on activation or restoration of function, potentially delivered locally via AAV vectors to minimize systemic exposure.

Genular Protein ID: 3857480734

Symbol: SYC1L_HUMAN

Name: Synaptonemal complex central element protein 1-like

UniProtKB Accession Codes:

A8MT33 A6NF23

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 2 Ensembl 1 ExpressionAtlas 1 GO 3 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 InterPro 1 KEGG 1 MANE-Select 1 MIM 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 1 SMR 1 STRING 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 15616553

Title: The sequence and analysis of duplication-rich human chromosome 16.

PubMed ID: 15616553

DOI: 10.1038/nature03187

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 242
  • Mass: 27397
  • Checksum: EA60AA7D1259D03E
  • Sequence:
    • MAGKLKPLNV EAPEATEEAE GQAKSLKTED LLAMVIKLQK EGSLEPQIED LISRINDLQQ 
AKKKSSEELR ETHSLWEALH RELDSLNGEK VHLEEVLGKK QEALRILQMH CQEKESEAQR 
LDVRGQLEDL MGQHKDLWEF HMLEQRLARE IRALERSKEQ LLSERRLVRA KLREVERRLH 
SPPEVEGAMA VNDGLKAELE IFGEQVRSAP EVGAGEGEAG PELPRARDEE DPEPPVAAPD 
AL