Details for: C12orf60

Gene ID: 144608

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: C12orf60

Ensembl ID: ENSG00000182993

Description: chromosome 12 open reading frame 60

Cell Significance Landscape

Associated with

Significant Cells

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

  • retinal rod cell CL0000604
    CSI 2.55
    rCSI 4.49%
    PRS 96.95
  • retinal cone cell CL0000573
    CSI 1.95
    rCSI 3.14%
    PRS 96.02
  • S cone cell CL0003050
    CSI 1.53
    rCSI 6.71%
    PRS 96.87
  • direct pathway medium spiny neuron CL4023026
    CSI 0.35
    rCSI 8.34%
    PRS 93.79
  • indirect pathway medium spiny neuron CL4023029
    CSI 0.32
    rCSI 7.63%
    PRS 93.47

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

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
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  • 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 [C12orf60](/details-gene/144608) is a protein-coding gene that encodes a largely uncharacterized protein. Current functional annotations suggest it participates in [protein binding](/details-go/GO:0005515). Expression data indicates a highly specialized role for this gene, as it is most significantly and specifically expressed in photoreceptor cells of the retina, including [retinal rod cell](/details-cell/CL0000604) and [retinal cone cell](/details-cell/CL0000573). This distinct expression pattern strongly suggests a function related to vision, photoreceptor maintenance, or retinal biology. ## Cellular Roles and Expression Landscape The expression profile of [C12orf60](/details-gene/144608) points toward a highly specific function within the central nervous system, particularly the retina. * **Retinal Photoreceptor Specificity:** **Overall**, the gene exhibits its highest significance in light-sensing cells. It is a top marker for [retinal rod cell](/details-cell/CL0000604) (CSI: 2.55), [retinal cone cell](/details-cell/CL0000573) (CSI: 1.95), and specifically [S cone cell](/details-cell/CL0003050) (CSI: 1.53). This pronounced expression in the primary cells responsible for phototransduction suggests that [C12orf60](/details-gene/144608) is likely involved in a core biological process unique to these cells, such as the phototransduction cascade, structural maintenance of outer segments, or metabolic support. * **Broader Neuronal Expression:** While its role in the retina is prominent, [C12orf60](/details-gene/144608) also shows modest but notable significance in striatal neurons, including [direct pathway medium spiny neuron](/details-cell/CL4023026) (CSI: 0.35) and [indirect pathway medium spiny neuron](/details-cell/CL4023029) (CSI: 0.32). This suggests a potential, albeit less critical, function in other neuronal subtypes beyond the visual system. ## Pathways and Molecular Function The functional role of [C12orf60](/details-gene/144608) is not well-defined, and it was first identified through large-scale cDNA sequencing projects [Link](https://doi.org/10.1038/ng1285), [Link](https://doi.org/10.1101/gr.2596504). * **Molecular Function:** The primary annotated molecular function for the C12orf60 protein is [protein binding](/details-go/GO:0005515). However, its specific interaction partners have not been identified. Given its high expression in photoreceptors, it is plausible that it interacts with proteins integral to the phototransduction machinery, the cytoskeleton of the outer segments, or trafficking of key components like opsins. ## Research Directions The highly specific expression of [C12orf60](/details-gene/144608) in retinal photoreceptors, coupled with its uncharacterized nature, makes it a compelling subject for further investigation, particularly in the context of retinal biology and disease. **Proposed Hypotheses:** 1. [C12orf60](/details-gene/144608) is a structural component of the photoreceptor outer segment, where it binds to and stabilizes key proteins involved in the architecture of the disc membranes. Loss of its function would therefore lead to progressive structural degradation and retinal degeneration. 2. The C12orf60 protein acts as an adaptor or scaffold protein within the phototransduction cascade, facilitating interactions between key signaling components. Its absence would impair the light response of both rods and cones. **Experimental Approach:** To test the hypothesis that [C12orf60](/details-gene/144608) is essential for photoreceptor structure and function, a knockout mouse model could be generated using CRISPR-Cas9. The phenotype of these mice could be comprehensively analyzed using: * **Electroretinography (ERG):** To measure the electrical responses of rods and cones to light, which would reveal functional deficits in the phototransduction pathway. * **Histology and Transmission Electron Microscopy (TEM):** To examine the retinal structure, specifically looking for signs of photoreceptor cell death, disorganization, or defects in the ultrastructure of the outer segments. * **Co-immunoprecipitation followed by Mass Spectrometry (Co-IP/MS):** Using retinal tissue lysates from wild-type mice to pull down the C12orf60 protein and identify its binding partners, which would provide direct evidence of its molecular interactions. **Therapeutic Potential:** Given its high specificity for retinal cells, [C12orf60](/details-gene/144608) represents a potential candidate gene for inherited retinal diseases. If loss-of-function mutations are identified as a cause of a retinal dystrophy, it could be an excellent target for gene replacement therapy using adeno-associated virus (AAV) vectors, a therapeutic modality with proven success in the eye. Its therapeutic potential hinges on first elucidating its fundamental biological role and its connection to human disease.

Genular Protein ID: 4160634561

Symbol: CL060_HUMAN

Name: Uncharacterized protein C12orf60

UniProtKB Accession Codes:

Q5U649 A8K1M7 Q5XKK8 Q8IXY2

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 4 Ensembl 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MANE-Select 1 MalaCards 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 8 SMR 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

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: 245
  • Mass: 27626
  • Checksum: C424D710741D7FD5
  • Sequence:
    • MSSESEKDKE RLIQAAKMFF FHVQDLASVI NTLTELFSRS MNTQILLMAV KNNSYIKDFF 
EQMLKIFKEM QSVVDARHDK IQKESLCSKV AMAMCSVVQK STNVEELHQS AKEVFKSAHT 
PVIISVLNSS NILGSLESSL SHLMKFPIMN LQLSDFYTED TKEQSDVTTS ERTRSPPGSS 
KTTMIDTLKK LQDVLKTEDS KNPTKSAADL LEQIVKAMGP ILEILQKAIK TMEMNISVFK 
KASDK