Details for: C6orf47

Gene ID: 57827

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: C6orf47

Ensembl ID: ENSG00000204439

Description: chromosome 6 open reading frame 47

Cell Significance Landscape

Associated with

Significant Cells

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

  • interstitial cell of Cajal CL0002088
    CSI 3.64
    rCSI 4.63%
    PRS 95.98
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 3.43
    rCSI 3.1%
    PRS 92.74
  • plasmacytoid dendritic cell, human CL0001058
    CSI 3.39
    rCSI 2.36%
    PRS 95.97
  • activated type II NK T cell CL0000931
    CSI 2.95
    rCSI 3.32%
    PRS 98.13
  • epithelial cell of lung CL0000082
    CSI 2.85
    rCSI 2.36%
    PRS 94.6
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 2.67
    rCSI 2.72%
    PRS 96.97
  • colon epithelial cell CL0011108
    CSI 2.54
    rCSI 2.67%
    PRS 91.73
  • goblet cell CL0000160
    CSI 2.33
    rCSI 2.2%
    PRS 91.63
  • mononuclear phagocyte CL0000113
    CSI 2.31
    rCSI 5.08%
    PRS 95.69
  • erythrocyte CL0000232
    CSI 2.29
    rCSI 5.21%
    PRS 91.59
  • ionocyte CL0005006
    CSI 2.26
    rCSI 2.42%
    PRS 94.57
  • transit amplifying cell of colon CL0009011
    CSI 2.11
    rCSI 2.48%
    PRS 93.6
  • colonocyte CL1000347
    CSI 1.82
    rCSI 2.6%
    PRS 91.97
  • club cell CL0000158
    CSI 1.81
    rCSI 2.66%
    PRS 90.23
  • mesenchymal cell CL0008019
    CSI 1.02
    rCSI 2.6%
    PRS 89.86

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 [C6orf47](/details-gene/57827) is a largely uncharacterized protein-coding gene located within the gene-dense Major Histocompatibility Complex (MHC) class III region on human chromosome 6 [Link](https://pubmed.ncbi.nlm.nih.gov/14656967/). Its primary annotated molecular function is [protein binding](https://www.ebi.ac.uk/QuickGO/term/GO:0005515). Expression data reveals a broad but distinct pattern, with high significance in diverse and specialized cell types. **Overall**, it is a key marker for [interstitial cell of Cajal](/details-cell/CL0002088) in the gastrointestinal tract, various hematopoietic lineages including [megakaryocyte-erythroid progenitor cell](/details-cell/CL0000050) and [plasmacytoid dendritic cell, human](/details-cell/CL0001058), and epithelial cells of mucosal tissues like the lung and colon. This distribution suggests a fundamental, yet context-specific, role in processes ranging from gut motility to immune surveillance and hematopoiesis. ## Cellular Roles and Expression Landscape The expression profile of [C6orf47](/details-gene/57827) indicates a multifaceted role across several physiological systems. **Overall**, its most significant expression is observed in [interstitial cell of Cajal](/details-cell/CL0002088) (CSI: 3.64), the pacemaker cells responsible for gastrointestinal motility, suggesting a specialized function in this context. The gene also shows high significance in a range of colonic cells, including [colon epithelial cell](/details-cell/CL0011108) and [transit amplifying cell of colon](/details-cell/CL0009011), underscoring a prominent role in the gut epithelium. Concurrently, [C6orf47](/details-gene/57827) is a notable marker within the hematopoietic and immune systems. It is highly significant in progenitor cells, such as [megakaryocyte-erythroid progenitor cell](/details-cell/CL0000050), as well as in mature immune cells critical for both innate and adaptive immunity, including [plasmacytoid dendritic cell, human](/details-cell/CL0001058), [activated type II NK T cell](/details-cell/CL0000931), and developing [double-positive, alpha-beta thymocyte](/details-cell/CL0000809). This pattern suggests involvement in both immune cell development and effector function. Furthermore, its expression in [epithelial cell of lung](/details-cell/CL0000082) points to a potential role in barrier tissues beyond the gut. The diverse array of cell types where [C6orf47](/details-gene/57827) is prominently expressed suggests it may be part of a fundamental cellular machinery that is adapted for specialized functions in different contexts. ## Pathways and Molecular Function The functional role of [C6orf47](/details-gene/57827) remains poorly defined, with its only significant Gene Ontology annotation being [protein binding](https://www.ebi.ac.uk/QuickGO/term/GO:0005515). This broad functional category is consistent with its potential role as an adaptor or scaffolding protein, participating in the formation of larger molecular complexes. This is further supported by phosphoproteomic studies that have identified its protein product [Link](https://doi.org/10.1021/pr300630k), suggesting it may be subject to post-translational regulation. The gene's location in the human MHC class III region is noteworthy [Link](https://pubmed.ncbi.nlm.nih.gov/2477242/). This genomic area is densely populated with genes involved in immunity and inflammation, which aligns with the observed high expression of [C6orf47](/details-gene/57827) in various immune cell populations, such as dendritic cells and T cells. Its protein-binding capacity could therefore be important for assembling signaling complexes involved in immune recognition or response pathways. ## Research Directions Given that [C6orf47](/details-gene/57827) is an uncharacterized gene with a distinct expression pattern, several avenues of research are warranted to elucidate its function. ### Proposed Hypotheses 1. **Role in Gut Motility:** Based on its top-ranking expression in [interstitial cell of Cajal](/details-cell/CL0002088), [C6orf47](/details-gene/57827) may function as a crucial component of a protein complex that regulates the generation or propagation of electrical slow waves, thereby controlling gastrointestinal peristalsis. 2. **Function in Innate Immunity:** The high significance of [C6orf47](/details-gene/57827) in [plasmacytoid dendritic cell, human](/details-cell/CL0001058), combined with its genomic location in the MHC class III region, suggests a role as an adaptor protein in innate immune signaling pathways, such as those involved in type I interferon production in response to viral pathogens. 3. **Involvement in Hematopoiesis:** Its notable expression in [megakaryocyte-erythroid progenitor cell](/details-cell/CL0000050) and developing thymocytes suggests that [C6orf47](/details-gene/57827) may be involved in lineage commitment or differentiation decisions during blood cell development. ### Key Experimental Approach To test the hypothesis regarding its role in gut motility, a targeted experimental approach is necessary. A conditional knockout mouse model could be generated to specifically delete [C6orf47](/details-gene/57827) in `Kit`-expressing cells, which would ablate its function primarily in interstitial cells of Cajal. Subsequent analysis of these mice using in vivo gastrointestinal transit assays and ex vivo intestinal manometry and electrophysiology would reveal any defects in motility or pacemaker activity. To identify its molecular partners, co-immunoprecipitation of the C6orf47 protein from primary interstitial cells of Cajal or a relevant cell line, followed by mass spectrometry, could uncover its binding partners and place it within a specific functional complex. ### Therapeutic Potential The therapeutic potential of [C6orf47](/details-gene/57827) is currently speculative. Its broad expression across multiple critical cell types, including immune and progenitor cells, suggests that systemic targeting could lead to significant off-target effects. However, if its function is proven to be central to pathologies characterized by abnormal gut motility (e.g., gastroparesis, chronic constipation) or specific immune dysfunctions, it could emerge as a viable drug target. As a protein-binding molecule, it would likely be more amenable to inhibition via small molecules designed to disrupt a specific protein-protein interaction rather than targeting with biologics. A detailed understanding of its function and structure is a prerequisite for any therapeutic development.

Genular Protein ID: 3125152584

Symbol: CF047_HUMAN

Name: Uncharacterized protein C6orf47

UniProtKB Accession Codes:

O95873 B0UXA1 B0UZ50 Q5SSS6 Q95IG0

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 DNASU 1 DisGeNET 1 EMBL 12 Ensembl 7 ExpressionAtlas 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MANE-Select 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 Pumba 1 RNAct 1 RefSeq 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 14656967

Title: Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse.

PubMed ID: 14656967

DOI: 10.1101/gr.1736803

PubMed ID: 14574404

Title: The DNA sequence and analysis of human chromosome 6.

PubMed ID: 14574404

DOI: 10.1038/nature02055

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

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

Sequence Information:

  • Length: 294
  • Mass: 31710
  • Checksum: 59ACE578FB60284D
  • Sequence:
    • MFLRRLGGWL PRPWGRRKPM RPDPPYPEPR RVDSSSENSG SDWDSAPETM EDVGHPKTKD 
SGALRVSGAA SEPSKEEPQV EQLGSKRMDS LKWDQPISST QESGRLEAGG ASPKLRWDHV 
DSGGTRRPGV SPEGGLSVPG PGAPLEKPGR REKLLGWLRG EPGAPSRYLG GPEECLQIST 
NLTLHLLELL ASALLALCSR PLRAALDTLG LRGPLGLWLH GLLSFLAALH GLHAVLSLLT 
AHPLHFACLF GLLQALVLAV SLREPNGDEA ATDWESEGLE REGEEQRGDP GKGL

Genular Protein ID: 3704567353

Symbol: Q9UMP7_HUMAN

Name: N/A

UniProtKB Accession Codes:

Q9UMP7

Database IDs:

AlphaFoldDB 1 BioGRID-ORCS 1 CTD 1 DNASU 1 DisGeNET 1 EMBL 2 GO 1 InterPro 1 KEGG 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PeptideAtlas 1 Pfam 1 RefSeq 1 SAM 2

Citations:

PubMed ID: 2477242

Title: Identification of multiple HTF-island associated genes in the human major histocompatibility complex class III region.

PubMed ID: 2477242

Sequence Information:

  • Length: 312
  • Mass: 33873
  • Checksum: 6E3EB35D71321E54
  • Sequence:
    • MFLRRLGGWL PRPWGRRKPM RPDPPYPEPR RVDSSSENSG SDWDSAPETM EDVGHPKTKD 
SGALRVSRAA SEPSKEEPQV EQLGSKRMDS LKWDQPISST QESGRLEAGG ASPKLRWDHV 
DSGGTRRPGV SPEGDSSVPG PGAPLEKPGR REKLLGWLRG EPGAPSRYLG GPEECLQIST 
NLTLHLLELL ASALLALCSR PLRAALDTLG LRGPLGLWLH GLLSFLAALH GLHAVLSLLT 
AHPLHFACLF GLLQALVLAV SSGSPMGMRR PLTGRVRGWR GKVRSRGETR ERGCDRGVGA 
KGEESVGFRR KV