Details for: EMCN

Gene ID: 51705

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: EMCN

Ensembl ID: ENSG00000164035

Description: endomucin

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • retinal blood vessel endothelial cell CL0002585
    CSI 19.01
    rCSI 30.35%
    PRS 88.98
  • cerebral cortex endothelial cell CL1001602
    CSI 18.35
    rCSI 31.74%
    PRS 78.78
  • myofibroblast cell CL0000186
    CSI 15.28
    rCSI 21.16%
    PRS 82.18
  • cardiac endothelial cell CL0010008
    CSI 15.18
    rCSI 61.25%
    PRS 86.2
  • cardiac muscle cell CL0000746
    CSI 14.93
    rCSI 21.42%
    PRS 76.76
  • endocardial cell CL0002350
    CSI 14.11
    rCSI 67.56%
    PRS 81.86
  • capillary endothelial cell CL0002144
    CSI 13.74
    rCSI 25.18%
    PRS 88.15
  • vasa recta ascending limb cell CL1001131
    CSI 13.25
    rCSI 59.97%
    PRS 90.66
  • pulmonary capillary endothelial cell CL4028001
    CSI 12.72
    rCSI 24.25%
    PRS 92.99
  • endothelial cell of artery CL1000413
    CSI 11.51
    rCSI 16.86%
    PRS 89.66
  • melanocyte CL0000148
    CSI 8.99
    rCSI 6.66%
    PRS 80.6
  • blood vessel endothelial cell CL0000071
    CSI 8.92
    rCSI 18.5%
    PRS 83.17
  • cardiac blood vessel endothelial cell CL0010006
    CSI 8.21
    rCSI 58.05%
    PRS 79.26
  • adipocyte CL0000136
    CSI 8.11
    rCSI 10.42%
    PRS 76.62
  • vascular associated smooth muscle cell CL0000359
    CSI 7.88
    rCSI 25.57%
    PRS 83.8
  • endothelial cell of lymphatic vessel CL0002138
    CSI 7.25
    rCSI 14.37%
    PRS 88.72
  • kidney loop of Henle thin ascending limb epithelial cell CL1001107
    CSI 7.03
    rCSI 18.17%
    PRS 82.1
  • type EC enteroendocrine cell CL0000577
    CSI 6.73
    rCSI 23.89%
    PRS 88.07
  • glutamatergic neuron CL0000679
    CSI 6.73
    rCSI 13.82%
    PRS 73.24
  • skin fibroblast CL0002620
    CSI 6.48
    rCSI 5.59%
    PRS 85.42
  • mesenchymal cell CL0008019
    CSI 6.42
    rCSI 16.31%
    PRS 79.65
  • endothelial cell of uterus CL0009095
    CSI 6.4
    rCSI 46.79%
    PRS 91.38
  • vein endothelial cell CL0002543
    CSI 6.04
    rCSI 16.48%
    PRS 90.37
  • pulmonary artery endothelial cell CL1001568
    CSI 5.8
    rCSI 7.89%
    PRS 91.96
  • mononuclear phagocyte CL0000113
    CSI 5.63
    rCSI 12.4%
    PRS 88.71
  • vein endothelial cell of respiratory system CL4033008
    CSI 5.55
    rCSI 38.12%
    PRS 90.2
  • vasa recta descending limb cell CL1001285
    CSI 5.17
    rCSI 41.23%
    PRS 91.36
  • renal interstitial pericyte CL1001318
    CSI 5
    rCSI 13.77%
    PRS 81.95
  • endothelial cell of periportal hepatic sinusoid CL0019021
    CSI 4.65
    rCSI 21.32%
    PRS 88.37
  • collagen secreting cell CL0000667
    CSI 4.64
    rCSI 26.62%
    PRS 89.57
  • endothelial cell of venule CL1000414
    CSI 3.84
    rCSI 34.06%
    PRS 90.97
  • lung endothelial cell CL1001567
    CSI 3.72
    rCSI 8.68%
    PRS 93.25
  • basal cell of epidermis CL0002187
    CSI 3.69
    rCSI 6.53%
    PRS 55.37
  • parietal epithelial cell CL1000452
    CSI 3.11
    rCSI 8.31%
    PRS 78.79
  • epithelial cell of proximal tubule CL0002306
    CSI 2.96
    rCSI 7.24%
    PRS 78.5
  • endothelial cell of pericentral hepatic sinusoid CL0019022
    CSI 2.75
    rCSI 8.48%
    PRS 88.74
  • melanocyte of skin CL1000458
    CSI 2.65
    rCSI 3.61%
    PRS 53.89
  • brain vascular cell CL4023072
    CSI 2.57
    rCSI 26.59%
    PRS 79.95
  • intestinal tuft cell CL0019032
    CSI 2.46
    rCSI 3.76%
    PRS 88.35
  • endothelial cell of vascular tree CL0002139
    CSI 2.4
    rCSI 13.11%
    PRS 82.15
  • mesangial cell CL0000650
    CSI 2.38
    rCSI 9.69%
    PRS 92.11
  • erythroid lineage cell CL0000764
    CSI 2.33
    rCSI 15%
    PRS 91.1
  • hematopoietic stem cell CL0000037
    CSI 2.19
    rCSI 1.45%
    PRS 87.65
  • prostate gland microvascular endothelial cell CL2000059
    CSI 1.67
    rCSI 40.04%
    PRS 91.2
  • kidney interstitial cell CL1000500
    CSI 1.54
    rCSI 25.27%
    PRS 87.87
  • indirect pathway medium spiny neuron CL4023029
    CSI 1.14
    rCSI 27.4%
    PRS 68.2
  • lung microvascular endothelial cell CL2000016
    CSI 1.05
    rCSI 20.25%
    PRS 91.25
  • stromal cell CL0000499
    CSI 0.81
    rCSI 2.28%
    PRS 81.1
  • mesenchymal stem cell CL0000134
    CSI 0.23
    rCSI 2.5%
    PRS 89.04

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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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 [EMCN](/details-gene/51705) is a protein-coding gene located on chromosome 4 that encodes endomucin, a membrane-bound O-sialoglycoprotein. Functionally, endomucin is annotated with a role in [hematopoietic stem cell homeostasis](/details-cell/CL0000037) ([GO:0061484](https://www.ebi.ac.uk/QuickGO/term/GO:0061484)) and has been shown to exhibit anti-adhesive activity ([Link](https://doi.org/10.1016/s0014-5793(01)02520-0)). Expression data highlights [EMCN](/details-gene/51705) as a prominent marker of the vascular endothelium, with exceptionally high significance scores across a wide range of [endothelial cell](/details-cell/CL0000115) subtypes from different tissues. This suggests a conserved and critical role for the gene in maintaining endothelial identity and function throughout the body. ## Cellular Roles and Expression Landscape The **Overall** expression profile of [EMCN](/details-gene/51705) establishes it as a quintessential marker of the endothelial lineage. The gene demonstrates its highest significance in a diverse array of endothelial cells, underscoring its widespread importance in the vasculature. Top-ranked cell types include [retinal blood vessel endothelial cell](/details-cell/CL0002585) (CSI: 19.01), [cerebral cortex endothelial cell](/details-cell/CL1001602) (CSI: 18.35), [cardiac endothelial cell](/details-cell/CL0010008) (CSI: 15.18), and [capillary endothelial cell](/details-cell/CL0002144) (CSI: 13.74). This broad endothelial expression pattern across specialized tissues like the retina, brain, and heart suggests a fundamental role in vascular biology. Beyond the endothelium, [EMCN](/details-gene/51705) also shows significant expression in cells associated with the cardiovascular system and connective tissue, such as [myofibroblast cell](/details-cell/CL0000186) (CSI: 15.28), [cardiac muscle cell](/details-cell/CL0000746) (CSI: 14.93), and [vascular associated smooth muscle cell](/details-cell/CL0000359) (CSI: 7.88). Its presence in [melanocyte](/details-cell/CL0000148) (CSI: 8.99) is consistent with studies noting its expression in both normal and diseased skin ([Link](https://doi.org/10.1046/j.1523-1747.2002.19647.x)). The data collectively points to [EMCN](/details-gene/51705) as a key component of the vascular microenvironment. ## Pathways and Molecular Function [EMCN](/details-gene/51705) encodes endomucin, a protein localized to the [plasma membrane](/details-cell/CL0000037) ([GO:0005886](https://www.ebi.ac.uk/QuickGO/term/GO:0005886)) and the [extracellular region](/details-cell/CL0000037) ([GO:0005576](https://www.ebi.ac.uk/QuickGO/term/GO:0005576)). Its primary molecular characteristic is that of a sialoglycoprotein that mediates cell-cell interactions. Research has demonstrated that endomucin possesses anti-adhesive properties, which may serve to regulate the attachment of other cells to the endothelium ([Link](https://doi.org/10.1016/s0014-5793(01)02520-0)). This function is consistent with its annotated biological process of [hematopoietic stem cell homeostasis](/details-cell/CL0000037) ([GO:0061484](https://www.ebi.ac.uk/QuickGO/term/GO:0061484)). Endothelial cells form a critical component of the hematopoietic stem cell niche in the bone marrow, and the regulation of stem cell adhesion and release is vital for homeostasis. [EMCN](/details-gene/51705), through its anti-adhesive nature, may play a direct role in modulating this process. The general molecular function of [protein binding](/details-cell/CL0000037) ([GO:0005515](https://www.ebi.ac.uk/QuickGO/term/GO:0005515)) further supports its role in mediating interactions at the cell surface. ## Research Directions The specific and high-level expression of [EMCN](/details-gene/51705) on the surface of endothelial cells, combined with its known anti-adhesive function, suggests several avenues for future investigation. **Proposed Hypotheses:** 1. Given its anti-adhesive properties, [EMCN](/details-gene/51705) may function as a gatekeeper for leukocyte extravasation. Under homeostatic conditions, its expression could create a non-permissive surface on the endothelium, preventing inappropriate immune cell adhesion. During inflammation, targeted downregulation of [EMCN](/details-gene/51705) at the site of injury may be a required step to allow for leukocyte binding and transmigration into tissues. 2. The expression of [EMCN](/details-gene/51705) in diseased skin ([Link](https://doi.org/10.1046/j.1523-1747.2002.19647.x)) and its general role as an endothelial marker suggest it could be co-opted during tumor angiogenesis to support cancer progression. Overexpression on tumor-associated blood vessels might influence the tumor microenvironment or serve as a biomarker for neovascularization in cancers such as melanoma. **Experimental Approach:** To test the hypothesis that [EMCN](/details-gene/51705) regulates leukocyte adhesion (Hypothesis 1), an in vitro flow chamber assay could be employed. Human endothelial cells (e.g., HUVECs) could be cultured on microfluidic slides and transfected with siRNA to specifically knock down [EMCN](/details-gene/51705]. The adhesion of primary human leukocytes (e.g., neutrophils or T-cells) under physiological shear stress would be quantified via microscopy. A significant increase in stable leukocyte adhesion to [EMCN](/details-gene/51705)-deficient endothelial cells, particularly following stimulation with inflammatory cytokines like TNF-α, would support its role as a negative regulator of immune cell trafficking. **Therapeutic Potential:** As a cell-surface protein highly and specifically expressed on the endothelium, [EMCN](/details-gene/51705) presents an attractive target for therapies aimed at the vasculature. If its involvement in tumor angiogenesis is confirmed, it could be a target for antibody-drug conjugates (ADCs) designed to deliver cytotoxic agents specifically to tumor blood vessels, thereby disrupting the tumor's nutrient supply. This strategy would involve therapeutic **inhibition** or targeted destruction of [EMCN](/details-gene/51705)-positive cells, making it a promising candidate for anti-angiogenic cancer treatments.

Genular Protein ID: 2007637296

Symbol: MUCEN_HUMAN

Name: Endomucin

UniProtKB Accession Codes:

Q9ULC0 A8K716 B4E347 Q8NEY5 Q8WWE7 Q9NRM8

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 13 Ensembl 3 ExpressionAtlas 1 GO 3 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 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 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 3 RNAct 1 RefSeq 3 STRING 1 SignaLink 1 SwissPalm 1 TopDownProteomics 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 11418125

Title: Identification of human endomucin-1 and -2 as membrane-bound O-sialoglycoproteins with anti-adhesive activity.

PubMed ID: 11418125

DOI: 10.1016/s0014-5793(01)02520-0

PubMed ID: 12485444

Title: Expression of endomucin, a novel endothelial sialomucin, in normal and diseased human skin.

PubMed ID: 12485444

DOI: 10.1046/j.1523-1747.2002.19647.x

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15815621

Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

PubMed ID: 15815621

DOI: 10.1038/nature03466

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: 14722670

Title: Identification of tumour antigens by serological analysis of cDNA expression cloning.

PubMed ID: 14722670

DOI: 10.1007/s00262-003-0471-y

Sequence Information:

  • Length: 261
  • Mass: 27452
  • Checksum: 6C88C34F7A81F7D2
  • Sequence:
    • MELLQVTILF LLPSICSSNS TGVLEAANNS LVVTTTKPSI TTPNTESLQK NVVTPTTGTT 
PKGTITNELL KMSLMSTATF LTSKDEGLKA TTTDVRKNDS IISNVTVTSV TLPNAVSTLQ 
SSKPKTETQS SIKTTEIPGS VLQPDASPSK TGTLTSIPVT IPENTSQSQV IGTEGGKNAS 
TSATSRSYSS IILPVVIALI VITLSVFVLV GLYRMCWKAD PGTPENGNDQ PQSDKESVKL 
LTVKTISHES GEHSAQGKTK N