Details for: ANKRD39

Gene ID: 51239

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: ANKRD39

Ensembl ID: ENSG00000213337

Description: ankyrin repeat domain 39

Cell Significance Landscape

Associated with

Significant Cells

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

  • melanocyte of skin CL1000458
    CSI 15.49
    rCSI 21.11%
    PRS 53.74
  • basal cell of epidermis CL0002187
    CSI 7
    rCSI 12.41%
    PRS 55.12
  • suprabasal keratinocyte CL4033013
    CSI 6.41
    rCSI 10.46%
    PRS 53.92
  • retina horizontal cell CL0000745
    CSI 6.39
    rCSI 9.74%
    PRS 82.67
  • chondrocyte CL0000138
    CSI 5.88
    rCSI 9.35%
    PRS 79.58
  • placental villous trophoblast CL2000060
    CSI 5.67
    rCSI 8.76%
    PRS 84.3
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 5.5
    rCSI 7.06%
    PRS 81.88
  • granulocyte monocyte progenitor cell CL0000557
    CSI 4.96
    rCSI 4.29%
    PRS 88.66
  • multi-ciliated epithelial cell CL0005012
    CSI 4.92
    rCSI 4.91%
    PRS 79.84
  • plasmacytoid dendritic cell, human CL0001058
    CSI 4.08
    rCSI 2.85%
    PRS 88.98
  • effector CD8-positive, alpha-beta T cell CL0001050
    CSI 3.98
    rCSI 3.03%
    PRS 95.38
  • activated type II NK T cell CL0000931
    CSI 3.74
    rCSI 4.21%
    PRS 95.09
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 3.59
    rCSI 4.35%
    PRS 65.92
  • pro-B cell CL0000826
    CSI 3.42
    rCSI 2.83%
    PRS 87.7
  • duct epithelial cell CL0000068
    CSI 3.24
    rCSI 4.73%
    PRS 89.62
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 3.12
    rCSI 5.5%
    PRS 69.22
  • early lymphoid progenitor CL0000936
    CSI 3.08
    rCSI 2.7%
    PRS 89.61
  • interneuron CL0000099
    CSI 3.04
    rCSI 6.11%
    PRS 77.65
  • plasmablast CL0000980
    CSI 3
    rCSI 2.36%
    PRS 89.22
  • effector CD4-positive, alpha-beta T cell CL0001044
    CSI 2.94
    rCSI 8.45%
    PRS 97.22
  • helper T cell CL0000912
    CSI 2.86
    rCSI 4.05%
    PRS 82.9
  • epithelial cell of lung CL0000082
    CSI 2.86
    rCSI 2.37%
    PRS 86.58
  • activated CD4-positive, alpha-beta T cell CL0000896
    CSI 2.86
    rCSI 2.64%
    PRS 95.99
  • ON-bipolar cell CL0000749
    CSI 2.85
    rCSI 4.24%
    PRS 85.17
  • cerebral cortex GABAergic interneuron CL0010011
    CSI 2.75
    rCSI 8.13%
    PRS 86.25
  • lung ciliated cell CL1000271
    CSI 2.74
    rCSI 3.17%
    PRS 78.99
  • CD4-positive helper T cell CL0000492
    CSI 2.7
    rCSI 2.04%
    PRS 94.85
  • ionocyte CL0005006
    CSI 2.68
    rCSI 2.87%
    PRS 87.53
  • epithelial cell of lower respiratory tract CL0002632
    CSI 2.67
    rCSI 2.07%
    PRS 88.84
  • CD4-positive, CD25-positive, alpha-beta regulatory T cell CL0000792
    CSI 2.67
    rCSI 2.62%
    PRS 95.37
  • mesodermal cell CL0000222
    CSI 2.67
    rCSI 3.2%
    PRS 83.83
  • innate lymphoid cell CL0001065
    CSI 2.57
    rCSI 5.31%
    PRS 81.13
  • neural crest cell CL0011012
    CSI 2.51
    rCSI 1.98%
    PRS 76.38
  • CD4-positive, alpha-beta cytotoxic T cell CL0000934
    CSI 2.15
    rCSI 2.95%
    PRS 96.37
  • ciliated epithelial cell CL0000067
    CSI 2.13
    rCSI 1.87%
    PRS 75.82
  • ciliated cell CL0000064
    CSI 2.01
    rCSI 3.26%
    PRS 80.29
  • sst GABAergic cortical interneuron CL4023017
    CSI 1.82
    rCSI 2.35%
    PRS 70.81
  • bronchus fibroblast of lung CL2000093
    CSI 1.75
    rCSI 1.43%
    PRS 84.93
  • cytotoxic T cell CL0000910
    CSI 1.69
    rCSI 9.7%
    PRS 86.86
  • club cell CL0000158
    CSI 1.65
    rCSI 2.41%
    PRS 80.58
  • T-helper 1 cell CL0000545
    CSI 1.59
    rCSI 2.86%
    PRS 95.72
  • peripheral nervous system neuron CL2000032
    CSI 1.47
    rCSI 2.01%
    PRS 78.2
  • type B pancreatic cell CL0000169
    CSI 1.46
    rCSI 3.23%
    PRS 85.31
  • effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL0001062
    CSI 1.44
    rCSI 7.21%
    PRS 94.67
  • mesenchymal cell CL0008019
    CSI 1.44
    rCSI 3.65%
    PRS 79.44
  • retinal cone cell CL0000573
    CSI 1.07
    rCSI 1.73%
    PRS 76.71
  • Cajal-Retzius cell CL0000695
    CSI 0.55
    rCSI 4.29%
    PRS 88.49
  • erythroid progenitor cell CL0000038
    CSI 0.35
    rCSI 2.02%
    PRS 89.06

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 [ANKRD39](/details-gene/51239) is a protein-coding gene located on chromosome 2q11.2 that encodes Ankyrin Repeat Domain 39, a protein whose function is not yet well characterized. Ankyrin repeats are motifs known to mediate protein-protein interactions, suggesting [ANKRD39](/details-gene/51239) likely acts as a scaffold or adaptor protein within cellular complexes. **Overall** expression data highlight its exceptionally high significance in skin cells, particularly [melanocyte of skin](/details-cell/CL1000458) and epidermal [basal cell of epidermis](/details-cell/CL0002187), suggesting a primary role in cutaneous biology. Its expression is also noted in a diverse array of other cell types, including progenitor cells, specialized sensory neurons, and various immune cell subsets, indicating broader, context-specific functions. One study identified its expression in CD34+ hematopoietic stem/progenitor cells, consistent with a potential role in development and differentiation ([Link](https://pubmed.ncbi.nlm.nih.gov/11042152/)). ## Cellular Roles and Expression Landscape The expression profile of [ANKRD39](/details-gene/51239) strongly indicates a specialized role in the integumentary system. **Overall**, the gene shows its highest significance in [melanocyte of skin](/details-cell/CL1000458) (CSI: 15.49), followed by [basal cell of epidermis](/details-cell/CL0002187) (CSI: 7.00) and [suprabasal keratinocyte](/details-cell/CL4033013) (CSI: 6.41). This pattern suggests that [ANKRD39](/details-gene/51239) may be integral to the function, differentiation, or structural organization of the epidermis. Beyond the skin, [ANKRD39](/details-gene/51239) demonstrates a broad but specific expression pattern in other tissues. It is a significant marker in specialized cell types such as [retina horizontal cell](/details-cell/CL0000745) (CSI: 6.39) and structural cells like [chondrocyte](/details-cell/CL0000138) (CSI: 5.88). Furthermore, its relevance is noted in several progenitor and developmental cell populations, including [placental villous trophoblast](/details-cell/CL2000060) (CSI: 5.67), [neuroblast (sensu Vertebrata)](/details-cell/CL0000031) (CSI: 5.50), and [granulocyte monocyte progenitor cell](/details-cell/CL0000557) (CSI: 4.96). This expression in multiple precursor cell types hints at a potential role in lineage specification or maintenance of an undifferentiated state. Finally, a consistent signal is observed across various immune cell lineages, including innate-like [plasmacytoid dendritic cell, human](/details-cell/CL0001058) (CSI: 4.08) and adaptive lymphocytes such as [effector CD8-positive, alpha-beta T cell](/details-cell/CL0001050) (CSI: 3.98) and [pro-B cell](/details-cell/CL0000826) (CSI: 3.42). This suggests that [ANKRD39](/details-gene/51239) may participate in the development or function of both the innate and adaptive immune systems. ## Pathways and Molecular Function The precise molecular function of [ANKRD39](/details-gene/51239) remains largely undefined, as reflected by its current high-level Gene Ontology annotations for [Biological_process](/details-go/GO:0008150), [Molecular_function](/details-go/GO:0003674), and [Cellular_component](/details-go/GO:0005575). However, its identity as an ankyrin repeat-containing protein provides a strong clue to its mechanism of action. Ankyrin repeats are one of the most common protein-protein interaction motifs in nature, typically forming elongated structures that act as scaffolds to assemble multi-protein complexes. Therefore, it is plausible that [ANKRD39](/details-gene/51239) functions as an adaptor or scaffolding protein. In the context of its high expression in melanocytes and keratinocytes, it may be involved in organizing protein complexes critical for melanin synthesis/transport, cell-cell adhesion, or cytoskeletal architecture. Its presence in various progenitor cells suggests a potential role in assembling signaling complexes that regulate cell fate decisions during differentiation. Similarly, in immune cells, it could serve as a platform for components of signal transduction pathways downstream of antigen or cytokine receptors. ## Research Directions The specific expression patterns and protein domain architecture of [ANKRD39](/details-gene/51239) provide a basis for several testable hypotheses regarding its function. 1. **Hypothesis on Skin Pigmentation:** Given its exceptional significance in [melanocyte of skin](/details-cell/CL1000458), [ANKRD39](/details-gene/51239) may be a critical regulator of melanogenesis or melanosome transport. It could act as a scaffold to link melanosomes to motor proteins or to organize the enzymatic machinery responsible for melanin synthesis. 2. **Hypothesis on Progenitor Cell Biology:** Based on its consistent expression across multiple progenitor cell types ([neuroblast (sensu Vertebrata)](/details-cell/CL0000031), [granulocyte monocyte progenitor cell](/details-cell/CL0000557), [pro-B cell](/details-cell/CL0000826)) and in hematopoietic stem cells ([Link](https://pubmed.ncbi.nlm.nih.gov/11042152/)), [ANKRD39](/details-gene/51239) may function as a general regulator of stemness or early lineage commitment, perhaps by scaffolding key transcription factors or signaling proteins that maintain pluripotency or drive initial differentiation steps. **Proposed Experiment:** To test the first hypothesis, a functional genomics approach in a relevant cell model is warranted. CRISPR-Cas9 could be used to knock out [ANKRD39](/details-gene/51239) in a human melanocyte cell line (e.g., MNT-1). The resulting phenotype would be assessed by quantifying melanin content, evaluating melanosome morphology and distribution via electron microscopy, and analyzing the expression of key melanocyte-specific genes (e.g., *TYR*, *MITF*, *PMEL*) using qRT-PCR and Western blot. Co-immunoprecipitation followed by mass spectrometry could also be employed to identify its protein interaction partners. **Therapeutic Potential:** The therapeutic potential of [ANKRD39](/details-gene/51239) is currently speculative due to the lack of functional data. However, its highly specific and significant expression in melanocytes suggests it could be a candidate for further investigation in pigmentation disorders or melanoma. If found to be essential for melanoma cell survival and overexpressed compared to normal tissues, its role as a scaffold protein could make it a target for therapeutic intervention, potentially through small molecules that disrupt its key protein-protein interactions. Inhibition would likely be the preferred strategy in a cancer context.

Genular Protein ID: 857860676

Symbol: ANR39_HUMAN

Name: Ankyrin repeat domain-containing protein 39

UniProtKB Accession Codes:

Q53RE8 Q59FU2 Q8N5X5 Q9P0S5

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 2 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 2 KEGG 1 MANE-Select 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRINTS 1 PRO 1 PROSITE 2 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 Pumba 1 RNAct 1 RefSeq 1 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 11042152

Title: Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells.

PubMed ID: 11042152

DOI: 10.1101/gr.140200

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: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

Sequence Information:

  • Length: 183
  • Mass: 19651
  • Checksum: 11C13234A456CD63
  • Sequence:
    • MATPRPCADG PCCSHPSAVL GVQQTLEEMD FERGIWSAAL NGDLGRVKHL IQKAEDPSQP 
DSAGYTALHY ASRNGHYAVC QFLLESGAKC DAQTHGGATA LHRASYCGHT EIARLLLSHG 
SNPRVVDDDG MTSLHKAAER GHGDICSLLL QHSPALKAIR DRKARLACDL LPCNSDLRDL 
LSS