Details for: SOX30

Gene ID: 11063

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: SOX30

Ensembl ID: ENSG00000039600

Description: SRY-box transcription factor 30

Cell Significance Landscape

Associated with

Significant Cells

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

  • ependymal cell CL0000065
    CSI 3.51
    rCSI 7.13%
    PRS 99.64

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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    • 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 [SOX30](/details-gene/11063) is a protein-coding gene located on chromosome 5q33.3 that encodes the SRY-box transcription factor 30. As a member of the SOX (SRY-box) family, it functions as a sequence-specific DNA-binding protein involved in the regulation of transcription. Functional annotations indicate that [SOX30](/details-gene/11063) can act as both a transcriptional activator and repressor ([GO:0001228](https://www.ebi.ac.uk/QuickGO/term/GO:0001228), [GO:0001227](https://www.ebi.ac.uk/QuickGO/term/GO:0001227)), playing significant roles in spermatid development ([GO:0007286](https://www.ebi.ac.uk/QuickGO/term/GO:0007286)) and the negative regulation of the Wnt signaling pathway ([GO:0030178](https://www.ebi.ac.uk/QuickGO/term/GO:0030178)). While initial studies highlighted its germ cell-specific expression ([Link](https://doi.org/10.1093/nar/27.12.2503)), expression data also points to a highly significant presence in [ependymal cells](/details-cell/CL0000065). Recent research has implicated [SOX30](/details-gene/11063) as a tumor suppressor, particularly in lung cancer, where it inhibits metastasis by modulating beta-catenin activity ([Link](https://doi.org/10.1016/j.ebiom.2018.04.026)). ## Cellular Roles and Expression Landscape The expression profile of [SOX30](/details-gene/11063) suggests specialized roles in distinct cellular contexts. **Overall** expression analysis identifies [ependymal cells](/details-cell/CL0000065) as the site of its most significant expression (CSI: 3.51). These epithelial cells line the ventricles of the brain and the central canal of the spinal cord, suggesting a potential role for [SOX30](/details-gene/11063) in the central nervous system, possibly related to cerebrospinal fluid homeostasis or blood-brain barrier maintenance. In addition to this finding, published literature provides crucial context, identifying [SOX30](/details-gene/11063) as a germ cell-specific gene, particularly important during male gametogenesis ([Link](https://doi.org/10.1093/nar/27.12.2503)). This is strongly supported by its functional annotation in spermatid development ([GO:0007286](https://www.ebi.ac.uk/QuickGO/term/GO:0007286)). This dual-context expression pattern in both the central nervous system and the reproductive system indicates that the function of [SOX30](/details-gene/11063) is highly dependent on the specific cellular environment. ## Pathways and Molecular Function [SOX30](/details-gene/11063) functions primarily as a DNA-binding transcription factor located in the nucleus ([GO:0005634](https://www.ebi.ac.uk/QuickGO/term/GO:0005634)) and associated with chromatin ([GO:0000785](https://www.ebi.ac.uk/QuickGO/term/GO:0000785)). Its molecular activities are diverse, encompassing both positive and negative regulation of transcription by RNA polymerase II ([GO:0045944](https://www.ebi.ac.uk/QuickGO/term/GO:0045944), [GO:0000122](https://www.ebi.ac.uk/QuickGO/term/GO:0000122)). A key function of [SOX30](/details-gene/11063) is its role as a negative regulator of the Wnt signaling pathway ([GO:0030178](https://www.ebi.ac.uk/QuickGO/term/GO:0030178)). Research has demonstrated that it achieves this by directly binding to beta-catenin ([GO:0008013](https://www.ebi.ac.uk/QuickGO/term/GO:0008013)), a central effector of the pathway. This interaction inhibits beta-catenin's transcriptional activity and promotes its degradation, thereby suppressing the expression of Wnt target genes involved in cell proliferation and migration ([Link](https://doi.org/10.1016/j.ebiom.2018.04.026)). This mechanism underpins its described tumor-suppressive properties. Furthermore, its involvement in spermatid development ([GO:0007286](https://www.ebi.ac.uk/QuickGO/term/GO:0007286)) and proacrosomal vesicle fusion ([GO:0120211](https://www.ebi.ac.uk/QuickGO/term/GO:0120211)) highlights its essential role in the intricate transcriptional programs that govern male fertility. ## Research Directions The established role of [SOX30](/details-gene/11063) as a Wnt signaling inhibitor and tumor suppressor in lung cancer provides a strong basis for further investigation into its clinical relevance and fundamental biology. Based on the available data, several testable hypotheses can be proposed: 1. **Hypothesis:** Epigenetic silencing (e.g., promoter hypermethylation) of [SOX30](/details-gene/11063) is a common mechanism contributing to metastasis in other epithelial cancers with aberrant Wnt signaling, such as colorectal or breast cancer. 2. **Hypothesis:** In [ependymal cells](/details-cell/CL0000065), [SOX30](/details-gene/11063) regulates the integrity of the blood-cerebrospinal fluid barrier by controlling the transcription of cell-cell junction proteins, and its expression is modulated in response to neuroinflammatory signals or corticosteroids ([GO:0031960](https://www.ebi.ac.uk/QuickGO/term/GO:0031960)). 3. **Hypothesis:** Mutations or copy number variations in the [SOX30](/details-gene/11063) gene are associated with specific forms of male infertility characterized by defects in spermatid maturation and acrosome formation. **Experimental Approach:** To test the first hypothesis regarding its role in other cancers, a compelling experiment would be to analyze patient-derived colorectal cancer datasets (e.g., from TCGA) to correlate [SOX30](/details-gene/11063) promoter methylation status with its mRNA expression levels and patient metastatic status. Experimentally, one could use CRISPR-Cas9 to knock out [SOX30](/details-gene/11063) in a low-metastatic colorectal cancer cell line. The impact on Wnt pathway activity could be measured via a TCF/LEF reporter assay, while the effect on metastatic potential could be assessed using in vitro transwell invasion assays and in vivo mouse models of metastasis. **Therapeutic Potential:** As a tumor suppressor that is often silenced in cancer, [SOX30](/details-gene/11063) itself is not a target for inhibition. Instead, therapeutic strategies would focus on its **reactivation**. If its silencing is due to promoter hypermethylation, treatment with epigenetic drugs such as DNA methyltransferase (DNMT) inhibitors could restore its expression and suppress metastasis. Alternatively, developing small molecules that mimic its inhibitory effect on the SOX30-beta-catenin interaction could serve as a targeted therapy for cancers with activated Wnt signaling.

Genular Protein ID: 4292268425

Symbol: SOX30_HUMAN

Name: Transcription factor SOX-30

UniProtKB Accession Codes:

O94993 O94995 Q8IYX6

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CDD 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 2 ExpressionAtlas 1 GO 20 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PDB 1 PDBsum 1 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 RNAct 1 RefSeq 3 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 10359848

Title: Identification of a novel Sry-related gene and its germ cell-specific expression.

PubMed ID: 10359848

DOI: 10.1093/nar/27.12.2503

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: 29739711

Title: SOX30 Inhibits Tumor Metastasis through Attenuating Wnt-Signaling via Transcriptional and Posttranslational Regulation of beta-Catenin in Lung Cancer.

PubMed ID: 29739711

DOI: 10.1016/j.ebiom.2018.04.026

Sequence Information:

  • Length: 753
  • Mass: 81854
  • Checksum: E9BF1409EE7FE81D
  • Sequence:
    • MERARPEPPP QPRPLRPAPP PLPVEGTSFW AAAMEPPPSS PTLSAAASAT LASSCGEAVA 
SGLQPAVRRL LQVKPEQVLL LPQPQAQNEE AAASSAQARL LQFRPDLRLL QPPTASDGAT 
SRPELHPVQP LALHVKAKKQ KLGPSLDQSV GPRGAVETGP RASRVVKLEG PGPALGYFRG 
DEKGKLEAEE VMRDSMQGGA GKSPAAIREG VIKTEEPERL LEDCRLGAEP ASNGLVHGSA 
EVILAPTSGA FGPHQQDLRI PLTLHTVPPG ARIQFQGAPP SELIRLTKVP LTPVPTKMQS 
LLEPSVKIET KDVPLTVLPS DAGIPDTPFS KDRNGHVKRP MNAFMVWARI HRPALAKANP 
AANNAEISVQ LGLEWNKLSE EQKKPYYDEA QKIKEKHREE FPGWVYQPRP GKRKRFPLSV 
SNVFSGTTQN IISTNPTTVY PYRSPTYSVV IPSLQNPITH PVGETSPAIQ LPTPAVQSPS 
PVTLFQPSVS SAAQVAVQDP SLPVYPALPP QRFTGPSQTD THQLHSEATH TVKQPTPVSL 
ESANRISSSA STAHARFATS TIQPPREYSS VSPCPRSAPI PQASPIPHPH VYQPPPLGHP 
ATLFGTPPRF SFHHPYFLPG PHYFPSSTCP YSRPPFGYGN FPSSMPECLS YYEDRYPKHE 
GIFSTLNRDY SFRDYSSECT HSENSRSCEN MNGTSYYNSH SHSGEENLNP VPQLDIGTLE 
NVFTAPTSTP SSIQQVNVTD SDEEEEEKVL RDL

Genular Protein ID: 2479629003

Symbol: B4DXW7_HUMAN

Name: N/A

UniProtKB Accession Codes:

B4DXW7

Database IDs:

Antibodypedia 1 Bgee 1 BioGRID-ORCS 1 CDD 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 2 GO 4 Gene3D 1 GeneTree 1 HGNC 1 HOGENOM 1 InterPro 3 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PROSITE 2 PROSITE-ProRule 1 PeptideAtlas 1 Pfam 1 Proteomes 2 ProteomicsDB 2 RefSeq 3 SAM 1 SMART 1 SUPFAM 1 UCSC 1 VEuPathDB 1

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 15372022

Title: The DNA sequence and comparative analysis of human chromosome 5.

PubMed ID: 15372022

DOI: 10.1038/nature02919

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

Sequence Information:

  • Length: 448
  • Mass: 49882
  • Checksum: 29894EEBBD98FCEF
  • Sequence:
    • MEKCCRGKEQ SLLCIQQGIP DTPFSKDRNG HVKRPMNAFM VWARIHRPAL AKANPAANNA 
EISVQLGLEW NKLSEEQKKP YYDEAQKIKE KHREEFPGWV YQPRPGKRKR FPLSVSNVFS 
GTTQNIISTN PTTVYPYRSP TYSVVIPSLQ NPITHPVGET SPAIQLPTPA VQSPSPVTLF 
QPSVSSAAQV AVQDPSLPVY PALPPQRFTG PSQTDTHQLH SEATHTVKQP TPVSLESANR 
ISSSASTAHA RFATSTIQPP REYSSVSPCP RSAPIPQASP IPHPHVYQPP PLGHPATLFG 
TPPRFSFHHP YFLPGPHYFP SSTCPYSRPP FGYGNFPSSM PECLSYYEDR YPKHEGIFST 
LNRDYSFRDY SSECTHSENS RSCENMNGTS YYNSHSHSGE ENLNPVPQLD IGTLENVFTA 
PTSTPSSIQQ VNVTDSDEEE EEKVLRDL