This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function ... See more...

Aliases for SOX4 Gene

Aliases for SOX4 Gene

  • SRY-Box Transcription Factor 4 2 3 5
  • SRY (Sex Determining Region Y)-Box 4 2 3
  • Transcription Factor SOX-4 3 4
  • SRY-Box 4 2 3
  • Ecotropic Viral Integration Site 16 3
  • SRY-Related HMG-Box Gene 4 3
  • CSS10 3
  • EVI16 3
  • SOX4 5

External Ids for SOX4 Gene

Previous GeneCards Identifiers for SOX4 Gene

  • GC06P021651
  • GC06P021701

Summaries for SOX4 Gene

Entrez Gene Summary for SOX4 Gene

  • This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for SOX4 Gene

SOX4 (SRY-Box Transcription Factor 4) is a Protein Coding gene. Diseases associated with SOX4 include Coffin-Siris Syndrome 10 and Coffin-Siris Syndrome 1. Among its related pathways are Signaling by GPCR and ERK Signaling. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is SOX11.

UniProtKB/Swiss-Prot Summary for SOX4 Gene

  • Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif (PubMed:30661772). Required for IL17A-producing Vgamma2-positive gamma-delta T-cell maturation and development, via binding to regulator loci of RORC to modulate expression (By similarity).

Gene Wiki entry for SOX4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SOX4 Gene

Genomics for SOX4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SOX4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J021592 Enhancer 0.3 CraniofacialAtlas 250.7 -1.1 -1081 0.2 PRDM1 SOX4 ENSG00000283480 HSALNG0048526 RF00017-4865
GH06J021586 Promoter/Enhancer 2 VISTA FANTOM5 ENCODE CraniofacialAtlas dbSUPER 17.2 -5.5 -5454 3.4 BCLAF1 MYC ZNF654 ZNF600 ZNF580 POLR2A ZSCAN16 ZIC2 ZBTB10 CTCF HSALNG0048526 SOX4 ENSG00000283480 piR-43164-056 RF00017-4865
GH06J021986 Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 12.5 +393.8 393774 2.4 IKZF1 ZNF592 REST BHLHE40 MNT ELF1 RXRA RARA GABPB1 RELA SOX4 lnc-PRL-4 piR-43105-568 PRL CASC15
GH06J020810 Enhancer 1.5 FANTOM5 Ensembl ENCODE CraniofacialAtlas 11.4 -783.0 -782990 3.9 NCOR1 IKZF1 JUND ZNF580 ZNF592 ATF2 NFIC CEBPB BHLHE40 ZNF639 SOX4 CDKAL1 ENSG00000233848 piR-50444-389
GH06J021263 Enhancer 1.4 FANTOM5 Ensembl ENCODE 11.2 -329.1 -329068 2.3 SP1 MYC ZNF600 ZNF580 ZNF592 ATF2 ZNF223 ZNF10 ZSCAN16 ZIC2 CDKAL1 SOX4 E2F3 ENSG00000287404 HSALNG0048495 HSALNG0048496
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOX4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SOX4

Top Transcription factor binding sites by QIAGEN in the SOX4 gene promoter:
  • AREB6
  • E47
  • FOXD3
  • Hand1
  • HTF
  • IRF-1
  • ITF-2
  • NCX
  • Pax-4a
  • STAT5B

Genomic Locations for SOX4 Gene

Latest Assembly
chr6:21,593,751-21,598,619
(GRCh38/hg38)
Size:
4,869 bases
Orientation:
Plus strand

Previous Assembly
chr6:21,593,982-21,598,850
(GRCh37/hg19 by Entrez Gene)
Size:
4,869 bases
Orientation:
Plus strand

chr6:21,593,972-21,598,847
(GRCh37/hg19 by Ensembl)
Size:
4,876 bases
Orientation:
Plus strand

Genomic View for SOX4 Gene

Genes around SOX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX4 Gene

Proteins for SOX4 Gene

  • Protein details for SOX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q06945-SOX4_HUMAN
    Recommended name:
    Transcription factor SOX-4
    Protein Accession:
    Q06945

    Protein attributes for SOX4 Gene

    Size:
    474 amino acids
    Molecular mass:
    47263 Da
    Quaternary structure:
    • Interacts with UBE2I.

neXtProt entry for SOX4 Gene

Post-translational modifications for SOX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SOX4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for SOX4

No data available for DME Specific Peptides for SOX4 Gene

Domains & Families for SOX4 Gene

Gene Families for SOX4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SOX4 Gene

Suggested Antigen Peptide Sequences for SOX4 Gene

GenScript: Design optimal peptide antigens:
  • Transcription factor SOX-4 (SOX4_HUMAN)
genes like me logo Genes that share domains with SOX4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SOX4 Gene

Function for SOX4 Gene

Molecular function for SOX4 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif (PubMed:30661772). Required for IL17A-producing Vgamma2-positive gamma-delta T-cell maturation and development, via binding to regulator loci of RORC to modulate expression (By similarity).
GENATLAS Biochemistry:
SRY related HMG box gene 4,transcriptional activator in embryonic heart,developing CNS,lung,tooth-bud,mesonephros,genitalia,pre B and T cells,controlled by progesterone,expressed in normal breast and in breast cancer cells,modulator of LINE retroposons promoter activity

Phenotypes From GWAS Catalog for SOX4 Gene

Gene Ontology (GO) - Molecular Function for SOX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IEA,ISS --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA,IDA 20049565
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA,ISS --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with SOX4: view
genes like me logo Genes that share phenotypes with SOX4: view

Human Phenotype Ontology for SOX4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SOX4 Gene

MGI Knock Outs for SOX4:

miRNA for SOX4 Gene

miRTarBase miRNAs that target SOX4
Targeted motifs for SOX4 Gene
HOMER Transcription Factor Regulatory Elements motif SOX4
  • Consensus sequence: YCTTTGTTCC Submotif: canonical Cell Type: proB GEO ID: GSE50066

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOX4

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for SOX4 Gene

Localization for SOX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SOX4 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Mitochondria (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SOX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA,IDA 16631117
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IEA --
GO:0005737 cytoplasm IEA,IDA 17875931
genes like me logo Genes that share ontologies with SOX4: view

Pathways & Interactions for SOX4 Gene

genes like me logo Genes that share pathways with SOX4: view

Pathways by source for SOX4 Gene

1 Qiagen pathway for SOX4 Gene
  • Molecular Mechanisms of Cancer

SIGNOR curated interactions for SOX4 Gene

Activates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SOX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA,ISS --
GO:0001841 neural tube formation IEA,ISS --
GO:0002328 pro-B cell differentiation IEA,ISS --
GO:0003183 mitral valve morphogenesis IEA,ISS --
GO:0003211 cardiac ventricle formation IEA,ISS --
genes like me logo Genes that share ontologies with SOX4: view

Drugs & Compounds for SOX4 Gene

(2) Drugs for SOX4 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for SOX4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SOX4: view

Transcripts for SOX4 Gene

mRNA/cDNA for SOX4 Gene

1 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOX4

Alternative Splicing Database (ASD) splice patterns (SP) for SOX4 Gene

No ASD Table

Relevant External Links for SOX4 Gene

GeneLoc Exon Structure for
SOX4

Expression for SOX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SOX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SOX4 Gene

This gene is overexpressed in Ovary (x4.9).

Protein differential expression in normal tissues from HIPED for SOX4 Gene

This gene is overexpressed in Brain (63.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SOX4 Gene



Protein tissue co-expression partners for SOX4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SOX4

SOURCE GeneReport for Unigene cluster for SOX4 Gene:

Hs.643910

mRNA Expression by UniProt/SwissProt for SOX4 Gene:

Q06945-SOX4_HUMAN
Tissue specificity: Testis, brain, and heart.

Evidence on tissue expression from TISSUES for SOX4 Gene

  • Lung(4.2)
  • Liver(4.2)
  • Nervous system(4.1)
  • Stomach(3.4)
  • Intestine(3.2)
  • Heart(3.2)
  • Blood(2.9)
  • Eye(2.8)
  • Kidney(2.8)
  • Muscle(2.7)
  • Skin(2.7)
  • Lymph node(2.4)
  • Bone marrow(2.3)
  • Spleen(2.2)
  • Pancreas(2.1)
genes like me logo Genes that share expression patterns with SOX4: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX4 Gene

Orthologs for SOX4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SOX4 29 30
  • 99.58 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SOX4 29 30
  • 91.45 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SOX4 29 30
  • 87.98 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sox4 29 16 30
  • 80 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sox4 29
  • 79.7 (n)
Oppossum
(Monodelphis domestica)
Mammalia SOX4 30
  • 79 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SOX4 30
  • 68 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 86 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sox4 29
  • 84.18 (n)
Str.9180 29
African clawed frog
(Xenopus laevis)
Amphibia MGC68880 29
Zebrafish
(Danio rerio)
Actinopterygii sox4b 29 30
  • 81.92 (n)
OneToMany
sox4a 30
  • 60 (a)
OneToMany
-- 29
Fruit Fly
(Drosophila melanogaster)
Insecta Sox14 30 31
  • 17 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea sem-2 30
  • 24 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10865 30
  • 20 (a)
OneToMany
Species where no ortholog for SOX4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SOX4 Gene

ENSEMBL:
Gene Tree for SOX4 (if available)
TreeFam:
Gene Tree for SOX4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SOX4: view image
Alliance of Genome Resources:
Additional Orthologs for SOX4

Paralogs for SOX4 Gene

(2) SIMAP similar genes for SOX4 Gene using alignment to 1 proteins:

  • SOX4_HUMAN
genes like me logo Genes that share paralogs with SOX4: view

Variants for SOX4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SOX4 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
1029670 Uncertain Significance: Coffin-Siris syndrome 10 21,595,280(+) C/A
NM_003107.3(SOX4):c.746C>A (p.Pro249His)
MISSENSE
870826 Uncertain Significance: not provided 21,594,812(+) T/A
NM_003107.3(SOX4):c.278T>A (p.Leu93Gln)
MISSENSE
873506 Uncertain Significance: SOX4-related neurodevelopmental disorder 21,595,000(+) G/C
NM_003107.3(SOX4):c.466G>C (p.Asp156His)
MISSENSE
931190 Uncertain Significance: Coffin-Siris syndrome 10 21,595,228(+) GCCGCCGCCGCCT/G
NM_003107.3(SOX4):c.697_708del (p.Ala233_Ser236del)
INFRAME_DELETION
982764 Uncertain Significance: Coffin-Siris syndrome 10 21,595,841(+) T/TC
NM_003107.3(SOX4):c.1308dup (p.Glu437fs)
FRAMESHIFT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SOX4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SOX4 Gene

Variant ID Type Subtype PubMed ID
nsv1145094 CNV deletion 24896259

Variation tolerance for SOX4 Gene

Residual Variation Intolerance Score: 41.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.10; 38.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SOX4 Gene

Human Gene Mutation Database (HGMD)
SOX4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SOX4
Leiden Open Variation Database (LOVD)
SOX4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SOX4 Gene

Disorders for SOX4 Gene

MalaCards: The human disease database

(12) MalaCards diseases for SOX4 Gene - From: LNC, OMI, CVR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
coffin-siris syndrome 10
  • css10
coffin-siris syndrome 1
  • css1
osteogenic sarcoma
  • osteosarcoma; osrc
adenoid cystic carcinoma
  • salivary gland adenoid cystic carcinoma
pediatric osteosarcoma
  • childhood osteosarcoma
- elite association - COSMIC cancer census association via MalaCards
Search SOX4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SOX4_HUMAN
  • Coffin-Siris syndrome 10 (CSS10) [MIM:618506]: A form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. CSS10 is characterized by mild to severe intellectual disability, global developmental delay, mild but distinct facial dysmorphism, fifth finger clinodactyly, and small stature. Hypotonia, ventricular septal defect, and spastic quadriparesis may also be present. CSS10 inheritance is autosomal dominant. {ECO:0000269 PubMed:30661772}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for SOX4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SOX4: view

No data available for Genatlas for SOX4 Gene

Publications for SOX4 Gene

  1. De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism. (PMID: 30661772) Zawerton A … Lefebvre V (American journal of human genetics 2019) 3 4 72
  2. Ubc9 interacts with SOX4 and represses its transcriptional activity. (PMID: 16631117) Pan X … Zhang X (Biochemical and biophysical research communications 2006) 3 4 22
  3. Assignment of Sox4 to mouse chromosome 13 bands A3-A5 by fluorescence in situ hybridization; refinement of the human SOX4 location to 6p22.3 and of SOX20 to chromosome 17p12.3. (PMID: 9730625) Critcher R … Farr CJ (Cytogenetics and cell genetics 1998) 2 3 22
  4. Characterization and mapping of the human SOX4 gene. (PMID: 8268656) Farr CJ … Goodfellow PN (Mammalian genome : official journal of the International Mammalian Genome Society 1993) 2 3 4
  5. Long non-coding RNA Sox4 promotes proliferation and migration by activating Wnt/β-catenin signaling pathway in osteosarcoma. (PMID: 29441981) Tian Z … Sun S (Die Pharmazie 2017) 3 72

Products for SOX4 Gene

Sources for SOX4 Gene