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Aliases for SOX9 Gene

Aliases for SOX9 Gene

  • SRY (Sex Determining Region Y)-Box 9 2 3
  • SRA1 3 6
  • CMD1 3 6
  • Campomelic Dysplasia, Autosomal Sex-Reversal 2
  • SRY (Sex-Determining Region Y)-Box 9 Protein 3
  • SRY-Related HMG-Box, Gene 9 3
  • Transcription Factor SOX-9 3
  • CMPD1 3

External Ids for SOX9 Gene

Previous HGNC Symbols for SOX9 Gene

  • CMD1
  • CMPD1

Previous GeneCards Identifiers for SOX9 Gene

  • GC17P069873
  • GC17P073111
  • GC17P070581
  • GC17P070714
  • GC17P067628
  • GC17P070117
  • GC17P065510

Summaries for SOX9 Gene

Entrez Gene Summary for SOX9 Gene

  • The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome campomelic dysplasia, frequently with sex reversal. [provided by RefSeq, Jul 2008]

GeneCards Summary for SOX9 Gene

SOX9 (SRY (Sex Determining Region Y)-Box 9) is a Protein Coding gene. Diseases associated with SOX9 include pierre robin syndrome and campomelic dysplasia. Among its related pathways are ERK Signaling and GPCR Pathway. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and protein kinase activity. An important paralog of this gene is SOX3.

UniProtKB/Swiss-Prot for SOX9 Gene

  • Plays an important role in the normal skeletal development. May regulate the expression of other genes involved in chondrogenesis by acting as a transcription factor for these genes

Gene Wiki entry for SOX9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX9 Gene

Genomics for SOX9 Gene

Regulatory Elements for SOX9 Gene

Genomic Location for SOX9 Gene

72,121,020 bp from pter
72,126,420 bp from pter
5,401 bases
Plus strand

Genomic View for SOX9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SOX9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX9 Gene

Proteins for SOX9 Gene

  • Protein details for SOX9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transcription factor SOX-9
    Protein Accession:
    Secondary Accessions:
    • Q53Y80

    Protein attributes for SOX9 Gene

    509 amino acids
    Molecular mass:
    56137 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for SOX9 Gene

neXtProt entry for SOX9 Gene

Proteomics data for SOX9 Gene at MOPED

Post-translational modifications for SOX9 Gene

  • Ubiquitination at Lys141
  • Modification sites at PhosphoSitePlus

Other Protein References for SOX9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SOX9 Gene

Domains for SOX9 Gene

Gene Families for SOX9 Gene

  • SOX :SRY (sex determining region Y)-boxes

Protein Domains for SOX9 Gene


Suggested Antigen Peptide Sequences for SOX9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • P48436
  • Contains 1 HMG box DNA-binding domain.
genes like me logo Genes that share domains with SOX9: view

Function for SOX9 Gene

Molecular function for SOX9 Gene

GENATLAS Biochemistry: SRY related HMG box gene 9,expressed in the genital ridge of both sexes,in chondrocytes and in non-skeletal tissues,likely involved in the differentiation of Sertoli cells,potent activator of the chondrocyte-specific enhancer of COL2A1,required for cartilage formation,important mediator of the BMP2 and Indian hedgehog (IHH) sinaling pathways in osteogenic cells,modulator of LINE retroposons promoter activity
UniProtKB/Swiss-Prot Function: Plays an important role in the normal skeletal development. May regulate the expression of other genes involved in chondrogenesis by acting as a transcription factor for these genes

Gene Ontology (GO) - Molecular Function for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding --
GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity --
GO:0001046 core promoter sequence-specific DNA binding IDA 20530484
GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA 20484372
GO:0001158 enhancer sequence-specific DNA binding ISS --
genes like me logo Genes that share ontologies with SOX9: view
genes like me logo Genes that share phenotypes with SOX9: view

Animal Models for SOX9 Gene

MGI Knock Outs for SOX9:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for SOX9 Gene

Localization for SOX9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX9 Gene

Subcellular locations from

Jensen Localization Image for SOX9 Gene COMPARTMENTS Subcellular localization image for SOX9 gene
Compartment Confidence
nucleus 5
extracellular 3
cytoskeleton 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 10805756
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex --
GO:0043234 protein complex IDA 20530484
GO:0044798 nuclear transcription factor complex IEA --
genes like me logo Genes that share ontologies with SOX9: view

Pathways for SOX9 Gene

genes like me logo Genes that share pathways with SOX9: view

Pathways by source for SOX9 Gene

Gene Ontology (GO) - Biological Process for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 8640233
GO:0001502 cartilage condensation ISS --
GO:0001503 ossification IEA --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001708 cell fate specification ISS --
genes like me logo Genes that share ontologies with SOX9: view

Compounds for SOX9 Gene

(21) Novoseek inferred chemical compound relationships for SOX9 Gene

Compound -log(P) Hits PubMed IDs
dmrt 70.8 2
glycosaminoglycan 64.3 12
alginate 53.1 3
cmps 46.7 2
testosterone 20.9 6
genes like me logo Genes that share compounds with SOX9: view

Transcripts for SOX9 Gene

mRNA/cDNA for SOX9 Gene

(205) Selected AceView cDNA sequences:
(6) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SOX9 Gene

SRY (sex determining region Y)-box 9:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SOX9 Gene

No ASD Table

Relevant External Links for SOX9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SOX9 Gene

mRNA expression in normal human tissues for SOX9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SOX9 Gene

This gene is overexpressed in Minor Salivary Gland (4.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SOX9 Gene

SOURCE GeneReport for Unigene cluster for SOX9 Gene Hs.647409

genes like me logo Genes that share expressions with SOX9: view

No data available for mRNA Expression by UniProt/SwissProt for SOX9 Gene

Orthologs for SOX9 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SOX9 35
  • 99.87 (n)
  • 99.8 (a)
SOX9 36
  • 100 (a)
(Bos Taurus)
Mammalia SOX9 35
  • 91.09 (n)
  • 92.67 (a)
SOX9 36
  • 95 (a)
(Canis familiaris)
Mammalia SOX9 35
  • 93.52 (n)
  • 94.3 (a)
SOX9 36
  • 96 (a)
(Mus musculus)
Mammalia Sox9 35
  • 89.35 (n)
  • 92.9 (a)
Sox9 16
Sox9 36
  • 97 (a)
(Monodelphis domestica)
Mammalia SOX9 36
  • 90 (a)
(Ornithorhynchus anatinus)
Mammalia SOX9 36
  • 88 (a)
(Rattus norvegicus)
Mammalia Sox9 35
  • 89.02 (n)
  • 92.7 (a)
(Gallus gallus)
Aves SOX9 35
  • 85.58 (n)
  • 88.82 (a)
SOX9 36
  • 87 (a)
(Anolis carolinensis)
Reptilia SOX9 36
  • 81 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1690 35
tropical clawed frog
(Silurana tropicalis)
Amphibia sox9 35
  • 77.59 (n)
  • 85.39 (a)
Str.15584 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11885 35
(Danio rerio)
Actinopterygii sox9a 35
  • 76.81 (n)
  • 81.11 (a)
sox9a 36
  • 79 (a)
sox9b 36
  • 68 (a)
fruit fly
(Drosophila melanogaster)
Insecta Sox100B 36
  • 28 (a)
Sox100B 37
  • 61 (a)
(Caenorhabditis elegans)
Secernentea sox-4 36
  • 34 (a)
Species with no ortholog for SOX9:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SOX9 Gene

Gene Tree for SOX9 (if available)
Gene Tree for SOX9 (if available)

Paralogs for SOX9 Gene

genes like me logo Genes that share paralogs with SOX9: view

Variants for SOX9 Gene

Sequence variations from dbSNP and Humsavar for SOX9 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs929651 -- 72,123,970(-) GGTGC(C/T)GCCGG synonymous-codon, reference
rs1042667 -- 72,124,410(+) GGCGA(A/C)GATGG utr-variant-3-prime
rs1042672 -- 72,125,197(+) TTTAT(C/G)ATATA utr-variant-3-prime
rs1042673 -- 72,125,198(+) TTATC(A/G)TATAT utr-variant-3-prime
rs1042678 -- 72,125,967(+) TCTCT(A/G)CATCT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SOX9 Gene

Variant ID Type Subtype PubMed ID
nsv833530 CNV Gain+Loss 17160897

Relevant External Links for SOX9 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SOX9 Gene

Disorders for SOX9 Gene

(1) OMIM Diseases for SOX9 Gene (608160)


  • Campomelic dysplasia (CMD1) [MIM:114290]: A rare, often lethal, osteochondrodysplasia characterized by congenital bowing and angulation of long bones. Other skeletal defects include unusually small scapula, deformed pelvis and spine, and a missing pair of ribs. Craniofacial and ear defects are common. Most patients die soon after birth due to respiratory distress which has been attributed to hypoplasia of the tracheobronchial cartilage and small thoracic cage. Up to two-thirds of affected XY individuals have genital defects or may develop as phenotypic females. {ECO:0000269 PubMed:10446171, ECO:0000269 PubMed:10951468, ECO:0000269 PubMed:11323423, ECO:0000269 PubMed:11754051, ECO:0000269 PubMed:12783851, ECO:0000269 PubMed:19921652, ECO:0000269 PubMed:20513132, ECO:0000269 PubMed:7485151, ECO:0000269 PubMed:9002675, ECO:0000269 PubMed:9452059}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 46,XX sex reversal 2 (SRXX2) [MIM:278850]: A condition in which male gonads develop in a genetic female (female to male sex reversal). {ECO:0000269 PubMed:21208124}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) University of Copenhagen DISEASES for SOX9 Gene

(28) Novoseek inferred disease relationships for SOX9 Gene

Disease -log(P) Hits PubMed IDs
campomelic dysplasia 97.1 74
osteochondrodysplasias 56.9 1
swyer syndrome 56.1 1
skeletal dysplasia 54.3 2
osteoarthritis 52.5 5

Relevant External Links for SOX9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SOX9: view

Publications for SOX9 Gene

  1. Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal. (PMID: 7485151) Kwok C. … Schafer A.J. (Am. J. Hum. Genet. 1995) 3 4 23
  2. Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene. (PMID: 7990924) Foster J.W. … Schafer A.J. (Nature 1994) 3 4 23
  3. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. (PMID: 8001137) Wagner T. … Scherer G. (Cell 1994) 3 4 23
  4. Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations. (PMID: 9002675) Meyer J. … Scherer G. (Hum. Mol. Genet. 1997) 3 4 23
  5. Functional and structural studies of wild type SOX9 and mutations causing campomelic dysplasia. (PMID: 10446171) McDowall S. … Harley V. (J. Biol. Chem. 1999) 3 4 23

Products for SOX9 Gene

Sources for SOX9 Gene

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