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 rever... See more...

Aliases for SOX9 Gene

Aliases for SOX9 Gene

  • SRY-Box Transcription Factor 9 2 3
  • SRY-Box 9 2 3 5
  • Transcription Factor SOX-9 3 4
  • SRY (Sex-Determining Region Y)-Box 9 Protein 3
  • Campomelic Dysplasia, Autosomal Sex-Reversal 2
  • SRY (Sex Determining Region Y)-Box 9 2
  • SRY (Sex Determining Region Y)-Box9 3
  • SRY-Related HMG-Box, Gene 9 3
  • SRXY10 3
  • SRXX2 3
  • CMPD1 3
  • SRA1 3
  • CMD1 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-Box Transcription Factor 9) is a Protein Coding gene. Diseases associated with SOX9 include Campomelic Dysplasia and 46,Xy Sex Reversal 10. Among its related pathways are Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers and Deactivation of the beta-catenin transactivating complex. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and protein kinase activity. An important paralog of this gene is SOX10.

UniProtKB/Swiss-Prot Summary for SOX9 Gene

  • Transcriptional regulator that plays a role in chondrocytes differentiation and skeletal development (PubMed:24038782). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with ZNF219 (By similarity).

Gene Wiki entry for SOX9 Gene

Additional gene information for SOX9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SOX9 Gene

Genomics for SOX9 Gene

GeneHancer (GH) Regulatory Elements for SOX9 Gene

Promoters and enhancers for SOX9 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
GH17J072116 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 750.6 +1.0 1035 12.1 SIN3A SP1 CTCF MLX RBPJ TCF7L2 CTBP1 NR2F1 NR2F6 ATF1 SOX9 SLC39A11 piR-47675-052 SOX9-AS1
GH17J072418 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 6.7 +300.9 300944 6.1 SIN3A ZNF24 SP1 ZBTB6 MLX RBPJ POLR2A NR2F1 NR2F6 CREB1 C17orf80 SOX9 ENSG00000263680 lnc-SOX9-7 LINC00511 LINC00673
GH17J072715 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 6 +595.2 595165 1.8 RBPJ POLR2A ATF1 CREB1 ZBTB33 ELF3 MAFK TFE3 ELF1 ZNF384 SOX9 SLC39A11 RF00017-2529 RF00017-2530
GH17J072385 Enhancer 1.3 Ensembl ENCODE dbSUPER 5 +269.7 269681 10.6 SP1 ZBTB6 MLX RBPJ NR2F6 ATF1 CREB1 MIXL1 ZNF362 RELA LINC00511 SOX9 lnc-SOX9-7 LINC02003 LINC00673
GH17J072444 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 2.3 +325.0 325030 3.9 SIN3A MLX RBPJ NR2F1 NR2F6 ATF1 CREB1 MIXL1 NFYC ZNF652 CDC42EP4 SSTR2 ENSG00000265010 SOX9 ENSG00000263680 lnc-SOX9-7 lnc-SOX9-8 LINC00511 LINC00673
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOX9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOX9 gene promoter:
  • MyoD
  • Nkx2-5
  • PPAR-gamma1
  • PPAR-gamma2
  • Sox9
  • SRY

Genomic Locations for SOX9 Gene

Genomic Locations for SOX9 Gene
chr17:72,121,020-72,126,420
(GRCh38/hg38)
Size:
5,401 bases
Orientation:
Plus strand
chr17:70,117,161-70,122,561
(GRCh37/hg19)
Size:
5,401 bases
Orientation:
Plus strand

Genomic View for SOX9 Gene

Genes around SOX9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    P48436-SOX9_HUMAN
    Recommended name:
    Transcription factor SOX-9
    Protein Accession:
    P48436
    Secondary Accessions:
    • Q53Y80

    Protein attributes for SOX9 Gene

    Size:
    509 amino acids
    Molecular mass:
    56137 Da
    Quaternary structure:
    • Interacts (via C-terminus) with ZNF219. Interacts with DDRGK1 (PubMed:28263186).

    Three dimensional structures from OCA and Proteopedia for SOX9 Gene

neXtProt entry for SOX9 Gene

Post-translational modifications for SOX9 Gene

  • Ubiquitinated. Ubiquitination leads to proteasomal degradation and is negatively regulated by DDRGK1.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SOX9 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for SOX9

No data available for DME Specific Peptides for SOX9 Gene

Domains & Families for SOX9 Gene

Gene Families for SOX9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SOX9 Gene

Suggested Antigen Peptide Sequences for SOX9 Gene

GenScript: Design optimal peptide antigens:
  • Transcription factor SOX-9 (SOX9_HUMAN)
genes like me logo Genes that share domains with SOX9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SOX9 Gene

Function for SOX9 Gene

Molecular function for SOX9 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional regulator that plays a role in chondrocytes differentiation and skeletal development (PubMed:24038782). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with ZNF219 (By similarity).
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

Phenotypes From GWAS Catalog for SOX9 Gene

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 IEA --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 20530484
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS,IDA 19274049
GO:0001158 enhancer sequence-specific DNA binding ISS,IEA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA,IDA 20484372
genes like me logo Genes that share ontologies with SOX9: view
genes like me logo Genes that share phenotypes with SOX9: view

Human Phenotype Ontology for SOX9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SOX9 Gene

MGI Knock Outs for SOX9:
  • Sox9 Sox9<tm2.1Crm>
  • Sox9 Sox9<tm1Crm>
  • Sox9 Sox9<tm1.1Gsr>
  • Sox9 Sox9<tm2.1Tlu>
  • Sox9 Sox9<tm2.1Haak>

Animal Model Products

CRISPR Products

Transcription Factor Targets for SOX9 Gene

Selected GeneGlobe predicted Target genes for SOX9
Targeted motifs for SOX9 Gene
HOMER Transcription Factor Regulatory Elements motif SOX9
  • Consensus sequence: AGGVNCCTTTGT Submotif: canonical Cell Type: Limb GEO ID: GSE73225

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOX9

Clone Products

  • Addgene plasmids for SOX9

No data available for Enzyme Numbers (IUBMB) for SOX9 Gene

Localization for SOX9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX9 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 SOX9 gene
Compartment Confidence
nucleus 5
extracellular 3
cytoskeleton 2
plasma membrane 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SOX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IEA --
GO:0032991 protein-containing complex IDA 20530484
GO:0044798 nuclear transcription factor complex IEA --
genes like me logo Genes that share ontologies with SOX9: view

Pathways & Interactions for SOX9 Gene

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

SIGNOR curated interactions for SOX9 Gene

Activates:
Inactivates:
Is activated by:

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,IEA --
GO:0001503 ossification IEA --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001708 cell fate specification ISS,IEA --
genes like me logo Genes that share ontologies with SOX9: view

Drugs & Compounds for SOX9 Gene

(11) Drugs for SOX9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(10) Additional Compounds for SOX9 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SOX9: view

Transcripts for SOX9 Gene

mRNA/cDNA for SOX9 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOX9

Clone Products

  • Addgene plasmids for SOX9

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

No ASD Table

Relevant External Links for SOX9 Gene

GeneLoc Exon Structure for
SOX9
ECgene alternative splicing isoforms for
SOX9

Expression for SOX9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x4.1).

Protein differential expression in normal tissues from HIPED for SOX9 Gene

This gene is overexpressed in Monocytes (42.6), Fetal testis (16.8), and Testis (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SOX9 Gene



Protein tissue co-expression partners for SOX9 Gene

NURSA nuclear receptor signaling pathways regulating expression of SOX9 Gene:

SOX9

SOURCE GeneReport for Unigene cluster for SOX9 Gene:

Hs.647409

Evidence on tissue expression from TISSUES for SOX9 Gene

  • Nervous system(4.7)
  • Eye(4.4)
  • Bone(2.7)
  • Intestine(2.6)
  • Pancreas(2.4)
  • Heart(2.3)
  • Kidney(2.3)
  • Muscle(2.3)
  • Bone marrow(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX9 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • chin
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • larynx
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • pituitary gland
  • scalp
  • skull
  • tongue
  • vocal cord
Thorax:
  • breast
  • bronchus
  • chest wall
  • clavicle
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
Abdomen:
  • kidney
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • placenta
  • prostate
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns 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
chimpanzee
(Pan troglodytes)
Mammalia SOX9 33 32
  • 99.87 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SOX9 33 32
  • 93.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SOX9 33 32
  • 91.09 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SOX9 33
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sox9 17 33 32
  • 89.35 (n)
rat
(Rattus norvegicus)
Mammalia Sox9 32
  • 89.02 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SOX9 33
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SOX9 33 32
  • 85.58 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SOX9 33
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sox9 32
  • 77.59 (n)
Str.15584 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.1690 32
zebrafish
(Danio rerio)
Actinopterygii sox9a 33 32 32
  • 76.81 (n)
OneToMany
sox9b 33
  • 68 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11885 32
fruit fly
(Drosophila melanogaster)
Insecta Sox100B 33 34
  • 28 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sox-4 33
  • 34 (a)
OneToMany
Species where no ortholog for SOX9 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for SOX9 (if available)
TreeFam:
Gene Tree for SOX9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SOX9: view image

Paralogs for SOX9 Gene

(3) SIMAP similar genes for SOX9 Gene using alignment to 12 proteins:

  • SOX9_HUMAN
  • S6CBB2_HUMAN
  • U5XJY7_HUMAN
  • U5XJZ1_HUMAN
  • U5XJZ4_HUMAN
  • U5XK44_HUMAN
  • U5XK50_HUMAN
  • U5XKW5_HUMAN
  • U5XKW9_HUMAN
  • U5XMM4_HUMAN
  • U5XN63_HUMAN
  • U5XN67_HUMAN
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 Variation AA Info Type
rs1042667 benign, Camptomelic dysplasia 72,124,410(+) A/C 3_prime_UTR_variant
rs1042673 benign, Camptomelic dysplasia 72,125,198(+) A/G 3_prime_UTR_variant
rs1042678 benign, Camptomelic dysplasia 72,125,967(+) G/A/C 3_prime_UTR_variant
rs104894647 pathogenic, Acampomelic campomelic dysplasia, Campomelic dysplasia (CMD1) [MIM:114290] 72,122,804(+) A/G coding_sequence_variant, missense_variant
rs1057518216 pathogenic, not provided, Camptomelic dysplasia 72,124,037(+) C/A/T coding_sequence_variant, stop_gained, synonymous_variant

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

Variant ID Type Subtype PubMed ID
esv3573809 CNV gain 25503493
nsv833530 CNV gain+loss 17160897

Variation tolerance for SOX9 Gene

Residual Variation Intolerance Score: 9.81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.75; 15.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SOX9 Gene

Human Gene Mutation Database (HGMD)
SOX9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SOX9

SNP Genotyping and Copy Number Assay Products

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

Disorders for SOX9 Gene

MalaCards: The human disease database

(41) MalaCards diseases for SOX9 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards