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SOX9 SRY-box 9 [ Homo sapiens (human) ]

Gene ID: 6662, updated on 24-Sep-2017
Official Symbol
SOX9provided by HGNC
Official Full Name
SRY-box 9provided by HGNC
Primary source
HGNC:HGNC:11204
See related
Ensembl:ENSG00000125398 MIM:608160; Vega:OTTHUMG00000166300
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CMD1; SRA1; CMPD1; SRXX2; SRXY10
Summary
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]
Orthologs
Location:
17q24.3
Exon count:
3
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 17 NC_000017.11 (72121020..72126420)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70117161..70122561)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2097 Neighboring gene SOX9 antisense RNA 1 Neighboring gene uncharacterized LOC107987249 Neighboring gene long intergenic non-protein coding RNA 2003 Neighboring gene long intergenic non-protein coding RNA 673

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
46,XY sex reversal 10
MedGen: C4225331 OMIM: 616425 GeneReviews: Not available
not available
Camptomelic dysplasia
MedGen: C1861922 OMIM: 114290 GeneReviews: Campomelic Dysplasia
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-26)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
NHGRI GWA Catalog
Genetic variation in prostate-specific antigen-detected prostate cancer and the effect of control selection on genetic association studies.
NHGRI GWA Catalog
Genetics of coronary artery calcification among African Americans, a meta-analysis.
NHGRI GWA Catalog
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
NHGRI GWA Catalog
Genome-wide association study of lung function decline in adults with and without asthma.
NHGRI GWA Catalog
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
NHGRI GWA Catalog
Identification of a susceptibility locus for severe adolescent idiopathic scoliosis on chromosome 17q24.3.
NHGRI GWA Catalog
  • Deactivation of the beta-catenin transactivating complex, organism-specific biosystem (from REACTOME)
    Deactivation of the beta-catenin transactivating complex, organism-specific biosystemThe mechanisms involved in downregulation of TCF-dependent transcription are not yet very well understood. beta-catenin is known to recruit a number of transcriptional repressors, including Reptin, S...
  • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
    Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
  • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
    Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Wnt, organism-specific biosystem (from REACTOME)
    Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
  • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
    Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
  • TCF dependent signaling in response to WNT, organism-specific biosystem (from REACTOME)
    TCF dependent signaling in response to WNT, organism-specific biosystem19 WNT ligands and 10 FZD receptors have been identified in human cells; interactions amongst these ligands and receptors vary in a developmental and tissue-specific manner and lead to activation of ...
  • cAMP signaling pathway, organism-specific biosystem (from KEGG)
    cAMP signaling pathway, organism-specific biosystemcAMP is one of the most common and universal second messengers, and its formation is promoted by adenylyl cyclase (AC) activation after ligation of G protein-coupled receptors (GPCRs) by ligands incl...
  • cAMP signaling pathway, conserved biosystem (from KEGG)
    cAMP signaling pathway, conserved biosystemcAMP is one of the most common and universal second messengers, and its formation is promoted by adenylyl cyclase (AC) activation after ligation of G protein-coupled receptors (GPCRs) by ligands incl...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
bHLH transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
beta-catenin binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enhancer binding IDA
Inferred from Direct Assay
more info
PubMed 
enhancer sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
pre-mRNA intronic binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein kinase A catalytic subunit binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor activity, sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor activity, sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
ERK1 and ERK2 cascade ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Harderian gland development IEA
Inferred from Electronic Annotation
more info
 
Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Sertoli cell development IEA
Inferred from Electronic Annotation
more info
 
Sertoli cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
astrocyte fate commitment IEA
Inferred from Electronic Annotation
more info
 
branching involved in ureteric bud morphogenesis IEA
Inferred from Electronic Annotation
more info
 
bronchus cartilage development IEA
Inferred from Electronic Annotation
more info
 
cAMP-mediated signaling IDA
Inferred from Direct Assay
more info
PubMed 
cartilage condensation ISS
Inferred from Sequence or Structural Similarity
more info
 
cartilage development ISS
Inferred from Sequence or Structural Similarity
more info
 
cell fate specification ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to epidermal growth factor stimulus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cellular response to heparin ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cellular response to interleukin-1 IEP
Inferred from Expression Pattern
more info
PubMed 
cellular response to mechanical stimulus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cellular response to retinoic acid IEP
Inferred from Expression Pattern
more info
PubMed 
cellular response to transforming growth factor beta stimulus IDA
Inferred from Direct Assay
more info
PubMed 
chondrocyte differentiation involved in endochondral bone morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
chondrocyte hypertrophy ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
cochlea morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
 
endocardial cushion morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
endocrine pancreas development IEA
Inferred from Electronic Annotation
more info
 
epidermal growth factor receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
epithelial cell proliferation involved in prostatic bud elongation ISS
Inferred from Sequence or Structural Similarity
more info
 
epithelial to mesenchymal transition ISS
Inferred from Sequence or Structural Similarity
more info
 
epithelial tube branching involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization IEA
Inferred from Electronic Annotation
more info
 
hair follicle development ISS
Inferred from Sequence or Structural Similarity
more info
 
heart valve development ISS
Inferred from Sequence or Structural Similarity
more info
 
heart valve formation IEA
Inferred from Electronic Annotation
more info
 
heart valve morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
intestinal epithelial structure maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
intrahepatic bile duct development IEA
Inferred from Electronic Annotation
more info
 
lacrimal gland development IEA
Inferred from Electronic Annotation
more info
 
limb bud formation IEA
Inferred from Electronic Annotation
more info
 
lung epithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
lung smooth muscle development IEA
Inferred from Electronic Annotation
more info
 
male germ-line sex determination ISS
Inferred from Sequence or Structural Similarity
more info
 
male gonad development IEP
Inferred from Expression Pattern
more info
PubMed 
male gonad development IMP
Inferred from Mutant Phenotype
more info
PubMed 
mammary gland development IEA
Inferred from Electronic Annotation
more info
 
metanephric nephron tubule formation ISS
Inferred from Sequence or Structural Similarity
more info
 
morphogenesis of a branching epithelium ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of biomineral tissue development ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of bone mineralization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of epithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of immune system process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of mesenchymal cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of myoblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of ossification ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of photoreceptor cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of pri-miRNA transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural crest cell development IEA
Inferred from Electronic Annotation
more info
 
notochord development IEA
Inferred from Electronic Annotation
more info
 
nucleosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
ossification IEA
Inferred from Electronic Annotation
more info
 
otic vesicle formation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cartilage development IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell proliferation involved in heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of chondrocyte differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of chondrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of epithelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of epithelial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of epithelial cell proliferation IEP
Inferred from Expression Pattern
more info
PubMed 
positive regulation of epithelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of extracellular matrix assembly IEA
Inferred from Electronic Annotation
more info
 
positive regulation of kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of male gonad development IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mesenchymal cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of mesenchymal stem cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of phosphatidylinositol 3-kinase signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
prostate gland development IEP
Inferred from Expression Pattern
more info
PubMed 
protein complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
protein kinase B signaling IEA
Inferred from Electronic Annotation
more info
 
protein localization to nucleus IEA
Inferred from Electronic Annotation
more info
 
regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of branching involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
 
regulation of cell adhesion IEA
Inferred from Electronic Annotation
more info
 
regulation of cell cycle process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell proliferation involved in tissue homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of epithelial cell proliferation involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
 
renal vesicle induction ISS
Inferred from Sequence or Structural Similarity
more info
 
retina development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
retinal rod cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
 
skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
somatic stem cell population maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
tissue homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
trachea cartilage development IEA
Inferred from Electronic Annotation
more info
 
transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
ureter morphogenesis IEA
Inferred from Electronic Annotation
more info
 
ureter smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
ureter urothelium development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear transcription factor complex IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
transcription factor SOX-9
Names
SRY (sex determining region Y)-box9
SRY (sex-determining region Y)-box 9 protein
SRY-related HMG-box, gene 9

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012490.1 RefSeqGene

    Range
    5001..10401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000346.3NP_000337.1  transcription factor SOX-9

    See identical proteins and their annotated locations for NP_000337.1

    Status: REVIEWED

    Source sequence(s)
    AC007461, BC007951, BC018276, Z46629
    Consensus CDS
    CCDS11689.1
    UniProtKB/Swiss-Prot
    P48436
    Related
    ENSP00000245479.2, OTTHUMP00000232537, ENST00000245479.2, OTTHUMT00000389032
    Conserved Domains (2) summary
    cd01388
    Location:104174
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
    pfam12444
    Location:2294
    Sox_N; Sox developmental protein N terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p7 Primary Assembly

    Range
    72121020..72126420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018928.2 Alternate CHM1_1.1

    Range
    70181222..70186622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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