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Sox9 Gene Detail
Summary
  • Symbol
    Sox9
  • Name
    SRY (sex determining region Y)-box 9
  • Synonyms
    2010306G03Rik
  • Feature Type
    protein coding gene
  • IDs
    MGI:98371
    NCBI Gene: 20682
  • Alliance
    gene page
  • Transcription Start Sites
    5 TSS
  • Regulated by
    Rr80, Rr1367, Rr335 ... (16 regulatory regions)
Location &
Maps
more
  • Sequence Map
    Chr11:112673050-112678586 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 11, 77.27 cM
  • Mapping Data
    12 experiments
Strain
Comparison
more
  • SNPs within 2kb
    174 from dbSNP Build 142
  • Strain Annotations
    18
  • PCR
    2
  • RFLP
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98371
 protein coding gene Chr11:112673036-112678586 (+)
129S1/SvImJ MGP_129S1SvImJ_G0019348
 protein coding gene Chr11:116538334-116543867 (+)
A/J MGP_AJ_G0019316
 protein coding gene Chr11:111532852-111538386 (+)
AKR/J MGP_AKRJ_G0019285
 protein coding gene Chr11:114803800-114809339 (+)
BALB/cJ MGP_BALBcJ_G0019290
 protein coding gene Chr11:111926681-111932214 (+)
C3H/HeJ MGP_C3HHeJ_G0019099
 protein coding gene Chr11:115158359-115163887 (+)
C57BL/6NJ MGP_C57BL6NJ_G0019740
 protein coding gene Chr11:120048049-120053585 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0017363
 protein coding gene Chr11:108628565-108634129 (+)
CAST/EiJ MGP_CASTEiJ_G0018652
 protein coding gene Chr11:116386380-116391596 (+)
CBA/J MGP_CBAJ_G0019068
 protein coding gene Chr11:124950884-124962491 (+)
DBA/2J MGP_DBA2J_G0019180
 protein coding gene Chr11:110975306-110980844 (+)
FVB/NJ MGP_FVBNJ_G0019171
 protein coding gene Chr11:110419902-110425428 (+)
LP/J MGP_LPJ_G0019250
 protein coding gene Chr11:116972212-116977753 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0019202
 protein coding gene Chr11:124129241-124136228 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0019777
 protein coding gene Chr11:115445002-115450553 (+)
PWK/PhJ MGP_PWKPhJ_G0018417
 protein coding gene Chr11:112156543-112161885 (+)
SPRET/EiJ MGP_SPRETEiJ_G0018209
 protein coding gene Chr11:115233760-115238993 (+)
WSB/EiJ MGP_WSBEiJ_G0018704
 protein coding gene Chr11:115381994-115387537 (+)



Homology
more
  • Human Ortholog
    SOX9, SRY-box transcription factor 9
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SOX9, SRY-box transcription factor 9
  • Synonyms
    CMD1, CMPD1, ENH13, SRA1, SRXX2, SRXY10, TES, TESCO
  • Links
    NCBI Gene ID: 6662
    neXtProt AC: NX_P48436
    UniProt: P48436

  • Chr Location
    17q24.3; chr17:72121020-72126416 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Sox9 mouse models; 3 with human SOX9 associations

Human Disease Mouse Models
      
IDs
 View 9 models
      
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    7 with disease annotations
  • References
    7 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    211 phenotypes from 18 alleles in 32 genetic backgrounds
    95 phenotypes from multigenic genotypes
    7 images
    335 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Null mutant heterozygotes and conditional knockout mutants display perinatal lethality with cleft palate, hypoplasia and distortion of numerous cartilage-derived skeletal structures, and premature mineralization in many bones. Specific conditional knockout mutations are sex-reversed. A heterozygous otic-vesicle-specific conditional gain-of-function mutation leads to various vestibular and hearing-related phenotypes.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    329
  • GO References
    99
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000000567 Ensembl Gene Model | MGI Sequence Detail 5537 C57BL/6J ±  kb
    transcript ENSMUST00000000579 Ensembl | MGI Sequence Detail 4135 Not Applicable  
    polypeptide ENSMUSP00000000579 Ensembl | MGI Sequence Detail 507 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 288
      Genomic 2
      cDNA 135
      Primer pair 60
      Other 91

      Microarray probesets 5
    Other
    Accession IDs
    less
    MGD-MRK-14510, MGI:1917265, MGI:2144464
    References
    more
    • Summaries
      All 2016
      Developmental Gene Expression 1679
      Diseases 7
      Gene Ontology 99
      Phenotypes 335
    • Earliest
      J:4011 Wright EM, et al., Seven new members of the Sox gene family expressed during mouse development. Nucleic Acids Res. 1993 Feb 11;21(3):744
    • Latest
      J:364151 Lahti L, et al., Sox9 and nuclear factor I transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors. Development. 2025 Mar 15;152(6):dev204421
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    03/25/2025
    MGI 6.24     		The Jackson Laboratory