SOX9 (SRY-box transcription factor 9) - Rat Genome Database

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Gene: SOX9 (SRY-box transcription factor 9) Canis lupus familiaris
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Symbol: SOX9
Name: SRY-box transcription factor 9
RGD ID: 12129154
Description: ENCODES a protein that exhibits beta-catenin binding (ortholog); bHLH transcription factor binding (ortholog); chromatin binding (ortholog); INVOLVED IN anterior head development (ortholog); aortic valve morphogenesis (ortholog); astrocyte fate commitment (ortholog); ASSOCIATED WITH 46,XX sex reversal 2 (ortholog); 46,XY sex reversal 10 (ortholog); Animal Mammary Neoplasms (ortholog); FOUND IN nucleoplasm (ortholog); nucleus (ortholog); protein-containing complex (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal); SRY-box 9; SRY-box containing protein 9; transcription factor SOX-9
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.198,275,049 - 8,278,172 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl98,275,049 - 8,278,172 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha99,564,949 - 9,568,092 (+)NCBI
ROS_Cfam_1.098,479,949 - 8,483,108 (-)NCBI
ROS_Cfam_1.0 Ensembl98,479,863 - 8,483,490 (-)Ensembl
UMICH_Zoey_3.198,522,923 - 8,526,068 (-)NCBI
UNSW_CanFamBas_1.098,777,560 - 8,780,707 (-)NCBI
UU_Cfam_GSD_1.098,722,828 - 8,725,975 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior head development  (ISO)
aortic valve morphogenesis  (ISO)
astrocyte fate commitment  (ISO)
branching involved in ureteric bud morphogenesis  (ISO)
bronchus cartilage development  (ISO)
cAMP-mediated signaling  (ISS)
cartilage condensation  (ISO,ISS)
cartilage development  (ISO,ISS)
cell differentiation  (IEA,ISO)
cell fate commitment  (ISO)
cell fate specification  (ISO,ISS)
cell-cell adhesion  (ISO)
cellular response to BMP stimulus  (ISS)
cellular response to epidermal growth factor stimulus  (ISS)
cellular response to heparin  (ISS)
cellular response to interleukin-1  (ISO)
cellular response to mechanical stimulus  (ISS)
cellular response to retinoic acid  (ISO)
cellular response to transforming growth factor beta stimulus  (ISO)
central nervous system development  (ISO)
chondrocyte development  (ISO)
chondrocyte differentiation  (IBA,ISO,ISS)
chondrocyte differentiation involved in endochondral bone morphogenesis  (ISS)
chondrocyte hypertrophy  (ISS)
chromatin remodeling  (ISS)
cochlea morphogenesis  (ISO,ISS)
cytoskeleton organization  (ISO)
endocardial cushion morphogenesis  (ISO,ISS)
endochondral bone morphogenesis  (ISO)
endocrine pancreas development  (ISO)
epidermal growth factor receptor signaling pathway  (ISS)
epithelial cell proliferation involved in prostatic bud elongation  (ISO,ISS)
epithelial to mesenchymal transition  (ISO,ISS)
epithelial tube branching involved in lung morphogenesis  (ISO)
ERK1 and ERK2 cascade  (ISS)
extracellular matrix organization  (ISO)
growth plate cartilage chondrocyte growth  (ISS)
hair follicle development  (ISO,ISS)
Harderian gland development  (ISO)
heart development  (IBA,ISO)
heart valve development  (ISS)
heart valve formation  (ISO)
heart valve morphogenesis  (ISO,ISS)
homeostasis of number of cells within a tissue  (ISO)
intestinal epithelial structure maintenance  (ISO,ISS)
intrahepatic bile duct development  (ISO)
lacrimal gland development  (ISO)
limb bud formation  (ISO)
lung epithelial cell differentiation  (ISO)
lung smooth muscle development  (ISO)
male germ-line sex determination  (ISO,ISS)
male gonad development  (ISO)
male sex determination  (ISO)
mammary gland development  (ISO)
metanephric nephron tubule formation  (ISO,ISS)
metanephric tubule development  (ISO)
morphogenesis of a branching epithelium  (ISO,ISS)
morphogenesis of an epithelium  (IBA)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of beta-catenin-TCF complex assembly  (ISO)
negative regulation of biomineral tissue development  (ISS)
negative regulation of bone mineralization  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO,ISS)
negative regulation of cell population proliferation  (ISO)
negative regulation of chondrocyte differentiation  (ISO,ISS)
negative regulation of epithelial cell differentiation  (ISO)
negative regulation of epithelial cell proliferation  (ISO,ISS)
negative regulation of fatty acid oxidation  (ISS)
negative regulation of gene expression  (ISO)
negative regulation of immune system process  (ISS)
negative regulation of mesenchymal cell apoptotic process  (ISO)
negative regulation of miRNA transcription  (ISO)
negative regulation of myoblast differentiation  (ISO,ISS)
negative regulation of ossification  (ISS)
negative regulation of osteoblast differentiation  (ISS)
negative regulation of photoreceptor cell differentiation  (ISO,ISS)
negative regulation of transcription by RNA polymerase II  (IBA)
negative regulation of transcription, DNA-templated  (ISO,ISS)
neural crest cell development  (ISO)
neural crest cell fate specification  (ISS)
Notch signaling pathway  (ISO)
notochord development  (ISO)
nucleosome assembly  (ISS)
oligodendrocyte differentiation  (IBA,ISO)
ossification  (ISO)
otic vesicle development  (ISO)
otic vesicle formation  (ISO,ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (ISS)
positive regulation of cartilage development  (ISO)
positive regulation of cell population proliferation  (ISO,ISS)
positive regulation of cell proliferation involved in heart morphogenesis  (ISO)
positive regulation of chondrocyte differentiation  (IBA,ISS)
positive regulation of chondrocyte proliferation  (ISO)
positive regulation of epithelial cell differentiation  (ISO,ISS)
positive regulation of epithelial cell migration  (ISO,ISS)
positive regulation of epithelial cell proliferation  (ISO,ISS)
positive regulation of extracellular matrix assembly  (ISO)
positive regulation of gene expression  (ISO,ISS)
positive regulation of kidney development  (ISS)
positive regulation of male gonad development  (ISS)
positive regulation of mesenchymal cell proliferation  (ISO,ISS)
positive regulation of mesenchymal stem cell differentiation  (ISS)
positive regulation of phosphatidylinositol 3-kinase signaling  (ISS)
positive regulation of protein catabolic process  (ISO)
positive regulation of protein phosphorylation  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO)
prostate gland development  (ISO)
prostate gland morphogenesis  (ISO)
protein kinase B signaling  (ISS)
protein localization to nucleus  (ISO)
protein-containing complex assembly  (ISS)
regulation of apoptotic process  (ISS)
regulation of branching involved in lung morphogenesis  (ISO)
regulation of cartilage development  (ISS)
regulation of cell adhesion  (ISO)
regulation of cell cycle process  (ISS)
regulation of cell differentiation  (ISO)
regulation of cell population proliferation  (ISO,ISS)
regulation of cell proliferation involved in tissue homeostasis  (ISO,ISS)
regulation of epithelial cell proliferation involved in lung morphogenesis  (ISO)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (IEA)
renal vesicle induction  (ISS)
response to fatty acid  (ISS)
retina development in camera-type eye  (ISO,ISS)
retinal rod cell differentiation  (ISO,ISS)
Sertoli cell development  (ISO)
Sertoli cell differentiation  (ISO,ISS)
signal transduction  (ISS)
skeletal system development  (ISS)
somatic stem cell population maintenance  (ISO,ISS)
spermatogenesis  (ISO,ISS)
tissue homeostasis  (ISS)
trachea cartilage development  (ISO)
ureter development  (ISO)
ureter morphogenesis  (ISO)
ureter smooth muscle cell differentiation  (ISO)
ureter urothelium development  (ISO)

Cellular Component

References
Additional References at PubMed
PMID:12840810   PMID:15596718   PMID:15814894   PMID:23978557   PMID:25010117   PMID:26184845   PMID:26423656   PMID:26428883   PMID:28094446   PMID:28365713  


Genomics

Comparative Map Data
SOX9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.198,275,049 - 8,278,172 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl98,275,049 - 8,278,172 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha99,564,949 - 9,568,092 (+)NCBI
ROS_Cfam_1.098,479,949 - 8,483,108 (-)NCBI
ROS_Cfam_1.0 Ensembl98,479,863 - 8,483,490 (-)Ensembl
UMICH_Zoey_3.198,522,923 - 8,526,068 (-)NCBI
UNSW_CanFamBas_1.098,777,560 - 8,780,707 (-)NCBI
UU_Cfam_GSD_1.098,722,828 - 8,725,975 (-)NCBI
SOX9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1772,121,020 - 72,126,416 (+)EnsemblGRCh38hg38GRCh38
GRCh381772,121,020 - 72,126,416 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371770,117,161 - 70,122,557 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361767,628,756 - 67,634,156 (+)NCBINCBI36hg18NCBI36
Build 341767,628,755 - 67,634,156NCBI
Celera1766,688,499 - 66,693,898 (+)NCBI
Cytogenetic Map17q24.3NCBI
HuRef1765,510,108 - 65,515,656 (+)NCBIHuRef
CHM1_11770,181,222 - 70,186,622 (+)NCBICHM1_1
Sox9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911112,673,036 - 112,678,583 (+)NCBIGRCm39mm39
GRCm39 Ensembl11112,673,050 - 112,678,586 (+)Ensembl
GRCm3811112,782,210 - 112,787,757 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11112,782,224 - 112,787,760 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711112,643,524 - 112,649,071 (+)NCBIGRCm37mm9NCBIm37
MGSCv3611112,598,314 - 112,603,839 (+)NCBImm8
Celera11124,540,008 - 124,545,554 (+)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1177.27NCBI
Sox9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21097,806,485 - 97,811,994 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)Ensembl
Rnor_6.010101,288,528 - 101,294,030 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10101,288,489 - 101,293,379 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010100,964,754 - 100,970,581 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410102,392,187 - 102,394,256 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110102,408,236 - 102,408,622 (+)NCBI
Celera1096,424,278 - 96,429,703 (+)NCBICelera
Cytogenetic Map10q32.1NCBI
Sox9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955478940,177 - 945,563 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955478941,684 - 945,563 (-)NCBIChiLan1.0ChiLan1.0
SOX9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11771,491,419 - 71,498,911 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01766,028,737 - 66,034,122 (+)NCBIMhudiblu_PPA_v0panPan3
Sox9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056028,350,254 - 8,354,855 (-)NCBI
SpeTri2.0NW_0049366551,849,044 - 1,852,648 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl128,642,158 - 8,647,315 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1128,642,154 - 8,647,315 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2129,029,449 - 9,032,820 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap12p13-p11NCBI
SOX9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11649,519,749 - 49,523,967 (-)NCBIChlSab1.1chlSab2
ChlSab1.11649,519,749 - 49,523,967 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1649,518,185 - 49,523,898 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607720,379,690 - 20,385,117 (-)NCBIVero_WHO_p1.0
Sox9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248012,296,353 - 2,300,853 (+)NCBIHetGla_female_1.0hetGla2


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 2 11 6 8 8 6 4
Low 3 5 11 6 6 6 4 4 4 2
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000007033
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl98,275,049 - 8,278,172 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845035905   ⟹   ENSCAFP00845028096
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl98,479,863 - 8,483,490 (-)Ensembl
RefSeq Acc Id: NM_001002978   ⟹   NP_001002978
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.198,275,049 - 8,278,172 (+)NCBI
Dog10K_Boxer_Tasha99,564,949 - 9,568,092 (+)NCBI
ROS_Cfam_1.098,479,949 - 8,483,108 (-)NCBI
UMICH_Zoey_3.198,522,923 - 8,526,068 (-)NCBI
UNSW_CanFamBas_1.098,777,560 - 8,780,707 (-)NCBI
UU_Cfam_GSD_1.098,722,828 - 8,725,975 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001002978 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAP69840 (Get FASTA)   NCBI Sequence Viewer  
  AAX33237 (Get FASTA)   NCBI Sequence Viewer  
  ABY81084 (Get FASTA)   NCBI Sequence Viewer  
  Q7YRJ7 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001002978   ⟸   NM_001002978
- UniProtKB: Q7YRJ7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSCAFP00845028096   ⟸   ENSCAFT00845035905


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000004374 Ensembl
  ENSCAFG00845020385 Ensembl, ENTREZGENE
Ensembl Protein ENSCAFP00845028096 ENTREZGENE
Ensembl Transcript ENSCAFT00845035905 ENTREZGENE
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot
InterPro HMG_box_dom UniProtKB/Swiss-Prot
  HMG_box_dom_sf UniProtKB/Swiss-Prot
  SOX-9 UniProtKB/Swiss-Prot
  Sox_N UniProtKB/Swiss-Prot
KEGG Report cfa:403464 UniProtKB/Swiss-Prot
NCBI Gene SOX9 ENTREZGENE
PANTHER PTHR45803:SF1 UniProtKB/Swiss-Prot
Pfam HMG_box UniProtKB/Swiss-Prot
  Sox_N UniProtKB/Swiss-Prot
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot
SMART HMG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot
UniProt Q7YRJ7 ENTREZGENE, UniProtKB/Swiss-Prot
VGNC ID VGNC:46684 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-06 SOX9  SRY-box transcription factor 9  SOX9  SRY-box 9  Symbol and/or name change 5135510 APPROVED