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

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Gene: SOX9 (SRY-box transcription factor 9) Sus scrofa
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Symbol: SOX9
Name: SRY-box transcription factor 9
RGD ID: 14090759
Description: ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific; bHLH transcription factor binding (ortholog); chromatin binding (ortholog); INVOLVED IN positive regulation of transcription by RNA polymerase II; anterior head development (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 nucleus; protein-containing complex (ortholog)
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: SOX-9; SRY (sex determining region Y)-box 9; SRY-box 9; transcription factor SOX-9
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

References
Additional References at PubMed
PMID:9154138   PMID:12203914   PMID:12606467   PMID:20530484   PMID:20950722   PMID:26430891   PMID:26634652   PMID:28580627   PMID:29254288   PMID:31319268  


Genomics

Comparative Map Data
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
(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
(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
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
(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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 hemolymphoid system musculoskeletal system nervous system reproductive system respiratory system
High
Medium 1
Low 8 3 3 3 22 2 1
Below cutoff 2 1 2 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000018780   ⟹   ENSSSCP00000018278
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl128,642,158 - 8,647,315 (-)Ensembl
RefSeq Acc Id: NM_213843   ⟹   NP_999008
RefSeq Status: VALIDATED
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1128,642,154 - 8,647,315 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_999008   ⟸   NM_213843
- Sequence:
RefSeq Acc Id: ENSSSCP00000018278   ⟸   ENSSSCT00000018780
Protein Domains
HMG box


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000017251 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00070002176 UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000018278 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00070003345 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000018780 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00070004042 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOX-9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sox_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report ssc:396840 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene SOX9 ENTREZGENE
PANTHER PTHR45803:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sox_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A4X1SLG8_PIG UniProtKB/TrEMBL
  B1VK42_PIG UniProtKB/TrEMBL
  B1VK43_PIG UniProtKB/TrEMBL
  F1RV30_PIG UniProtKB/TrEMBL
  O18896 ENTREZGENE
  Q71VI1_PIG UniProtKB/TrEMBL
  SOX9_PIG UniProtKB/Swiss-Prot
VGNC ID VGNC:99053 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-06-18 SOX9  SRY-box transcription factor 9  SOX9  SRY-box 9  Symbol and/or name change 5135510 APPROVED