Sox9 (SRY-box transcription factor 9) - Rat Genome Database

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Gene: Sox9 (SRY-box transcription factor 9) Chinchilla lanigera
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Symbol: Sox9
Name: SRY-box transcription factor 9
RGD ID: 8833996
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); apoptotic process (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: MODEL
Previously known as: SRY (sex determining region Y)-box 9; SRY-box 9; transcription factor SOX-9
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955478940,177 - 945,563 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955478941,684 - 945,563 (-)NCBIChiLan1.0ChiLan1.0
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)
apoptotic process  (ISO)
astrocyte fate commitment  (ISO)
bone mineralization  (ISO)
branching involved in ureteric bud morphogenesis  (ISO)
bronchus cartilage development  (ISO)
cAMP-mediated signaling  (ISO)
canonical Wnt signaling pathway  (ISO)
cartilage condensation  (ISO)
cartilage development  (ISO)
cell fate commitment  (ISO)
cell population proliferation  (ISO)
cell proliferation involved in heart morphogenesis  (ISO)
cell-cell adhesion  (ISO)
cellular response to epidermal growth factor stimulus  (ISO)
cellular response to heparin  (ISO)
cellular response to interleukin-1  (ISO)
cellular response to mechanical stimulus  (ISO)
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  (ISO)
chondrocyte differentiation involved in endochondral bone morphogenesis  (ISO)
chondrocyte hypertrophy  (ISO)
chromatin remodeling  (ISO)
cochlea morphogenesis  (ISO)
cytoskeleton organization  (ISO)
endocardial cushion morphogenesis  (ISO)
endochondral bone morphogenesis  (ISO)
endocrine pancreas development  (ISO)
epidermal growth factor receptor signaling pathway  (ISO)
epithelial cell proliferation  (ISO)
epithelial cell proliferation involved in prostatic bud elongation  (ISO)
epithelial to mesenchymal transition  (ISO)
epithelial tube branching involved in lung morphogenesis  (ISO)
ERK1 and ERK2 cascade  (ISO)
extracellular matrix assembly  (ISO)
extracellular matrix organization  (ISO)
gene expression  (ISO)
glandular epithelial cell differentiation  (ISO)
glial cell fate specification  (ISO)
growth plate cartilage chondrocyte growth  (ISO)
hair follicle development  (ISO)
Harderian gland development  (ISO)
heart development  (ISO)
heart valve development  (ISO)
heart valve formation  (ISO)
heart valve morphogenesis  (ISO)
homeostasis of number of cells within a tissue  (ISO)
intestinal epithelial cell differentiation  (ISO)
intestinal epithelial structure maintenance  (ISO)
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)
male gonad development  (ISO)
male sex determination  (ISO)
mammary gland development  (ISO)
mesenchymal cell apoptotic process  (ISO)
mesenchymal cell proliferation  (ISO)
metanephric nephron tubule formation  (ISO)
metanephric tubule development  (ISO)
morphogenesis of a branching epithelium  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of beta-catenin-TCF complex assembly  (ISO)
negative regulation of biomineral tissue development  (ISO)
negative regulation of bone mineralization  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO)
negative regulation of chondrocyte differentiation  (ISO)
negative regulation of DNA-templated transcription  (ISO)
negative regulation of epithelial cell differentiation  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of fatty acid oxidation  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of immune system process  (ISO)
negative regulation of mesenchymal cell apoptotic process  (ISO)
negative regulation of miRNA transcription  (ISO)
negative regulation of myoblast differentiation  (ISO)
negative regulation of ossification  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of photoreceptor cell differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
neural crest cell development  (ISO)
neuron fate specification  (ISO)
Notch signaling pathway  (ISO)
notochord development  (ISO)
nucleosome assembly  (ISO)
oligodendrocyte differentiation  (ISO)
ossification  (ISO)
otic vesicle development  (ISO)
otic vesicle formation  (ISO)
phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
positive regulation of branching involved in ureteric bud morphogenesis  (ISO)
positive regulation of cartilage development  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell proliferation involved in heart morphogenesis  (ISO)
positive regulation of chondrocyte differentiation  (ISO)
positive regulation of chondrocyte proliferation  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of epithelial cell differentiation  (ISO)
positive regulation of epithelial cell migration  (ISO)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of extracellular matrix assembly  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of kidney development  (ISO)
positive regulation of male gonad development  (ISO)
positive regulation of mesenchymal cell proliferation  (ISO)
positive regulation of mesenchymal stem cell differentiation  (ISO)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
positive regulation of protein catabolic process  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of stem cell proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
prostate gland development  (ISO)
prostate gland morphogenesis  (ISO)
protein localization to nucleus  (ISO)
protein phosphorylation  (ISO)
protein-containing complex assembly  (ISO)
regulation of branching involved in lung morphogenesis  (ISO)
regulation of cell adhesion  (ISO)
regulation of cell cycle process  (ISO)
regulation of cell differentiation  (ISO)
regulation of cell population proliferation  (ISO)
regulation of cell proliferation involved in tissue homeostasis  (ISO)
regulation of epithelial cell proliferation involved in lung morphogenesis  (ISO)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
renal vesicle induction  (ISO)
response to fatty acid  (ISO)
response to organic cyclic compound  (ISO)
retina development in camera-type eye  (ISO)
retinal rod cell differentiation  (ISO)
Sertoli cell development  (ISO)
Sertoli cell differentiation  (ISO)
signal transduction  (ISO)
skeletal system development  (ISO)
somatic stem cell population maintenance  (ISO)
spermatogenesis  (ISO)
stem cell proliferation  (ISO)
tissue homeostasis  (ISO)
trachea cartilage development  (ISO)
transcription by RNA polymerase II  (ISO)
type I pneumocyte differentiation  (ISO)
ureter development  (ISO)
ureter morphogenesis  (ISO)
ureter smooth muscle cell differentiation  (ISO)
ureter urothelium development  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381772,121,020 - 72,126,416 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1772,121,020 - 72,126,416 (+)EnsemblGRCh38hg38GRCh38
GRCh371770,117,161 - 70,122,557 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361767,628,756 - 67,634,156 (+)NCBINCBI36Build 36hg18NCBI36
Build 341767,628,755 - 67,634,156NCBI
Celera1766,688,499 - 66,693,898 (+)NCBICelera
Cytogenetic Map17q24.3NCBI
HuRef1765,510,108 - 65,515,656 (+)NCBIHuRef
CHM1_11770,181,222 - 70,186,622 (+)NCBICHM1_1
T2T-CHM13v2.01772,994,224 - 72,999,619 (+)NCBIT2T-CHM13v2.0
Sox9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911112,673,036 - 112,678,583 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11112,673,050 - 112,678,586 (+)EnsemblGRCm39 Ensembl
GRCm3811112,782,210 - 112,787,757 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11112,782,224 - 112,787,760 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711112,643,524 - 112,649,071 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611112,598,314 - 112,603,839 (+)NCBIMGSCv36mm8
Celera11124,540,008 - 124,545,554 (+)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1177.27NCBI
Sox9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81098,305,744 - 98,311,250 (+)NCBIGRCr8
mRatBN7.21097,806,485 - 97,811,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10102,866,804 - 102,872,316 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010102,329,807 - 102,335,320 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01097,726,102 - 97,731,622 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110102,408,236 - 102,408,622 (+)NCBI
Celera1096,424,278 - 96,429,703 (+)NCBICelera
Cytogenetic Map10q32.1NCBI
SOX9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21988,118,202 - 88,123,589 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11792,942,486 - 92,947,874 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01766,028,737 - 66,034,122 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11771,491,419 - 71,498,911 (+)NCBIpanpan1.1PanPan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.098,479,949 - 8,483,108 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl98,479,863 - 8,483,490 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.198,522,923 - 8,526,068 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.098,777,560 - 8,780,707 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.098,722,828 - 8,725,975 (-)NCBIUU_Cfam_GSD_1.0
Sox9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056028,350,254 - 8,354,855 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366551,847,272 - 1,852,705 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1649,518,185 - 49,523,898 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607720,379,690 - 20,385,117 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248012,296,168 - 2,301,596 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248012,296,353 - 2,300,853 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Ensembl Acc Id: ENSCLAT00000009498   ⟹   ENSCLAP00000009369
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_004955478940,177 - 945,563 (-)Ensembl
RefSeq Acc Id: XM_005402098   ⟹   XP_005402155
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955478941,684 - 945,563 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005402155 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000009369
  ENSCLAP00000009369.1
RefSeq Acc Id: XP_005402155   ⟸   XM_005402098
- UniProtKB: A0A8C2V2L2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCLAP00000009369   ⟸   ENSCLAT00000009498
Protein Domains
HMG box


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000006507 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000009498 ENTREZGENE
  ENSCLAT00000009498.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  Sox_N UniProtKB/TrEMBL
  SOX_TF UniProtKB/TrEMBL
NCBI Gene LOC102020005 ENTREZGENE
PANTHER PTHR45803:SF1 UniProtKB/TrEMBL
  SOX100B UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  Sox_N UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A8C2V2L2 ENTREZGENE, UniProtKB/TrEMBL


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
2016-08-16 Sox9  SRY-box 9    SRY (sex determining region Y)-box 9  Symbol and/or name change 5135510 APPROVED
2015-08-25 Sox9  SRY (sex determining region Y)-box 9  LOC102020005  transcription factor SOX-9-like  Symbol and/or name change 5135510 APPROVED