| Tag | Content |
|---|---|
| Uniprot ID | F1LYL9 |
| Entrez ID | 140586 |
| Genbank protein ID | EDM06505.1 |
| Genbank nucleotide ID | NM_080403.1 |
| Ensembl protein ID | ENSRNOP00000003511 |
| Ensembl nucleotide ID | ENSRNOG00000002607 |
| Gene name | Transcription factor SOX-9 |
| Gene symbol | Sox9 |
| Organism | Rattus norvegicus |
| NCBI taxa ID | 10116 |
| Cleft type | |
| Developmental stage | |
| Data sources | Homology search |
| Reference | |
| Functional description | Transcription factor that plays a key role in chondrocytes differentiation and skeletal development (By similarity). Specifically binds the 5'-ACAAAG-3' DNA motif present in enhancers and super-enhancers and promotes expression of genes important for chondrogenesis, including cartilage matrix protein-coding genes COL2A1, COL4A2, COL9A1, COL11A2 and ACAN, SOX5 and SOX6 (PubMed:26150426). Also binds to some promoter regions (By similarity). Plays a central role in successive steps of chondrocyte differentiation (By similarity). Absolutely required for precartilaginous condensation, the first step in chondrogenesis during which skeletal progenitors differentiate into prechondrocytes (By similarity). Together with SOX5 and SOX6, required for overt chondrogenesis when condensed prechondrocytes differentiate into early stage chondrocytes, the second step in chondrogenesis (By similarity). Later, required to direct hypertrophic maturation and block osteoblast differentiation of growth plate chondrocytes: maintains chondrocyte columnar proliferation, delays prehypertrophy and then prevents osteoblastic differentiation of chondrocytes by lowering beta-catenin (CTNNB1) signaling and RUNX2 expression (By similarity). Also required for chondrocyte hypertrophy, both indirectly, by keeping the lineage fate of chondrocytes, and directly, by remaining present in upper hypertrophic cells and transactivating COL10A1 along with MEF2C (By similarity). Low lipid levels are the main nutritional determinant for chondrogenic commitment of skeletal progenitor cells: when lipids levels are low, FOXO (FOXO1 and FOXO3) transcription factors promote expression of SOX9, which induces chondrogenic commitment and suppresses fatty acid oxidation (By similarity). Mechanistically, helps, but is not required, to remove epigenetic signatures of transcriptional repression and deposit active promoter and enhancer marks at chondrocyte-specific genes (By similarity). Acts in cooperation with the Hedgehog pathway-dependent GLI (GLI1 and GLI3) transcription factors (By similarity). In addition to cartilage development, also acts as a regulator of proliferation and differentiation in epithelial stem/progenitor cells: involved in the lung epithelium during branching morphogenesis, by balancing proliferation and differentiation and regulating the extracellular matrix (By similarity). Controls epithelial branching during kidney development (By similarity). |
| Sequence | MNLLDPFMKM TDEQEKGLSG APSPTMSEDS AGSPCPSGSG SDTENTRPQE NTFPKGEPDL 60 KKESEEDKFP VCIREAVSQV LKGYDWTLVP MPVRVNGSSK NKPHVKRPMN AFMVWAQAAR 120 RKLADQYPHL HNAELSKTLG KLWRLLNESE KRPFVEEAER LRVQHKKDHP DYKYQPRRRK 180 SVKNGQAEAE EATEQTHISP NAIFKALQAD SPHSSSGMSE VHSPGEHSGQ SQGPPTPPTT 240 PKTDVQAGKV DLKREGRPLA EGGRQPPIDF RDVDIGELSS DVISNIETFD VNEFDQYLPP 300 NGHPGVPATH GQVSYTGSYG ISSTAPTPAT AGHVWMSKQQ APPPPPQQPP QAPQAPQAPP 360 QQQAPPQPQQ APQQQQAHTL TTLSSEPGQS QRTHIKTEQL SPSHYSEQQQ HSPQQISYSP 420 FNLPHYNPSY PTITRSQYDY TDHQNSGSYY SHAAGQGSGL YSTFTYMNPA QRPMYTPIAD 480 TSGVPSIPQT HSPQHWEQPV YTQLTRP 507 |
Abbreviation :
CLO : cleft lip only. CPO : cleft palate only.
CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.
| Relation | Gene symbol | Entrez ID | UniProt ID | Cleft type | Developmental stage | Species | Evidence | Details |
|---|---|---|---|---|---|---|---|---|
| 1:1 ortholog | SOX9 | 106503295 | A0A452FKA9 | Capra hircus | Prediction | More>> | ||
| 1:1 ortholog | SOX9 | 6662 | P48436 | Homo sapiens | Publication | More>> | ||
| 1:1 ortholog | Sox9 | 20682 | Q04887 | CPO | E14.5 | Mus musculus | Publication | More>> |
| 1:1 ortholog | SOX9 | H2QDR6 | Pan troglodytes | Prediction | More>> | |||
| 1:1 ortholog | SOX9 | 396840 | F1RV30 | Sus scrofa | Prediction | More>> | ||
| 1:1 ortholog | Sox9 | 140586 | F1LYL9 | Rattus norvegicus | Prediction | More>> | ||
| 1:1 ortholog | sox9a | 60641 | Q9DFH2 | Danio rerio | Prediction | More>> |
| GO ID | GO Term |
|---|---|
| GO:0044798 | nuclear transcription factor complex |
| GO:0005654 | nucleoplasm |
| GO:0005634 | nucleus |
| GO:0032991 | protein-containing complex |
| GO:0005667 | transcription factor complex |
| GO:0008013 | beta-catenin binding |
| GO:0043425 | bHLH transcription factor binding |
| GO:0003682 | chromatin binding |
| GO:0035326 | cis-regulatory region binding |
| GO:0000987 | cis-regulatory region sequence-specific DNA binding |
| GO:0001228 | DNA-binding transcription activator activity, RNA polymerase II-specific |
| GO:0003700 | DNA-binding transcription factor activity |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific |
| GO:0097157 | pre-mRNA intronic binding |
| GO:0034236 | protein kinase A catalytic subunit binding |
| GO:0000978 | RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| GO:0043565 | sequence-specific DNA binding |
| GO:0044212 | transcription regulatory region DNA binding |
| GO:0000976 | transcription regulatory region sequence-specific DNA binding |
| GO:0097065 | anterior head development |
| GO:0003180 | aortic valve morphogenesis |
| GO:0060018 | astrocyte fate commitment |
| GO:0001658 | branching involved in ureteric bud morphogenesis |
| GO:0060532 | bronchus cartilage development |
| GO:0019933 | cAMP-mediated signaling |
| GO:0001502 | cartilage condensation |
| GO:0051216 | cartilage development |
| GO:0030154 | cell differentiation |
| GO:0045165 | cell fate commitment |
| GO:0001708 | cell fate specification |
| GO:0098609 | cell-cell adhesion |
| GO:0071364 | cellular response to epidermal growth factor stimulus |
| GO:0071504 | cellular response to heparin |
| GO:0071347 | cellular response to interleukin-1 |
| GO:0071260 | cellular response to mechanical stimulus |
| GO:0071300 | cellular response to retinoic acid |
| GO:0071560 | cellular response to transforming growth factor beta stimulus |
| GO:0007417 | central nervous system development |
| GO:0002063 | chondrocyte development |
| GO:0002062 | chondrocyte differentiation |
| GO:0003413 | chondrocyte differentiation involved in endochondral bone morphogenesis |
| GO:0003415 | chondrocyte hypertrophy |
| GO:0006338 | chromatin remodeling |
| GO:0090103 | cochlea morphogenesis |
| GO:0007010 | cytoskeleton organization |
| GO:0003203 | endocardial cushion morphogenesis |
| GO:0060350 | endochondral bone morphogenesis |
| GO:0031018 | endocrine pancreas development |
| GO:0007173 | epidermal growth factor receptor signaling pathway |
| GO:0060517 | epithelial cell proliferation involved in prostatic bud elongation |
| GO:0001837 | epithelial to mesenchymal transition |
| GO:0060441 | epithelial tube branching involved in lung morphogenesis |
| GO:0070371 | ERK1 and ERK2 cascade |
| GO:0030198 | extracellular matrix organization |
| GO:0001942 | hair follicle development |
| GO:0070384 | Harderian gland development |
| GO:0007507 | heart development |
| GO:0003170 | heart valve development |
| GO:0003188 | heart valve formation |
| GO:0003179 | heart valve morphogenesis |
| GO:0048873 | homeostasis of number of cells within a tissue |
| GO:0060729 | intestinal epithelial structure maintenance |
| GO:0035622 | intrahepatic bile duct development |
| GO:0032808 | lacrimal gland development |
| GO:0060174 | limb bud formation |
| GO:0060487 | lung epithelial cell differentiation |
| GO:0061145 | lung smooth muscle development |
| GO:0019100 | male germ-line sex determination |
| GO:0008584 | male gonad development |
| GO:0030238 | male sex determination |
| GO:0030879 | mammary gland development |
| GO:0072289 | metanephric nephron tubule formation |
| GO:0072170 | metanephric tubule development |
| GO:0061138 | morphogenesis of a branching epithelium |
| GO:0002009 | morphogenesis of an epithelium |
| GO:0043066 | negative regulation of apoptotic process |
| GO:0070168 | negative regulation of biomineral tissue development |
| GO:0030502 | negative regulation of bone mineralization |
| GO:0090090 | negative regulation of canonical Wnt signaling pathway |
| GO:0008285 | negative regulation of cell population proliferation |
| GO:0032331 | negative regulation of chondrocyte differentiation |
| GO:0030857 | negative regulation of epithelial cell differentiation |
| GO:0050680 | negative regulation of epithelial cell proliferation |
| GO:0010629 | negative regulation of gene expression |
| GO:0002683 | negative regulation of immune system process |
| GO:2001054 | negative regulation of mesenchymal cell apoptotic process |
| GO:0045662 | negative regulation of myoblast differentiation |
| GO:0030279 | negative regulation of ossification |
| GO:0046533 | negative regulation of photoreceptor cell differentiation |
| GO:1902894 | negative regulation of pri-miRNA transcription by RNA polymerase II |
| GO:0000122 | negative regulation of transcription by RNA polymerase II |
| GO:0045892 | negative regulation of transcription, DNA-templated |
| GO:0014032 | neural crest cell development |
| GO:0007219 | Notch signaling pathway |
| GO:0030903 | notochord development |
| GO:0006334 | nucleosome assembly |
| GO:0048709 | oligodendrocyte differentiation |
| GO:0001503 | ossification |
| GO:0071599 | otic vesicle development |
| GO:0030916 | otic vesicle formation |
| GO:0090190 | positive regulation of branching involved in ureteric bud morphogenesis |
| GO:0061036 | positive regulation of cartilage development |
| GO:0008284 | positive regulation of cell population proliferation |
| GO:2000138 | positive regulation of cell proliferation involved in heart morphogenesis |
| GO:0032332 | positive regulation of chondrocyte differentiation |
| GO:1902732 | positive regulation of chondrocyte proliferation |
| GO:0030858 | positive regulation of epithelial cell differentiation |
| GO:0010634 | positive regulation of epithelial cell migration |
| GO:0050679 | positive regulation of epithelial cell proliferation |
| GO:1901203 | positive regulation of extracellular matrix assembly |
| GO:0010628 | positive regulation of gene expression |
| GO:0090184 | positive regulation of kidney development |
| GO:2000020 | positive regulation of male gonad development |
| GO:0002053 | positive regulation of mesenchymal cell proliferation |
| GO:2000741 | positive regulation of mesenchymal stem cell differentiation |
| GO:0014068 | positive regulation of phosphatidylinositol 3-kinase signaling |
| GO:0045732 | positive regulation of protein catabolic process |
| GO:0001934 | positive regulation of protein phosphorylation |
| GO:0045944 | positive regulation of transcription by RNA polymerase II |
| GO:0045893 | positive regulation of transcription, DNA-templated |
| GO:0030850 | prostate gland development |
| GO:0060512 | prostate gland morphogenesis |
| GO:0043491 | protein kinase B signaling |
| GO:0034504 | protein localization to nucleus |
| GO:0065003 | protein-containing complex assembly |
| GO:0042981 | regulation of apoptotic process |
| GO:0061046 | regulation of branching involved in lung morphogenesis |
| GO:0030155 | regulation of cell adhesion |
| GO:0010564 | regulation of cell cycle process |
| GO:0045595 | regulation of cell differentiation |
| GO:0042127 | regulation of cell population proliferation |
| GO:0060784 | regulation of cell proliferation involved in tissue homeostasis |
| GO:2000794 | regulation of epithelial cell proliferation involved in lung morphogenesis |
| GO:0010468 | regulation of gene expression |
| GO:0006357 | regulation of transcription by RNA polymerase II |
| GO:0072034 | renal vesicle induction |
| GO:0060041 | retina development in camera-type eye |
| GO:0060221 | retinal rod cell differentiation |
| GO:0060009 | Sertoli cell development |
| GO:0060008 | Sertoli cell differentiation |
| GO:0007165 | signal transduction |
| GO:0001501 | skeletal system development |
| GO:0035019 | somatic stem cell population maintenance |
| GO:0007283 | spermatogenesis |
| GO:0001894 | tissue homeostasis |
| GO:0060534 | trachea cartilage development |
| GO:0072189 | ureter development |
| GO:0072197 | ureter morphogenesis |
| GO:0072193 | ureter smooth muscle cell differentiation |
| GO:0072190 | ureter urothelium development |
| PROSITE ID | PROSITE Term |
|---|---|
| PS50118 | HMG_BOX_2 |