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Protein

Transcription factor SOX-9

Gene

SOX9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays an important role in the normal skeletal development. May regulate the expression of other genes involved in chondrogenesis by acting as a transcription factor for these genes.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi105 – 173HMG boxPROSITE-ProRule annotationAdd BLAST69

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • core promoter sequence-specific DNA binding Source: UniProtKB
  • enhancer binding Source: UniProtKB
  • enhancer sequence-specific DNA binding Source: UniProtKB
  • pre-mRNA intronic binding Source: Ensembl
  • protein kinase A catalytic subunit binding Source: UniProtKB
  • protein kinase activity Source: UniProtKB
  • transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: UniProtKB
  • transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding Source: UniProtKB
  • transcription factor activity, sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000125398-MONOMER.
ReactomeiR-HSA-3769402. Deactivation of the beta-catenin transactivating complex.
SignaLinkiP48436.
SIGNORiP48436.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor SOX-9
Gene namesi
Name:SOX9
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:11204. SOX9.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • nuclear transcription factor complex Source: Ensembl
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • protein complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Campomelic dysplasia (CMD1)10 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare, often lethal, osteochondrodysplasia characterized by congenital bowing and angulation of long bones. Other skeletal defects include unusually small scapula, deformed pelvis and spine, and a missing pair of ribs. Craniofacial and ear defects are common. Most patients die soon after birth due to respiratory distress which has been attributed to hypoplasia of the tracheobronchial cartilage and small thoracic cage. Up to two-thirds of affected XY individuals have genital defects or may develop as phenotypic females.
See also OMIM:114290
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06364276A → E in CMD1; dimerization and the resulting capacity to activate promoters via dimeric binding sites is lost; other features of the protein function remain unaltered. 1 PublicationCorresponds to variant rs137853128dbSNPEnsembl.1
Natural variantiVAR_003735108P → L in CMD1. 1 Publication1
Natural variantiVAR_003736112F → L in CMD1; loss of DNA binding. 2 Publications1
Natural variantiVAR_003737112F → S in CMD1. 1 Publication1
Natural variantiVAR_063643113M → T in CMD1. 1 Publication1
Natural variantiVAR_063644113M → V in CMD1; residual DNA binding and transactivation of regulated genes. 1 Publication1
Natural variantiVAR_003738119A → V in CMD1; almost no loss of DNA binding. 2 Publications1
Natural variantiVAR_003739143W → R in CMD1. 1 Publication1
Natural variantiVAR_003740152R → P in CMD1. 1 Publication1
Natural variantiVAR_008529154F → L in CMD1; 5% of wild-type DNA binding activity; transcriptional activation is only reduced to 26% of wild-type activity. 1 PublicationCorresponds to variant rs137853129dbSNPEnsembl.1
Natural variantiVAR_008530158A → T in CMD1; 17% of wild-type DNA binding activity; shows a 2-fold reduction in nuclear import efficiency; transcriptional activation is only reduced to 62% of wild-type activity. 1 PublicationCorresponds to variant rs137853130dbSNPEnsembl.1
Natural variantiVAR_063645165H → Q in CMD1; residual DNA binding and transactivation of regulated genes. 1 Publication1
Natural variantiVAR_008531165H → Y in CMD1; loss of DNA binding. 2 PublicationsCorresponds to variant rs28940282dbSNPEnsembl.1
Natural variantiVAR_063646170P → L in CMD1. 1 Publication1
Natural variantiVAR_003741170P → R in CMD1. 2 Publications1
Natural variantiVAR_063647173K → E in CMD1. 1 PublicationCorresponds to variant rs104894647dbSNPEnsembl.1
Natural variantiVAR_003742354 – 356Missing in CMD1. 3
46,XX sex reversal 2 (SRXX2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA condition in which male gonads develop in a genetic female (female to male sex reversal).
See also OMIM:278850
46,XY sex reversal 10 (SRXY10)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder of sex development. Affected individuals have a 46,XY karyotype, show gonadal dysgenesis with streak gonads, look like normal females at birth, do not develop secondary sexual characteristics at puberty and do not menstruate.
See also OMIM:616425

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi6662.
MalaCardsiSOX9.
MIMi114290. phenotype.
278850. phenotype.
616425. phenotype.
OpenTargetsiENSG00000125398.
Orphaneti2138. 46,XX ovotesticular disorder of sex development.
393. 46,XX testicular disorder of sex development.
140. Campomelic dysplasia.
718. Isolated Pierre Robin syndrome.
PharmGKBiPA36041.

Polymorphism and mutation databases

BioMutaiSOX9.
DMDMi1351096.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000487391 – 509Transcription factor SOX-9Add BLAST509

Proteomic databases

EPDiP48436.
MaxQBiP48436.
PaxDbiP48436.
PeptideAtlasiP48436.
PRIDEiP48436.

PTM databases

iPTMnetiP48436.
PhosphoSitePlusiP48436.

Expressioni

Gene expression databases

BgeeiENSG00000125398.
CleanExiHS_SOX9.
GenevisibleiP48436. HS.

Organism-specific databases

HPAiCAB022456.
CAB068240.
HPA001758.

Interactioni

GO - Molecular functioni

  • protein kinase A catalytic subunit binding Source: UniProtKB

Protein-protein interaction databases

BioGridi112545. 17 interactors.
DIPiDIP-61319N.
IntActiP48436. 1 interactor.
STRINGi9606.ENSP00000245479.

Structurei

Secondary structure

1509
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi111 – 126Combined sources16
Helixi132 – 143Combined sources12
Helixi148 – 168Combined sources21

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1S9Mmodel-A101-177[»]
1SX9model-A101-177[»]
4EUWX-ray2.77A98-181[»]
ProteinModelPortaliP48436.
SMRiP48436.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi339 – 378Gln/Pro-richAdd BLAST40
Compositional biasi342 – 346Poly-Pro5

Sequence similaritiesi

Contains 1 HMG box DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0527. Eukaryota.
ENOG410XT0K. LUCA.
GeneTreeiENSGT00760000118988.
HOGENOMiHOG000108876.
HOVERGENiHBG002061.
InParanoidiP48436.
KOiK18435.
OMAiTITRSQY.
OrthoDBiEOG091G0EKD.
PhylomeDBiP48436.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
InterProiIPR009071. HMG_box_dom.
IPR029548. SOX-9.
IPR022151. Sox_N.
[Graphical view]
PANTHERiPTHR10270:SF212. PTHR10270:SF212. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF12444. Sox_N. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P48436-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNLLDPFMKM TDEQEKGLSG APSPTMSEDS AGSPCPSGSG SDTENTRPQE
60 70 80 90 100
NTFPKGEPDL KKESEEDKFP VCIREAVSQV LKGYDWTLVP MPVRVNGSSK
110 120 130 140 150
NKPHVKRPMN AFMVWAQAAR RKLADQYPHL HNAELSKTLG KLWRLLNESE
160 170 180 190 200
KRPFVEEAER LRVQHKKDHP DYKYQPRRRK SVKNGQAEAE EATEQTHISP
210 220 230 240 250
NAIFKALQAD SPHSSSGMSE VHSPGEHSGQ SQGPPTPPTT PKTDVQPGKA
260 270 280 290 300
DLKREGRPLP EGGRQPPIDF RDVDIGELSS DVISNIETFD VNEFDQYLPP
310 320 330 340 350
NGHPGVPATH GQVTYTGSYG ISSTAATPAS AGHVWMSKQQ APPPPPQQPP
360 370 380 390 400
QAPPAPQAPP QPQAAPPQQP AAPPQQPQAH TLTTLSSEPG QSQRTHIKTE
410 420 430 440 450
QLSPSHYSEQ QQHSPQQIAY SPFNLPHYSP SYPPITRSQY DYTDHQNSSS
460 470 480 490 500
YYSHAAGQGT GLYSTFTYMN PAQRPMYTPI ADTSGVPSIP QTHSPQHWEQ

PVYTQLTRP
Length:509
Mass (Da):56,137
Last modified:February 1, 1996 - v1
Checksum:i9289CFBB8D6631A2
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06364276A → E in CMD1; dimerization and the resulting capacity to activate promoters via dimeric binding sites is lost; other features of the protein function remain unaltered. 1 PublicationCorresponds to variant rs137853128dbSNPEnsembl.1
Natural variantiVAR_003735108P → L in CMD1. 1 Publication1
Natural variantiVAR_003736112F → L in CMD1; loss of DNA binding. 2 Publications1
Natural variantiVAR_003737112F → S in CMD1. 1 Publication1
Natural variantiVAR_063643113M → T in CMD1. 1 Publication1
Natural variantiVAR_063644113M → V in CMD1; residual DNA binding and transactivation of regulated genes. 1 Publication1
Natural variantiVAR_003738119A → V in CMD1; almost no loss of DNA binding. 2 Publications1
Natural variantiVAR_003739143W → R in CMD1. 1 Publication1
Natural variantiVAR_003740152R → P in CMD1. 1 Publication1
Natural variantiVAR_008529154F → L in CMD1; 5% of wild-type DNA binding activity; transcriptional activation is only reduced to 26% of wild-type activity. 1 PublicationCorresponds to variant rs137853129dbSNPEnsembl.1
Natural variantiVAR_008530158A → T in CMD1; 17% of wild-type DNA binding activity; shows a 2-fold reduction in nuclear import efficiency; transcriptional activation is only reduced to 62% of wild-type activity. 1 PublicationCorresponds to variant rs137853130dbSNPEnsembl.1
Natural variantiVAR_063645165H → Q in CMD1; residual DNA binding and transactivation of regulated genes. 1 Publication1
Natural variantiVAR_008531165H → Y in CMD1; loss of DNA binding. 2 PublicationsCorresponds to variant rs28940282dbSNPEnsembl.1
Natural variantiVAR_063646170P → L in CMD1. 1 Publication1
Natural variantiVAR_003741170P → R in CMD1. 2 Publications1
Natural variantiVAR_063647173K → E in CMD1. 1 PublicationCorresponds to variant rs104894647dbSNPEnsembl.1
Natural variantiVAR_003742354 – 356Missing in CMD1. 3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46629 mRNA. Translation: CAA86598.1.
S74506, S74504, S74505 Genomic DNA. Translation: AAB32870.1.
BT006875 mRNA. Translation: AAP35521.1.
CH471099 Genomic DNA. Translation: EAW89102.1.
BC007951 mRNA. Translation: AAH07951.1.
BC056420 mRNA. Translation: AAH56420.1.
CCDSiCCDS11689.1.
PIRiA55204.
RefSeqiNP_000337.1. NM_000346.3.
UniGeneiHs.647409.

Genome annotation databases

EnsembliENST00000245479; ENSP00000245479; ENSG00000125398.
GeneIDi6662.
KEGGihsa:6662.
UCSCiuc002jiw.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46629 mRNA. Translation: CAA86598.1.
S74506, S74504, S74505 Genomic DNA. Translation: AAB32870.1.
BT006875 mRNA. Translation: AAP35521.1.
CH471099 Genomic DNA. Translation: EAW89102.1.
BC007951 mRNA. Translation: AAH07951.1.
BC056420 mRNA. Translation: AAH56420.1.
CCDSiCCDS11689.1.
PIRiA55204.
RefSeqiNP_000337.1. NM_000346.3.
UniGeneiHs.647409.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1S9Mmodel-A101-177[»]
1SX9model-A101-177[»]
4EUWX-ray2.77A98-181[»]
ProteinModelPortaliP48436.
SMRiP48436.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112545. 17 interactors.
DIPiDIP-61319N.
IntActiP48436. 1 interactor.
STRINGi9606.ENSP00000245479.

PTM databases

iPTMnetiP48436.
PhosphoSitePlusiP48436.

Polymorphism and mutation databases

BioMutaiSOX9.
DMDMi1351096.

Proteomic databases

EPDiP48436.
MaxQBiP48436.
PaxDbiP48436.
PeptideAtlasiP48436.
PRIDEiP48436.

Protocols and materials databases

DNASUi6662.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000245479; ENSP00000245479; ENSG00000125398.
GeneIDi6662.
KEGGihsa:6662.
UCSCiuc002jiw.4. human.

Organism-specific databases

CTDi6662.
DisGeNETi6662.
GeneCardsiSOX9.
GeneReviewsiSOX9.
HGNCiHGNC:11204. SOX9.
HPAiCAB022456.
CAB068240.
HPA001758.
MalaCardsiSOX9.
MIMi114290. phenotype.
278850. phenotype.
608160. gene.
616425. phenotype.
neXtProtiNX_P48436.
OpenTargetsiENSG00000125398.
Orphaneti2138. 46,XX ovotesticular disorder of sex development.
393. 46,XX testicular disorder of sex development.
140. Campomelic dysplasia.
718. Isolated Pierre Robin syndrome.
PharmGKBiPA36041.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0527. Eukaryota.
ENOG410XT0K. LUCA.
GeneTreeiENSGT00760000118988.
HOGENOMiHOG000108876.
HOVERGENiHBG002061.
InParanoidiP48436.
KOiK18435.
OMAiTITRSQY.
OrthoDBiEOG091G0EKD.
PhylomeDBiP48436.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000125398-MONOMER.
ReactomeiR-HSA-3769402. Deactivation of the beta-catenin transactivating complex.
SignaLinkiP48436.
SIGNORiP48436.

Miscellaneous databases

ChiTaRSiSOX9. human.
GeneWikiiSOX9.
GenomeRNAii6662.
PROiP48436.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000125398.
CleanExiHS_SOX9.
GenevisibleiP48436. HS.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
InterProiIPR009071. HMG_box_dom.
IPR029548. SOX-9.
IPR022151. Sox_N.
[Graphical view]
PANTHERiPTHR10270:SF212. PTHR10270:SF212. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF12444. Sox_N. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSOX9_HUMAN
AccessioniPrimary (citable) accession number: P48436
Secondary accession number(s): Q53Y80
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 2, 2016
This is version 172 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.