SOX6 (SRY-box transcription factor 6)

Gene

• Entrez ID: 55553
• Gene name: SRY-box transcription factor 6
• Gene symbol: SOX6
• Synonyms: HSSOX6, SOXD, TOLCAS
• Chromosome: 11
• Chromosome location: 11p15.2
• Summary: This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT003203	hsa-miR-1-3p	Luciferase reporter assay	20081117
MIRT004658	hsa-miR-499a-5p	Luciferase reporter assay	20081117
MIRT006113	hsa-miR-155-5p	Luciferase reporter assay, qRT-PCR, Western blot	21989846
MIRT052901	hsa-miR-16-5p	Luciferase reporter assay, qRT-PCR, Western blot	24852767
MIRT438545	hsa-miR-208a-3p	Luciferase reporter assay, Western blot	25023649
MIRT554044	hsa-miR-3148	PAR-CLIP	21572407
MIRT554045	hsa-miR-4668-5p	PAR-CLIP	21572407
MIRT554046	hsa-miR-562	PAR-CLIP	21572407
MIRT554047	hsa-miR-651-3p	PAR-CLIP	21572407
MIRT554048	hsa-miR-548n	PAR-CLIP	21572407
MIRT554049	hsa-miR-19a-3p	PAR-CLIP	21572407
MIRT554050	hsa-miR-19b-3p	PAR-CLIP	21572407
MIRT732043	hsa-miR-1269a	Luciferase reporter assay, qRT-PCR	26692953
MIRT734812	hsa-miR-132-3p	Luciferase reporter assay, Western blot	27556448
MIRT735019	hsa-miR-202-3p	Luciferase reporter assay, Western blot	26770366
MIRT783355	hsa-miR-1273h-5p	HITS-CLIP	27418678
MIRT783602	hsa-miR-129-5p	HITS-CLIP	27418678
MIRT784510	hsa-miR-30b-3p	HITS-CLIP	27418678
MIRT784523	hsa-miR-30c-1-3p	HITS-CLIP	27418678
MIRT784535	hsa-miR-30c-2-3p	HITS-CLIP	27418678
MIRT784585	hsa-miR-3122	HITS-CLIP	27418678
MIRT785246	hsa-miR-3689a-3p	HITS-CLIP	27418678
MIRT785259	hsa-miR-3689b-3p	HITS-CLIP	27418678
MIRT785272	hsa-miR-3689c	HITS-CLIP	27418678
MIRT785439	hsa-miR-3913-5p	HITS-CLIP	27418678
MIRT786046	hsa-miR-450a-1-3p	HITS-CLIP	27418678
MIRT788320	hsa-miR-6513-5p	HITS-CLIP	27418678
MIRT788484	hsa-miR-6731-5p	HITS-CLIP	27418678
MIRT788690	hsa-miR-6779-5p	HITS-CLIP	27418678
MIRT788702	hsa-miR-6780a-5p	HITS-CLIP	27418678
MIRT788735	hsa-miR-6788-5p	HITS-CLIP	27418678
MIRT789265	hsa-miR-6878-5p	HITS-CLIP	27418678
MIRT789858	hsa-miR-8085	HITS-CLIP	27418678
MIRT789902	hsa-miR-887-5p	HITS-CLIP	27418678

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription regulatory region sequence-specific DNA binding	IDA	26525805
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001217	Function	DNA-binding transcription repressor activity	ISS
GO:0001502	Process	Cartilage condensation	ISS
GO:0002062	Process	Chondrocyte differentiation	ISS
GO:0003677	Function	DNA binding	NAS	1614875
GO:0003700	Function	DNA-binding transcription factor activity	NAS	1614875
GO:0005515	Function	Protein binding	IPI	21262861
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA
GO:0005634	Component	Nucleus	NAS	1614875
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006355	Process	Regulation of transcription, DNA-templated	NAS	1614875
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007417	Process	Central nervous system development	IBA	21873635
GO:0007517	Process	Muscle organ development	NAS	11255018
GO:0021529	Process	Spinal cord oligodendrocyte cell differentiation	ISS
GO:0032332	Process	Positive regulation of chondrocyte differentiation	IBA	21873635
GO:0032332	Process	Positive regulation of chondrocyte differentiation	IDA	21401405
GO:0045165	Process	Cell fate commitment	IBA	21873635
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IEA
GO:0048708	Process	Astrocyte differentiation	IEA
GO:0051216	Process	Cartilage development	ISS
GO:0061036	Process	Positive regulation of cartilage development	IDA	21401405
GO:0071560	Process	Cellular response to transforming growth factor beta stimulus	IDA	21401405
GO:2000726	Process	Negative regulation of cardiac muscle cell differentiation	IMP	20081117
GO:2000741	Process	Positive regulation of mesenchymal stem cell differentiation	IDA	21401405

Other IDs

• MIM: 607257
• HGNC: 16421
• e!Ensembl: ENSG00000110693

Protein

• UniProt ID: P35712
• Protein name: Transcription factor SOX-6
• Protein function: Transcription factor that plays a key role in several developmental processes, including neurogenesis, chondrocytes differentiation and cartilage formation. Specifically binds the 5'-AACAAT-3' DNA motif present in enhancers and super-enhancers and promotes expression of genes important for chondrogenesis. Required for overt chondrogenesis when condensed prechondrocytes differentiate into early stage chondrocytes: SOX5 and SOX6 cooperatively bind with SOX9 on active enhancers and super-enhancers associated with cartilage-specific genes, and thereby potentiate SOX9's ability to transactivate. Not involved in precartilaginous condensation, the first step in chondrogenesis, during which skeletal progenitors differentiate into prechondrocytes. Together with SOX5, required to form and maintain a pool of highly proliferating chondroblasts between epiphyses and metaphyses, to form columnar chondroblasts, delay chondrocyte prehypertrophy but promote hypertrophy, and to delay terminal differentiation of chondrocytes on contact with ossification fronts. Binds to the proximal promoter region of the myelin protein MPZ gene, and is thereby involved in the differentiation of oligodendroglia in the developing spinal tube. Binds to the gene promoter of MBP and acts as a transcriptional repressor.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00505	HMG_box	621 → 689	HMG (high mobility group) box	Domain

• Sequence:

  MSSKQATSPFACAADGEDAMTQDLTSREKEEGSDQHVASHLPLHPIMHNKPHSEELPTLV
  STIQQDADWDSVLSSQQRMESENNKLCSLYSFRNTSTSPHKPDEGSRDREIMTSVTFGTP
  ERRKGSLADVVDTLKQKKLEEMTRTEQEDSSCMEKLLSKDWKEKMERLNTSELLGEIKGT
  PESLAEKERQLSTMITQLISLREQLLAAHDEQKKLAASQIEKQRQQMDLARQQQEQIARQ
  QQQLLQQQHKINLLQQQIQVQGHMPPLMIPIFPHDQRTLAAAAAAQQGFLFPPGITYKPG
  DNYPVQFIPSTMAAAAASGLSPLQLQKGHVSHPQINQRLKGLSDRFGRNLDTFEHGGGHS
  YNHKQIEQLYAAQLASMQVSPGAKMPSTPQPPNTAGTVSPTGIKNEKRGTSPVTQVKDEA
  AAQPLNLSSRPKTAEPVKSPTSPTQNLFPASKTSPVNLPNKSSIPSPIGGSLGRGSSLDI
  LSSLNSPALFGDQDTVMKAIQEARKMREQIQREQQQQQPHGVDGKLSSINNMGLNSCRNE
  KERTRFENLGPQLTGKSNEDGKLGPGVIDLTRPEDAEGSKAMNGSAAKLQQYYCWPTGGA
  TVAEARVYRDARGRASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWK
  SMSNQEKQPYYEEQARLSKIHLEKYPNYKYKPRPKRTCIVDGKKLRIGEYKQLMRSRRQE
  MRQFFTVGQQPQIPITTGTGVVYPGAITMATTTPSPQMTSDCSSTSASPEPSLPVIQSTY
  GMKTDGGSLAGNEMINGEDEMEMYDDYEDDPKSDYSSENEAPEAVSAN

• Sequence length: 828

Pathways

Reactome:

Deactivation of the beta-catenin transactivating complex

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Coronary artery disease	Coronary Artery Disease	rs137852988, rs121918313, rs-1, rs121918529, rs121918531, rs137852340, rs405509, rs1555800701, rs1215189537	29212778
Obesity	Obesity	rs34911341, rs74315349, rs1474810899, rs121918111, rs796065034, rs753856820, rs796065035, rs121918112, rs-1, rs104894023, rs137852821, rs1580764441, rs137852822, rs137852823, rs137852824, rs13447324, rs121913562, rs121913564, rs74315393, rs121913556, rs2989924, rs193922650, rs193922685, rs193922687, rs751160202, rs1421085, rs747681609, rs1553400259, rs13447339, rs370479598, rs1554394014, rs1553174844, rs756232889, rs369841551, rs1557670950, rs1571321748, rs148538980, rs1572820988, rs1591461970, rs1419374563, rs745921568, rs144159890, rs1570714352, rs779783209, rs1573250294, rs1573254045, rs1580744791, rs1580746829, rs6548238, rs7138803, rs7754840	19714249
Osteoporosis	Osteoporosis	rs72658152, rs72667023, rs587776916, rs72656370, rs768615287	19714249

Unknown
Disease name	Disease term	dbSNP ID	References
Mental depression	Major Depressive Disorder	rs587778876, rs587778877	29942085
Cardiovascular diseases	Cardiovascular Diseases		30595370
Mood disorder	Mood Disorders		29942085