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Aliases for SOX6 Gene

Aliases for SOX6 Gene

  • SRY-Box 6 2 3 5
  • SRY (Sex Determining Region Y)-Box 6 2 3
  • Transcription Factor SOX-6 3
  • SRY-Box Containing Gene 6 3
  • SRY Box 6 2
  • HSSOX6 3
  • SOXD 3

External Ids for SOX6 Gene

Previous GeneCards Identifiers for SOX6 Gene

  • GC11M017086
  • GC11M016740
  • GC11M016032
  • GC11M015957
  • GC11M015673

Summaries for SOX6 Gene

Entrez Gene Summary for SOX6 Gene

  • 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]

GeneCards Summary for SOX6 Gene

SOX6 (SRY-Box 6) is a Protein Coding gene. Diseases associated with SOX6 include Multiple Synostoses Syndrome. Among its related pathways are Signaling by Wnt and ERK Signaling. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is SOX5.

UniProtKB/Swiss-Prot for SOX6 Gene

  • Transcriptional activator. Binds specifically to the DNA sequence 5-AACAAT-3. Plays a key role in several developmental processes, including neurogenesis and skeleton formation.

Gene Wiki entry for SOX6 Gene

Additional gene information for SOX6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX6 Gene

Genomics for SOX6 Gene

GeneHancer (GH) Regulatory Elements for SOX6 Gene

Promoters and enhancers for SOX6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J016737 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.6 550 3 HDGF FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B SOX6 C11orf58 SNORD14A SNORD14B PIR48413
GH11J016401 Promoter/Enhancer 2.1 VISTA UCNEbase EPDnew ENCODE 650.1 +336.5 336484 2.8 ELF3 FOXA2 THAP11 KLF11 ZBTB25 MIER2 PPARG SP1 RCOR2 NR2C1 SOX6 GC11P016359 GC11M016482
GH11J016396 Promoter/Enhancer 1 EPDnew ENCODE 650.1 +342.4 342431 1.9 SP1 AFF1 HNF1A TAF1 HMG20A REST PPARG SOX6 GC11P016359 GC11M016482
GH11J016741 Enhancer 0.7 Ensembl dbSUPER 650.7 -1.9 -1910 0.6 ZNF610 POLR2A ZIC2 ZNF18 SOX6 GC11M016777 C11orf58
GH11J016740 Enhancer 0.6 FANTOM5 dbSUPER 650.7 -1.4 -1371 0.4 ZBTB33 MLLT1 SOX6 GC11M016777 C11orf58
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOX6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOX6 gene promoter:
  • C/EBPalpha
  • C/EBPbeta
  • LyF-1
  • AREB6
  • CREB
  • deltaCREB
  • Sox5

Genomic Locations for SOX6 Gene

Genomic Locations for SOX6 Gene
chr11:15,966,449-16,739,591
(GRCh38/hg38)
Size:
773,143 bases
Orientation:
Minus strand
chr11:15,987,995-16,761,138
(GRCh37/hg19)
Size:
773,144 bases
Orientation:
Minus strand

Genomic View for SOX6 Gene

Genes around SOX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX6 Gene

Proteins for SOX6 Gene

  • Protein details for SOX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35712-SOX6_HUMAN
    Recommended name:
    Transcription factor SOX-6
    Protein Accession:
    P35712
    Secondary Accessions:
    • Q86VX7
    • Q9BXQ3
    • Q9BXQ4
    • Q9BXQ5
    • Q9H0I8

    Protein attributes for SOX6 Gene

    Size:
    828 amino acids
    Molecular mass:
    91921 Da
    Quaternary structure:
    • Interacts with DAZAP2.
    SequenceCaution:
    • Sequence=BC037866; Type=Frameshift; Positions=505; Evidence={ECO:0000305};

    Alternative splice isoforms for SOX6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SOX6 Gene

Post-translational modifications for SOX6 Gene

Antibody Products

  • Abcam antibodies for SOX6
  • Boster Bio Antibodies for SOX6

No data available for DME Specific Peptides for SOX6 Gene

Domains & Families for SOX6 Gene

Gene Families for SOX6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SOX6 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SOX6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SOX6: view

No data available for UniProtKB/Swiss-Prot for SOX6 Gene

Function for SOX6 Gene

Molecular function for SOX6 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator. Binds specifically to the DNA sequence 5-AACAAT-3. Plays a key role in several developmental processes, including neurogenesis and skeleton formation.

Phenotypes From GWAS Catalog for SOX6 Gene

Gene Ontology (GO) - Molecular Function for SOX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding NAS 1614875
GO:0003700 DNA binding transcription factor activity IEA,NAS 1614875
genes like me logo Genes that share ontologies with SOX6: view
genes like me logo Genes that share phenotypes with SOX6: view

Animal Models for SOX6 Gene

MGI Knock Outs for SOX6:

Animal Model Products

CRISPR Products

Targeted motifs for SOX6 Gene
HOMER Transcription Factor Regulatory Elements motif SOX6
  • Consensus sequence: CCATTGTTNY Submotif: canonical Cell Type: Myotubes GEO ID: GSE32627

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOX6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for SOX6 Gene

Localization for SOX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX6 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SOX6 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SOX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,NAS 1614875
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with SOX6: view

Pathways & Interactions for SOX6 Gene

genes like me logo Genes that share pathways with SOX6: view

Gene Ontology (GO) - Biological Process for SOX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0000902 cell morphogenesis IEA --
GO:0001701 in utero embryonic development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated NAS 1614875
genes like me logo Genes that share ontologies with SOX6: view

No data available for SIGNOR curated interactions for SOX6 Gene

Drugs & Compounds for SOX6 Gene

(1) Additional Compounds for SOX6 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SOX6: view

Transcripts for SOX6 Gene

mRNA/cDNA for SOX6 Gene

Unigene Clusters for SOX6 Gene

SRY (sex determining region Y)-box 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SOX6

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SOX6 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b
SP1: - - - - - - - -
SP2: - - - - -
SP3: - - - - - -
SP4: - - -
SP5: - -

Relevant External Links for SOX6 Gene

GeneLoc Exon Structure for
SOX6
ECgene alternative splicing isoforms for
SOX6

Expression for SOX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SOX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SOX6 Gene

This gene is overexpressed in Muscle - Skeletal (x4.7).

Protein differential expression in normal tissues from HIPED for SOX6 Gene

This gene is overexpressed in Adipocyte (61.5) and Peripheral blood mononuclear cells (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SOX6 Gene



Protein tissue co-expression partners for SOX6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SOX6 Gene:

SOX6

SOURCE GeneReport for Unigene cluster for SOX6 Gene:

Hs.368226

mRNA Expression by UniProt/SwissProt for SOX6 Gene:

P35712-SOX6_HUMAN
Tissue specificity: Expressed in a wide variety of tissues, most abundantly in skeletal muscle.

Evidence on tissue expression from TISSUES for SOX6 Gene

  • Blood(4.2)
  • Liver(4.1)
  • Nervous system(2.6)
  • Muscle(2)
genes like me logo Genes that share expression patterns with SOX6: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX6 Gene

Orthologs for SOX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SOX6 34 33
  • 99.6 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SOX6 34 33
  • 96.43 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SOX6 34 33
  • 94.71 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SOX6 34
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sox6 16 34 33
  • 92.46 (n)
rat
(Rattus norvegicus)
Mammalia Sox6 33
  • 92.45 (n)
oppossum
(Monodelphis domestica)
Mammalia SOX6 34
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves SOX6 34 33
  • 87.26 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SOX6 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sox6 33
  • 79.18 (n)
zebrafish
(Danio rerio)
Actinopterygii sox6 34 33
  • 76.4 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11718 33
fruit fly
(Drosophila melanogaster)
Insecta Sox102F 34 35
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea egl-13 34 35
  • 31 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea Cin.10481 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10481 33
Species where no ortholog for SOX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SOX6 Gene

ENSEMBL:
Gene Tree for SOX6 (if available)
TreeFam:
Gene Tree for SOX6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SOX6: view image

Paralogs for SOX6 Gene

Paralogs for SOX6 Gene

(10) SIMAP similar genes for SOX6 Gene using alignment to 6 proteins:

  • SOX6_HUMAN
  • E9PN02_HUMAN
  • E9PQ67_HUMAN
  • E9PQ78_HUMAN
  • E9PQL4_HUMAN
  • L8EBC2_HUMAN
genes like me logo Genes that share paralogs with SOX6: view

Variants for SOX6 Gene

Sequence variations from dbSNP and Humsavar for SOX6 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000001559 -- 16,060,239(-) T/C intron_variant
rs1000005858 -- 16,414,553(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000013408 -- 16,006,122(-) C/A/T intron_variant
rs1000030490 -- 16,401,361(-) G/A intron_variant
rs1000032666 -- 16,315,086(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SOX6 Gene

Variant ID Type Subtype PubMed ID
dgv1662n54 CNV loss 21841781
dgv326e212 CNV loss 25503493
esv1378524 CNV insertion 17803354
esv2051843 CNV deletion 18987734
esv2461915 CNV deletion 19546169
esv2631763 CNV deletion 19546169
esv2666456 CNV deletion 23128226
esv2740786 CNV deletion 23290073
esv2740902 CNV deletion 23290073
esv2744134 CNV deletion 23290073
esv2744135 CNV deletion 23290073
esv2744136 CNV deletion 23290073
esv2744137 CNV deletion 23290073
esv2744138 CNV deletion 23290073
esv2744139 CNV deletion 23290073
esv3307050 CNV mobile element insertion 20981092
esv3308313 CNV mobile element insertion 20981092
esv3358765 CNV insertion 20981092
esv3361836 CNV insertion 20981092
esv3578272 CNV gain 25503493
esv3579388 CNV loss 25503493
esv3579391 CNV loss 25503493
esv8667 CNV gain 19470904
nsv435922 CNV deletion 17901297
nsv467710 CNV loss 19166990
nsv477230 CNV novel sequence insertion 20440878
nsv477567 CNV novel sequence insertion 20440878
nsv478212 CNV novel sequence insertion 20440878
nsv510244 OTHER sequence alteration 20534489
nsv553562 CNV loss 21841781
nsv553565 CNV loss 21841781
nsv553566 CNV gain 21841781
nsv832074 CNV loss 17160897
nsv832075 CNV gain 17160897
nsv957186 CNV deletion 24416366

Variation tolerance for SOX6 Gene

Residual Variation Intolerance Score: 2.23% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.04; 21.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SOX6 Gene

Human Gene Mutation Database (HGMD)
SOX6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SOX6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SOX6 Gene

Disorders for SOX6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SOX6 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
multiple synostoses syndrome
  • symphalangism-brachydactyly syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SOX6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SOX6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SOX6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SOX6 Gene

Publications for SOX6 Gene

  1. Cloning, characterization and chromosome mapping of the human SOX6 gene. (PMID: 11255018) Cohen-Barak O … Brilliant MH (Gene 2001) 2 3 4 22 58
  2. Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males. (PMID: 19714249) Liu YZ … Deng HW (PloS one 2009) 3 22 44 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. (PMID: 20548944) Hsu YH … Kiel DP (PLoS genetics 2010) 3 44 58

Products for SOX6 Gene

Sources for SOX6 Gene

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