Human Gene SOX6 (uc001mme.3) Description and Page Index
  Description: Homo sapiens SRY (sex determining region Y)-box 6 (SOX6), transcript variant 4, mRNA.
RefSeq Summary (NM_001145819): 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].
Transcript (Including UTRs)
   Position: hg19 chr11:15,987,995-16,424,413 Size: 436,419 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr11:15,994,355-16,424,380 Size: 430,026 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:15,987,995-16,424,413)mRNA (may differ from genome)Protein (841 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SOX6_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-6;
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.
SUBUNIT: Interacts with DAZAP2 (By similarity).
INTERACTION: O15266:SHOX; NbExp=3; IntAct=EBI-3505706, EBI-3505698;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in a wide variety of tissues, most abundantly in skeletal muscle.
PTM: Sumoylation inhibits the transcriptional activity.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
SEQUENCE CAUTION: Sequence=BC037866; Type=Frameshift; Positions=505;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SOX6
CDC HuGE Published Literature: SOX6
Positive Disease Associations: Bone mineral density (hip) , Myocardial Infarction , Obesity , obesity and osteoporosis
Related Studies:
  1. Bone mineral density (hip)
    Rivadeneira ,et al. 2009, Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies, Nature genetics 2009 41- 11 : 1199-206. [PubMed 19801982]
  2. Myocardial Infarction
    , , . [PubMed 0]
  3. Obesity
    Yao-Zhong Liu et al. PloS one 2010, Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males., PloS one. [PubMed 19714249]
    Our findings, together with the prior biological evidence, suggest the SOX6 genes importance in co-regulation of obesity and osteoporosis.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SOX6
Diseases sorted by gene-association score: multiple synostoses syndrome (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.04 RPKM in Testis
Total median expression: 48.63 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -0.9033-0.027 Picture PostScript Text
3' UTR -1805.306360-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on P35712
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000902 cell morphogenesis
GO:0001701 in utero embryonic development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007517 muscle organ development
GO:0009791 post-embryonic development
GO:0010468 regulation of gene expression
GO:0016458 gene silencing
GO:0021778 oligodendrocyte cell fate specification
GO:0030097 hemopoiesis
GO:0030218 erythrocyte differentiation
GO:0032332 positive regulation of chondrocyte differentiation
GO:0042692 muscle cell differentiation
GO:0045165 cell fate commitment
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048708 astrocyte differentiation
GO:0048709 oligodendrocyte differentiation
GO:0048821 erythrocyte development
GO:0051216 cartilage development
GO:0055007 cardiac muscle cell differentiation
GO:0061036 positive regulation of cartilage development
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:2000726 negative regulation of cardiac muscle cell differentiation
GO:2000741 positive regulation of mesenchymal stem cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AF309034 - Homo sapiens SOX6 mRNA, complete cds.
BC037866 - Homo sapiens SRY (sex determining region Y)-box 6, mRNA (cDNA clone IMAGE:5273203), with apparent retained intron.
BC047064 - Homo sapiens SRY (sex determining region Y)-box 6, mRNA (cDNA clone MGC:48285 IMAGE:5269193), complete cds.
AL136780 - Homo sapiens mRNA; cDNA DKFZp434N1217 (from clone DKFZp434N1217).
AM392594 - Synthetic construct Homo sapiens clone IMAGE:100002389 for hypothetical protein (SOX6 gene).
AM392730 - Synthetic construct Homo sapiens clone IMAGE:100002390 for hypothetical protein (SOX6 gene).
AB463289 - Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.
AM393356 - Synthetic construct Homo sapiens clone IMAGE:100001775 for hypothetical protein (SOX6 gene).
AK097455 - Homo sapiens cDNA FLJ40136 fis, clone TESTI2012550, moderately similar to TRANSCRIPTION FACTOR SOX-6.
AK310506 - Homo sapiens cDNA, FLJ17548.
AL833302 - Homo sapiens mRNA; cDNA DKFZp451M129 (from clone DKFZp451M129).
BC029429 - Homo sapiens SRY (sex determining region Y)-box 6, mRNA (cDNA clone IMAGE:4046207), with apparent retained intron.
AK021785 - Homo sapiens cDNA FLJ11723 fis, clone HEMBA1005314.
HZ464144 - WO 2015194610-A/580: Kit and method for detecting lung cancer.
LY498045 - KR 1020170018409-A/580: KIT OR DEVICE FOR DETECTING LUNG CANCER, AND LUNG CANCER DETECTION METHOD.
MA143308 - WO 2018056432-A/23: A method of detecting hemolysis of blood sample and a chip for detecting hemolysis.
MS997111 - Sequence 580 from Patent EP3159416.
HZ464125 - WO 2015194610-A/561: Kit and method for detecting lung cancer.
HZ482409 - JP 2015535430-A/2915: TERMINALLY MODIFIED RNA.
HZ792340 - JP 2016504050-A/4085: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC515072 - Sequence 5325 from Patent WO2014113089.
LF160640 - JP 2016513950-A/706: Oligomers with improved off-target profile.
LP951740 - Sequence 246 from Patent WO2017157650.
LQ072660 - Sequence 2984 from Patent EP2964234.
LY498026 - KR 1020170018409-A/561: KIT OR DEVICE FOR DETECTING LUNG CANCER, AND LUNG CANCER DETECTION METHOD.
MA143292 - WO 2018056432-A/7: A method of detecting hemolysis of blood sample and a chip for detecting hemolysis.
MS997092 - Sequence 561 from Patent EP3159416.
JA483748 - Sequence 56 from Patent EP2303292.
JD557207 - Sequence 538231 from Patent EP1572962.
JD557815 - Sequence 538839 from Patent EP1572962.
JD208009 - Sequence 189033 from Patent EP1572962.
JD394999 - Sequence 376023 from Patent EP1572962.
JD450013 - Sequence 431037 from Patent EP1572962.
JD507810 - Sequence 488834 from Patent EP1572962.
JA483746 - Sequence 54 from Patent EP2303292.
JD043670 - Sequence 24694 from Patent EP1572962.
JD301260 - Sequence 282284 from Patent EP1572962.
X65663 - H.sapiens Sox-6 mRNA.
MA646161 - JP 2017113010-A/4085: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA734045 - JP 2017140048-A/2915: TERMINALLY MODIFIED RNA.
MA803214 - JP 2018183181-A/4085: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P35712 (Reactome details) participates in the following event(s):

R-HSA-5626938 Beta-catenin binds SOX proteins
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001145819, NP_001139291, P35712, Q86VX7, Q9BXQ3, Q9BXQ4, Q9BXQ5, Q9H0I8, SOX6_HUMAN
UCSC ID: uc001mme.3
RefSeq Accession: NM_001145819
Protein: P35712 (aka SOX6_HUMAN)
CCDS: CCDS7821.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001145819.1
exon count: 16CDS single in 3' UTR: no RNA size: 8919
ORF size: 2526CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5220.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.