Human Gene SOX4 (uc003ndi.3)
  Description: Homo sapiens SRY (sex determining region Y)-box 4 (SOX4), mRNA.
RefSeq Summary (NM_003107): This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr6:21,593,972-21,598,849 Size: 4,878 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr6:21,594,766-21,596,190 Size: 1,425 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:21,593,972-21,598,849)mRNA (may differ from genome)Protein (474 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOX4_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-4;
FUNCTION: Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.
SUBUNIT: Interacts with UBE2I.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Testis, brain, and heart.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/SOX4ID42358ch6p22.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SOX4
CDC HuGE Published Literature: SOX4

-  MalaCards Disease Associations
  MalaCards Gene Search: SOX4
Diseases sorted by gene-association score: deafness, autosomal dominant 31 (8), deafness, autosomal dominant 21 (7), deafness, autosomal dominant 13 (4)

-  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: 29.27 RPKM in Ovary
Total median expression: 304.38 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 -323.91794-0.408 Picture PostScript Text
3' UTR -798.352659-0.300 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
IPR017386 - SOX-12/11/4a

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

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on Q06945
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 orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0001501 skeletal system development
GO:0001841 neural tube formation
GO:0002328 pro-B cell differentiation
GO:0003183 mitral valve morphogenesis
GO:0003211 cardiac ventricle formation
GO:0003215 cardiac right ventricle morphogenesis
GO:0003289 atrial septum primum morphogenesis
GO:0003357 noradrenergic neuron differentiation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0007507 heart development
GO:0008284 positive regulation of cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0014009 glial cell proliferation
GO:0021510 spinal cord development
GO:0021522 spinal cord motor neuron differentiation
GO:0021782 glial cell development
GO:0030177 positive regulation of Wnt signaling pathway
GO:0030217 T cell differentiation
GO:0031018 endocrine pancreas development
GO:0031397 negative regulation of protein ubiquitination
GO:0031647 regulation of protein stability
GO:0032024 positive regulation of insulin secretion
GO:0035019 somatic stem cell population maintenance
GO:0035910 ascending aorta morphogenesis
GO:0042593 glucose homeostasis
GO:0042769 DNA damage response, detection of DNA damage
GO:0043065 positive regulation of apoptotic process
GO:0045727 positive regulation of translation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048485 sympathetic nervous system development
GO:0050821 protein stabilization
GO:0060070 canonical Wnt signaling pathway
GO:0060174 limb bud formation
GO:0060412 ventricular septum morphogenesis
GO:0060548 negative regulation of cell death
GO:0060563 neuroepithelial cell differentiation
GO:0060993 kidney morphogenesis
GO:0071333 cellular response to glucose stimulus
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:2000761 positive regulation of N-terminal peptidyl-lysine acetylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0044798 nuclear transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  JD092790 - Sequence 73814 from Patent EP1572962.
JD219792 - Sequence 200816 from Patent EP1572962.
AF070669 - Homo sapiens sox mRNA, partial 5'UTR.
AF124147 - Homo sapiens SOX4 mRNA, 5' untranslated region.
JD533525 - Sequence 514549 from Patent EP1572962.
JD445814 - Sequence 426838 from Patent EP1572962.
BC072668 - Homo sapiens SRY (sex determining region Y)-box 4, mRNA (cDNA clone MGC:71240 IMAGE:6584346), complete cds.
JD534951 - Sequence 515975 from Patent EP1572962.
JD485254 - Sequence 466278 from Patent EP1572962.
JD296546 - Sequence 277570 from Patent EP1572962.
JD327028 - Sequence 308052 from Patent EP1572962.
X70683 - H.sapiens mRNA for SOX-4 protein.
JD334016 - Sequence 315040 from Patent EP1572962.
JD037446 - Sequence 18470 from Patent EP1572962.
JD330136 - Sequence 311160 from Patent EP1572962.
JD525186 - Sequence 506210 from Patent EP1572962.
JD175210 - Sequence 156234 from Patent EP1572962.
JD151367 - Sequence 132391 from Patent EP1572962.
JD191637 - Sequence 172661 from Patent EP1572962.
AB385573 - Synthetic construct DNA, clone: pF1KB9430, Homo sapiens SOX4 gene for transcription factor SOX-4, complete cds, without stop codon, in Flexi system.
EU446655 - Synthetic construct Homo sapiens clone IMAGE:100070345; IMAGE:100011864; FLH257198.01L SRY (sex determining region Y)-box 4 (SOX4) gene, encodes complete protein.
X65661 - H.sapiens Sox-4 mRNA.
JD211267 - Sequence 192291 from Patent EP1572962.
JD525064 - Sequence 506088 from Patent EP1572962.
JD129532 - Sequence 110556 from Patent EP1572962.
JD408454 - Sequence 389478 from Patent EP1572962.
JD472776 - Sequence 453800 from Patent EP1572962.
JD406948 - Sequence 387972 from Patent EP1572962.
JD228446 - Sequence 209470 from Patent EP1572962.
JD037177 - Sequence 18201 from Patent EP1572962.
JD307477 - Sequence 288501 from Patent EP1572962.
JD341646 - Sequence 322670 from Patent EP1572962.
JD461125 - Sequence 442149 from Patent EP1572962.
JD100194 - Sequence 81218 from Patent EP1572962.
JD159591 - Sequence 140615 from Patent EP1572962.
JD058234 - Sequence 39258 from Patent EP1572962.
JD329387 - Sequence 310411 from Patent EP1572962.
JD180054 - Sequence 161078 from Patent EP1572962.
JD069003 - Sequence 50027 from Patent EP1572962.
AJ420500 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1977059.
JD326631 - Sequence 307655 from Patent EP1572962.
JD503722 - Sequence 484746 from Patent EP1572962.
JD502466 - Sequence 483490 from Patent EP1572962.
JD265138 - Sequence 246162 from Patent EP1572962.
JD410358 - Sequence 391382 from Patent EP1572962.
JD496329 - Sequence 477353 from Patent EP1572962.
JD087839 - Sequence 68863 from Patent EP1572962.
JD106572 - Sequence 87596 from Patent EP1572962.

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

Protein Q06945 (Reactome details) participates in the following event(s):

R-HSA-5626938 Beta-catenin binds SOX proteins
R-HSA-5665608 TCF: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_003107, NP_003098, Q06945, SOX4_HUMAN
UCSC ID: uc003ndi.3
RefSeq Accession: NM_003107
Protein: Q06945 (aka SOX4_HUMAN)
CCDS: CCDS4547.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SOX4:
coffin-siris (Coffin-Siris Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003107.2
exon count: 1CDS single in 3' UTR: no RNA size: 4912
ORF size: 1425CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2961.50frame shift in genome: no % Coverage: 99.31
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.