Mouse Gene Sox1 (ENSMUST00000180353.1) Description and Page Index
  Description: Mus musculus SRY (sex determining region Y)-box 1 (Sox1), mRNA. (from RefSeq NM_009233)
Gencode Transcript: ENSMUST00000180353.1
Gencode Gene: ENSMUSG00000096014.1
Transcript (Including UTRs)
   Position: mm10 chr8:12,395,295-12,400,126 Size: 4,832 Total Exon Count: 1 Strand: +
Coding Region
   Position: mm10 chr8:12,396,361-12,397,536 Size: 1,176 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:12,395,295-12,400,126)mRNA (may differ from genome)Protein (391 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SOX1_MOUSE
DESCRIPTION: RecName: Full=Transcription factor SOX-1;
FUNCTION: Transcriptional activator. May function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation (By similarity).
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Mainly in the developing central nervous system. Expressed in developing urogenital ridge.
SIMILARITY: Contains 1 HMG box DNA-binding domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -416.601066-0.391 Picture PostScript Text
3' UTR -740.302590-0.286 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
IPR022097 - TF_SOX

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain
PF12336 - SOX transcription factor

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on P53783
FrontTopSide
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-  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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region 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:0003677 DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001764 neuron migration
GO:0002089 lens morphogenesis in camera-type eye
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007399 nervous system development
GO:0021521 ventral spinal cord interneuron specification
GO:0021879 forebrain neuron differentiation
GO:0021884 forebrain neuron development
GO:0030900 forebrain development
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AB108672 - Mus musculus Sox1 mRNA for transcriptional factor SOX1, complete cds.
BC172600 - Synthetic construct Mus musculus clone IMAGE:100069408, MGC:199310 SRY-box containing gene 1 (Sox1) mRNA, encodes complete protein.
BC172706 - Synthetic construct Mus musculus clone IMAGE:100069514, MGC:199416 SRY-box containing gene 1 (Sox1) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_009233, P53783, Sox-1, SOX1_MOUSE, uc009kwa.1, uc009kwa.2, uc009kwa.3
UCSC ID: uc009kwa.3
RefSeq Accession: NM_009233
Protein: P53783 (aka SOX1_MOUSE)
CCDS: CCDS57605.1

-  Gene Model Information
  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.