Mouse Gene Vsx2 (ENSMUST00000021665.11) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus visual system homeobox 2 (Vsx2), transcript variant 2, mRNA. (from RefSeq NM_007701)
RefSeq Summary (NM_007701): This gene encodes a member of the Vsx (visual system homeobox) family which belongs to the larger PRD homeobox class. The encoded protein is required for eye organogenesis and controls retinal development. Disruption of this gene is associated with ocular retardation J (orJ), a mouse disease which causes microphthalmia, retinal degeneration and optic nerve aplasia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014].
Gencode Transcript: ENSMUST00000021665.11
Gencode Gene: ENSMUSG00000021239.12
Transcript (Including UTRs)
   Position: mm10 chr12:84,569,762-84,595,457 Size: 25,696 Total Exon Count: 5 Strand: +
Coding Region
   Position: mm10 chr12:84,569,943-84,593,454 Size: 23,512 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:84,569,762-84,595,457)mRNA (may differ from genome)Protein (361 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
MGIPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=C. elegans ceh-10 homeo domain containing homolog, isoform CRA_b; SubName: Full=Visual system homeobox 2;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 homeobox DNA-binding domain.

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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -71.60181-0.396 Picture PostScript Text
3' UTR -660.802003-0.330 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
IPR023339 - CVC
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR003654 - OAR_dom

Pfam Domains:
PF00046 - Homeobox domain
PF03826 - OAR domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q80WF9
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AK143461 - Mus musculus 14 days embryo eyeball cDNA, RIKEN full-length enriched library, clone:E630012G02 product:C. elegans ceh-10 homeo domain containing homolog, full insert sequence.
BC058806 - Mus musculus visual system homeobox 2, mRNA (cDNA clone MGC:65308 IMAGE:6492679), complete cds.
BC031869 - Mus musculus visual system homeobox 2, mRNA (cDNA clone MGC:30502 IMAGE:4480964), complete cds.
BC051245 - Mus musculus visual system homeobox 2, mRNA (cDNA clone MGC:58960 IMAGE:6494544), complete cds.
L34808 - Mus musculus (clone 6) homeobox protein (Chx10) mRNA, complete cds.
AK162139 - Mus musculus in vitro fertilized eggs cDNA, RIKEN full-length enriched library, clone:7420434P22 product:C. elegans ceh-10 homeo domain containing homolog, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: Chx10, mCG_5514, NM_007701, Q80WF9, Q80WF9_MOUSE, uc007ofm.1, uc007ofm.2, uc007ofm.3
UCSC ID: uc007ofm.3
RefSeq Accession: NM_007701
Protein: Q80WF9 CCDS: CCDS36493.1, CCDS79136.1

+  Gene Model Information
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-  Methods, Credits, and Use Restrictions
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