Mouse Gene Vsx1 (ENSMUST00000046095.9) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus visual system homeobox 1 (Vsx1), mRNA. (from RefSeq NM_054068)
Gencode Transcript: ENSMUST00000046095.9
Gencode Gene: ENSMUSG00000033080.9
Transcript (Including UTRs)
   Position: mm10 chr2:150,680,702-150,689,360 Size: 8,659 Total Exon Count: 5 Strand: -
Coding Region
   Position: mm10 chr2:150,683,001-150,688,960 Size: 5,960 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 (chr2:150,680,702-150,689,360)mRNA (may differ from genome)Protein (363 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
MGIPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Visual system homeobox 1; AltName: Full=Homeodomain protein RINX; AltName: Full=Retinal inner nuclear layer homeobox protein; AltName: Full=Transcription factor VSX1;
FUNCTION: Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster. May regulate the activity of the LCR and the cone opsin genes at earlier stages of development (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: In the adult, expressed exclusively in the cells of the neural retina with expression restricted to postnatal cone bipolar interneurons.
DEVELOPMENTAL STAGE: Expressed at P5, solely within the inner nuclear layer (INL) of the central neuroretina. By days P6 and P7, expression expands peripherally during neurogenesis. By P12, expression is restricted to the outer margin of the INL and reaches the outer periphery of the neuroretina.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 CVC domain.
SIMILARITY: Contains 1 homeobox 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 -156.40400-0.391 Picture PostScript Text
3' UTR -693.202299-0.302 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

Pfam Domains:
PF00046 - Homeobox domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q91V10
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
No orthologGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
 RGDEnsembl WormBase 
 Protein Sequence  Protein Sequence 
 Alignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007601 visual perception
GO:0042551 neuron maturation
GO:0048666 neuron development
GO:0050896 response to stimulus
GO:0060040 retinal bipolar neuron differentiation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC057647 - Mus musculus visual system homeobox 1 homolog (zebrafish), mRNA (cDNA clone MGC:67932 IMAGE:4511665), complete cds.
AK044393 - Mus musculus adult retina cDNA, RIKEN full-length enriched library, clone:A930010K22 product:TRANSCRIPTION FACTOR VSX1 (VISUAL SYSTEM HOMEOBOX 1) (HOMEODOMAIN PROTEIN RINX), full insert sequence.
AK044687 - Mus musculus adult retina cDNA, RIKEN full-length enriched library, clone:A930033D24 product:visual system homeobox 1 homolog (zebrafish), full insert sequence.
BC138456 - Mus musculus visual system homeobox 1 homolog (zebrafish), mRNA (cDNA clone MGC:170081 IMAGE:8861476), complete cds.
BC138460 - Mus musculus visual system homeobox 1 homolog (zebrafish), mRNA (cDNA clone MGC:170085 IMAGE:8861480), complete cds.
AY056825 - Mus musculus transcription factor VSX1 (Vsx1) mRNA, complete cds.
AF391758 - Mus musculus homeodomain protein RINX (Rinx) mRNA, complete cds.
AF395732 - Mus musculus visual system homeobox 1 (Vsx1) mRNA, complete cds.
AK157311 - Mus musculus activated spleen cDNA, RIKEN full-length enriched library, clone:F830210J18 product:visual system homeobox 1 homolog (zebrafish), full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_054068, Q91V10, Rinx, uc008muh.1, uc008muh.2, uc008muh.3, VSX1_MOUSE
UCSC ID: uc008muh.3
RefSeq Accession: NM_054068
Protein: Q91V10 (aka VSX1_MOUSE)
CCDS: CCDS16860.1

+  Gene Model Information
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