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Protein

Visual system homeobox 1

Gene

Vsx1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi171 – 23060HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • neuron development Source: MGI
  • neuron maturation Source: MGI
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • response to stimulus Source: UniProtKB-KW
  • retinal bipolar neuron differentiation Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • visual perception Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Sensory transduction, Transcription, Transcription regulation, Vision

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Visual system homeobox 1
Alternative name(s):
Homeodomain protein RINX
Retinal inner nuclear layer homeobox protein
Transcription factor VSX1
Gene namesi
Name:Vsx1
Synonyms:Rinx
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1890816. Vsx1.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 363363Visual system homeobox 1PRO_0000049356Add
BLAST

Proteomic databases

PRIDEiQ91V10.

PTM databases

PhosphoSiteiQ91V10.

Expressioni

Tissue specificityi

In the adult, expressed exclusively in the cells of the neural retina with expression restricted to postnatal cone bipolar interneurons.

Developmental stagei

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.

Gene expression databases

BgeeiQ91V10.
CleanExiMM_VSX1.
ExpressionAtlasiQ91V10. baseline.
GenevisibleiQ91V10. MM.

Interactioni

Protein-protein interaction databases

BioGridi227900. 1 interaction.
STRINGi10090.ENSMUSP00000039088.

Structurei

3D structure databases

ProteinModelPortaliQ91V10.
SMRiQ91V10. Positions 178-227.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini231 – 28353CVCPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi31 – 388Octapeptide motif
Motifi168 – 1736Nuclear localization signalSequence Analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi44 – 12784Pro-richAdd
BLAST
Compositional biasi80 – 9314Gly/Leu-richAdd
BLAST
Compositional biasi142 – 15211Asp/Glu-rich (acidic)Add
BLAST

Sequence similaritiesi

Belongs to the paired homeobox family.Curated
Contains 1 CVC domain.PROSITE-ProRule annotation
Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiNOG237888.
GeneTreeiENSGT00800000124086.
HOGENOMiHOG000115909.
HOVERGENiHBG036251.
InParanoidiQ91V10.
KOiK09335.
OMAiKVSPEHG.
OrthoDBiEOG76474B.
PhylomeDBiQ91V10.
TreeFamiTF350743.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR023339. CVC.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS51496. CVC. 1 hit.
PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q91V10-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTGRDGLSDA RSRSRALAPG CPPTGSRLRS FAINDLLGLE ADLPTPAEPG
60 70 80 90 100
LRSNSGDPAE AIGSGPGPGP GLCGSCPARG ALPLGLGLLC GFGAQPPSAA
110 120 130 140 150
AAARARCLLL ADLRLLPSAG PEPAVAQGPV HPPPALGSQQ RSESVSTSDG
160 170 180 190 200
DSPSEEKNDP KMSLILGKRK KRRHRTVFTA HQLEELEKAF GEAHYPDVYA
210 220 230 240 250
REMLAAKTEL PEDRIQVWFQ NRRAKWRKRE KRWGGSSVMA EYGLYGAMVR
260 270 280 290 300
HCIPLPDSVL NSADSLQGSC APWLLGMHKK STGMRKPESE DKLAGLWEFD
310 320 330 340 350
HLKKGANKDE DGPERGPDET TQNPENSLED VAIDLSSSSR QETKKMPPGS
360
STQLPQPPQV GAS
Length:363
Mass (Da):38,755
Last modified:December 1, 2001 - v1
Checksum:iE250D452C77228C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY056825 mRNA. Translation: AAL11431.1.
AF395732 mRNA. Translation: AAL08947.1.
AF391757 Genomic DNA. Translation: AAL09584.1.
AF391758 mRNA. Translation: AAL09585.1.
BC057647 mRNA. Translation: AAH57647.1.
CCDSiCCDS16860.1.
PIRiJC7750.
RefSeqiNP_473409.1. NM_054068.2.
UniGeneiMm.207061.

Genome annotation databases

EnsembliENSMUST00000046095; ENSMUSP00000039088; ENSMUSG00000033080.
GeneIDi114889.
KEGGimmu:114889.
UCSCiuc008muh.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY056825 mRNA. Translation: AAL11431.1.
AF395732 mRNA. Translation: AAL08947.1.
AF391757 Genomic DNA. Translation: AAL09584.1.
AF391758 mRNA. Translation: AAL09585.1.
BC057647 mRNA. Translation: AAH57647.1.
CCDSiCCDS16860.1.
PIRiJC7750.
RefSeqiNP_473409.1. NM_054068.2.
UniGeneiMm.207061.

3D structure databases

ProteinModelPortaliQ91V10.
SMRiQ91V10. Positions 178-227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi227900. 1 interaction.
STRINGi10090.ENSMUSP00000039088.

PTM databases

PhosphoSiteiQ91V10.

Proteomic databases

PRIDEiQ91V10.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000046095; ENSMUSP00000039088; ENSMUSG00000033080.
GeneIDi114889.
KEGGimmu:114889.
UCSCiuc008muh.2. mouse.

Organism-specific databases

CTDi30813.
MGIiMGI:1890816. Vsx1.

Phylogenomic databases

eggNOGiNOG237888.
GeneTreeiENSGT00800000124086.
HOGENOMiHOG000115909.
HOVERGENiHBG036251.
InParanoidiQ91V10.
KOiK09335.
OMAiKVSPEHG.
OrthoDBiEOG76474B.
PhylomeDBiQ91V10.
TreeFamiTF350743.

Miscellaneous databases

NextBioi368909.
PROiQ91V10.
SOURCEiSearch...

Gene expression databases

BgeeiQ91V10.
CleanExiMM_VSX1.
ExpressionAtlasiQ91V10. baseline.
GenevisibleiQ91V10. MM.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR023339. CVC.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS51496. CVC. 1 hit.
PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Vsx1, a rapidly evolving paired-like homeobox gene expressed in cone bipolar cells."
    Chow R.L., Snow B., Novak J., Looser J., Freund C., Vidgen D., Ploder L., McInnes R.R.
    Mech. Dev. 109:315-322(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/c.
    Tissue: Retina.
  2. "Isolation and characterization of Vsx1, a novel mouse CVC paired-like homeobox gene expressed during embryogenesis and in the retina."
    Ohtoshi A., Justice M.J., Behringer R.R.
    Biochem. Biophys. Res. Commun. 286:133-140(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Swiss.
  3. "Expression of rinx/vsx1 during postnatal eye development in cone-bipolar, differentiating ganglion, and lens fiber cells."
    Hayashi T., Huang J., Deeb S.S.
    Jpn. J. Ophthalmol. 49:93-105(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: 129/SvJ.
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Eye.

Entry informationi

Entry nameiVSX1_MOUSE
AccessioniPrimary (citable) accession number: Q91V10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: December 1, 2001
Last modified: July 22, 2015
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.