Q9NZR4 · VSX1_HUMAN

  • Protein
    Visual system homeobox 1
  • Gene
    VSX1
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster (PubMed:10903837).
May regulate the activity of the LCR and the cone opsin genes at earlier stages of development (PubMed:10903837).
Dispensable in early retinal development (By similarity).

Features

Showing features for dna binding.

136550100150200250300350
TypeIDPosition(s)Description
DNA binding164-223Homeobox

GO annotations

all annotationsall molecular functionvirus receptor activitydna bindingrna bindingcytoskeletal motor activitycatalytic activitygtpase activitystructural molecule activitytransporter activitycytoskeletal protein bindinglipid bindingcyclase activityantioxidant activityoxidoreductase activitytransferase activityhydrolase activitylyase activityisomerase activityligase activityprotein tag activitycargo receptor activityhistone bindingprotein folding chaperonetranslation regulator activitynutrient reservoir activityreceptor ligand activitymolecular transducer activitymolecular adaptor activitytoxin activitycell adhesion mediator activitymolecular function regulator activityvirus coreceptor activitycatalytic activity, acting on a proteincatalytic activity, acting on dnacatalytic activity, acting on rnamolecular carrier activitytranscription regulator activitygeneral transcription initiation factor activitymolecular sensor activitymolecular sequestering activityatp-dependent activityother molecular functionall biological processmitotic cell cyclecytokinesiscytoplasmic translationimmune system processmuscle system processcirculatory system processrenal system processrespiratory system processcarbohydrate metabolic processgeneration of precursor metabolites and energydna replicationdna repairdna recombinationchromatin organizationdna-templated transcriptionregulation of dna-templated transcriptiontrna metabolic processprotein foldingprotein glycosylationamino acid metabolic processmodified amino acid metabolic processlipid metabolic processvitamin metabolic processsulfur compound metabolic processintracellular protein transportnucleocytoplasmic transportautophagyinflammatory responsemitochondrion organizationcytoskeleton organizationmicrotubule-based movementperoxisome organizationlysosome organizationchromosome segregationcell adhesionestablishment or maintenance of cell polarityprogrammed cell deathphotosynthesismrna metabolic processsnrna metabolic processvesicle-mediated transportreproductive processdigestive system processsignalingcell differentiationprotein catabolic processextracellular matrix organizationregulatory ncrna-mediated gene silencingtelomere organizationcell junction organizationwound healingribosome biogenesiscilium organizationanatomical structure developmentcell motilitynervous system processendocrine processprotein maturationtransmembrane transportnucleobase-containing small molecule metabolic processhepaticobiliary system processmembrane organizationprotein-containing complex assemblycell wall organization or biogenesisnitrogen cycle metabolic processprotein localization to plasma membranedefense response to other organismdetoxificationmeiotic nuclear divisionmitotic nuclear divisionmitochondrial gene expressioncarbohydrate derivative metabolic processother biological processall cellular componentnuclear chromosomeextracellular regionextracellular spacecell wallnucleusnuclear envelopenucleoplasmchromosomenucleolusmitochondrionlysosomeendosomevacuoleperoxisomeendoplasmic reticulumgolgi apparatuslipid dropletmicrotubule organizing centercytosolribosomecytoskeletonplasma membraneciliumplastidthylakoidexternal encapsulating structureextracellular matrixcytoplasmic vesicleorganelleother cellular component
Cell color indicative of number of GO terms
AspectTerm
Cellular Componentchromatin
Cellular Componentnucleus
Molecular FunctionDNA-binding transcription factor activity
Molecular FunctionDNA-binding transcription factor activity, RNA polymerase II-specific
Molecular Functionsequence-specific double-stranded DNA binding
Molecular Functiontranscription cis-regulatory region binding
Biological Processneuron development
Biological Processneuron maturation
Biological Processregulation of DNA-templated transcription
Biological Processretinal bipolar neuron differentiation
Biological Processvisual perception

Keywords

Enzyme and pathway databases

Community curation (1)

The subsequence KASPTLGKRKKRRHRTVFTAHQLEELEKAFSEAHYPDVYAREMLAVKTELPEDRIQVWFQNRRAKWRKREKRWGGSSVMA, which contains the Homeodomain domain, shows transcriptional repressor activity in a high-throughput recruitment assay.

Names & Taxonomy

Protein names

  • Recommended name
    Visual system homeobox 1
  • Alternative names
    • Homeodomain protein RINX
    • Retinal inner nuclear layer homeobox protein
    • Transcription factor VSX1

Gene names

    • Name
      VSX1
    • Synonyms
      RINX
Community curation (1)

Organism names

  • Taxonomic identifier
  • Taxonomic lineage
    Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo

Accessions

  • Primary accession
    Q9NZR4
  • Secondary accessions
    • B9EGJ4
    • D1MF28
    • Q0GM60
    • Q0GM61
    • Q0GM62

Proteomes

Organism-specific databases

Subcellular Location

Keywords

Disease & Variants

Involvement in disease

Keratoconus 1 (KTCN1)

  • Note
    • The disease is caused by variants affecting the gene represented in this entry
  • Description
    Frequent corneal dystrophy with an incidence that varies from 50 to 230 per 100'000. The cornea assumes a conical shape as a result of a progressive non-inflammatory thinning of the corneal stroma. Keratoconus is most often an isolated sporadic condition with cases of autosomal dominant and autosomal recessive transmission.
  • See also
    MIM:148300
Natural variants in KTCN1
Variant IDPosition(s)ChangeDescription
VAR_06667017L>Pin KTCN1; dbSNP:rs74315436
VAR_014244159L>Min KTCN1; uncertain significance; dbSNP:rs74315434
VAR_014245160G>Din KTCN1; uncertain significance; dbSNP:rs74315433
VAR_014246166R>Win KTCN1; sporadic; dbSNP:rs74315432
VAR_063100175Q>Hin KTCN1; dbSNP:rs771561481
VAR_076692239G>Rin KTCN1; uncertain significance; dbSNP:rs749663315
VAR_014247244H>Rin KTCN1; uncertain significance; dbSNP:rs148957473
VAR_014248247P>Rin KTCN1; uncertain significance; also in a patient with retinal dysfunction; dbSNP:rs576300014

Craniofacial anomalies and anterior segment dysgenesis syndrome (CAASDS)

  • Note
    • The disease is caused by variants affecting the gene represented in this entry
  • Description
    A disorder with extremely variable expressivity. Clinical features include wide interpupillary distance, abnormal corneal endothelium, unusual pinnae, partially to completely empty sella turcica, posterior fossa cyst, anterior encephalocele, and/or hydrocephalus.
  • See also
    MIM:614195
Natural variants in CAASDS
Variant IDPosition(s)ChangeDescription
VAR_066672256A>Sin CAASDS; dbSNP:rs74315435

Features

Showing features for natural variant.

TypeIDPosition(s)Description
Natural variantVAR_06667017in KTCN1; dbSNP:rs74315436
Natural variantVAR_066671131in dbSNP:rs6050307
Natural variantVAR_014243144in dbSNP:rs140122268
Natural variantVAR_014244159in KTCN1; uncertain significance; dbSNP:rs74315434
Natural variantVAR_014245160in KTCN1; uncertain significance; dbSNP:rs74315433
Natural variantVAR_014246166in KTCN1; sporadic; dbSNP:rs74315432
Natural variantVAR_063100175in KTCN1; dbSNP:rs771561481
Natural variantVAR_076692239in KTCN1; uncertain significance; dbSNP:rs749663315
Natural variantVAR_014247244in KTCN1; uncertain significance; dbSNP:rs148957473
Natural variantVAR_014248247in KTCN1; uncertain significance; also in a patient with retinal dysfunction; dbSNP:rs576300014
Natural variantVAR_066672256in CAASDS; dbSNP:rs74315435

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 493 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

Keywords

Organism-specific databases

Miscellaneous

Genetic variation databases

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00000493551-365Visual system homeobox 1

Proteomic databases

PTM databases

Expression

Tissue specificity

In the adult eye, expressed in lens, iris, ciliary body, choroid, optical nerve head and, most strongly, in retina, but not expressed in sclera and cornea. According to PubMed:11978762, expressed in adult retina but not in lens and cornea. Within adult retina, found exclusively in the inner nuclear layer. Isoform 1, isoform 2, isoform 3 and isoform 4 expressed in adult retina, but not in brain, heart, kidney, liver, lung, pancreas, placenta and skeletal muscle. Not expressed in thymus and spleen. Expressed in embryonic craniofacial tissue. Expressed in fetal (week 14) retina. Strongly expressed in neonatal retina, weakly in neonatal lens, choroid and cornea (day 1, 4; month 9).

Gene expression databases

Organism-specific databases

Interaction

Binary interactions

TypeEntry 1Entry 2Number of experimentsIntact
BINARY Q9NZR4BAG6 P46379-23EBI-21789837, EBI-10988864

Protein-protein interaction databases

Miscellaneous

Structure

Family & Domains

Features

Showing features for compositional bias, region, motif, domain.

TypeIDPosition(s)Description
Compositional bias1-15Polar residues
Region1-37Disordered
Motif31-38Octapeptide motif
Region113-167Disordered
Compositional bias136-158Basic and acidic residues
Motif161-166Nuclear localization signal
Domain224-277CVC
Region290-365Disordered
Compositional bias297-315Polar residues

Sequence similarities

Belongs to the paired homeobox family.

Keywords

Phylogenomic databases

Family and domain databases

Sequence & Isoforms

Align isoforms (8)
  • Sequence status
    Complete

This entry describes 8 isoforms produced by Alternative splicing. Additional isoforms seem to exist.

Q9NZR4-1

This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

  • Name
    1
  • Synonyms
    L1
  • Note
    Major form.
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Length
    365
  • Mass (Da)
    38,431
  • Last updated
    2001-03-01 v2
  • Checksum
    C58BE94767D66FCB
MTGRDSLSDGRTSSRALVPGGSPRGSRPRGFAITDLLGLEAELPAPAGPGQGSGCEGPAVAPCPGPGLDGSSLARGALPLGLGLLCGFGTQPPAAARAPCLLLADVPFLPPRGPEPAAPLAPSRPPPALGRQKRSDSVSTSDEDSQSEDRNDLKASPTLGKRKKRRHRTVFTAHQLEELEKAFSEAHYPDVYAREMLAVKTELPEDRIQVWFQNRRAKWRKREKRWGGSSVMAEYGLYGAMVRHCIPLPDSVLNSAEGGLLGSCAPWLLGMHKKSMGMIRKPGSEDKLAGLWGSDHFKEGSSQSESGSQRGSDKVSPENGLEDVAIDLSSSARQETKKVHPGAGAQGGSNSTALEGPQPGKVGAT

Q9NZR4-2

  • Name
    2
  • Synonyms
    S1, L3
  • Note
    Major form.
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical
    • 211-239: WFQNRRAKWRKREKRWGGSSVMAEYGLYG → SGVPFLRSKDTTENVSFPHSVSQSAVPSL
    • 240-365: Missing

Q9NZR4-3

  • Name
    3
  • Synonyms
    S2
  • Note
    Minor form.
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical
    • 141-141: S → SGNQARAFRSCPCPLGSEPRRGHRPSPHRTPGPSGPDLGGEPRARPRRGRGIRGAAPPAPCCILNPCLSSGVLFPQRCETATTWFRVEPFDETLGSSTTISRGPFFPPAPGASLRLWQLRGSGRPGPVVVTSSTEQ
    • 211-239: WFQNRRAKWRKREKRWGGSSVMAEYGLYG → SGVPFLRSKDTTENVSFPHSVSQSAVPSL
    • 240-365: Missing

Q9NZR4-4

  • Name
    4
  • Synonyms
    S3
  • Note
    Minor form.
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Q9NZR4-5

  • Name
    5
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Q9NZR4-6

  • Name
    6
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Q9NZR4-7

  • Name
    7
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical
    • 210-236: VWFQNRRAKWRKREKRWGGSSVMAEYG → CKLLLLEAPVHWTLQETHRLPRPRGGA
    • 237-365: Missing

Q9NZR4-8

  • Name
    8
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical
    • 270-301: GMHKKSMGMIRKPGSEDKLAGLWGSDHFKEGS → VQTSAPGGSRSLDFAGDTQAPQTPWWCLMTFS
    • 302-365: Missing

Features

Showing features for compositional bias, alternative sequence.

TypeIDPosition(s)Description
Compositional bias1-15Polar residues
Compositional bias136-158Basic and acidic residues
Alternative sequenceVSP_002299141in isoform 3
Alternative sequenceVSP_002300142-143in isoform 4
Alternative sequenceVSP_002301144-365in isoform 4
Alternative sequenceVSP_039140210-218in isoform 6
Alternative sequenceVSP_039141210-236in isoform 7
Alternative sequenceVSP_002302211-239in isoform 2 and isoform 3
Alternative sequenceVSP_039142219-365in isoform 6
Alternative sequenceVSP_039143237-365in isoform 7
Alternative sequenceVSP_002303240-365in isoform 2 and isoform 3
Alternative sequenceVSP_039144270-280in isoform 5
Alternative sequenceVSP_039145270-301in isoform 8
Alternative sequenceVSP_039146281-365in isoform 5
Compositional bias297-315Polar residues
Alternative sequenceVSP_039147302-365in isoform 8

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AF176797
EMBL· GenBank· DDBJ
AAF37425.2
EMBL· GenBank· DDBJ
mRNA
AF251033
EMBL· GenBank· DDBJ
AAF99656.1
EMBL· GenBank· DDBJ
mRNA
AF251034
EMBL· GenBank· DDBJ
AAF99657.1
EMBL· GenBank· DDBJ
mRNA
DQ854807
EMBL· GenBank· DDBJ
ABI23973.1
EMBL· GenBank· DDBJ
mRNA
DQ854808
EMBL· GenBank· DDBJ
ABI23974.1
EMBL· GenBank· DDBJ
mRNA
DQ854809
EMBL· GenBank· DDBJ
ABI23975.1
EMBL· GenBank· DDBJ
mRNA
DQ854810
EMBL· GenBank· DDBJ
ABI23976.1
EMBL· GenBank· DDBJ
mRNA
DQ854811
EMBL· GenBank· DDBJ
ABI23977.1
EMBL· GenBank· DDBJ
mRNA
DQ854812
EMBL· GenBank· DDBJ
ABI23978.1
EMBL· GenBank· DDBJ
mRNA
AL080312
EMBL· GenBank· DDBJ
-Genomic DNA No translation available.
BC126228
EMBL· GenBank· DDBJ
AAI26229.1
EMBL· GenBank· DDBJ
mRNA
BC136497
EMBL· GenBank· DDBJ
AAI36498.1
EMBL· GenBank· DDBJ
mRNA
GU138372
EMBL· GenBank· DDBJ
ACZ01961.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

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