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Protein

Visual system homeobox 1

Gene

vsx1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

May be involved in maintenance as well as cellular differentiation of retinal interneurons, such as bipolar cells. May play a role in establishing interneuronal cell classes in nonsensory as well as sensory systems.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi151 – 210HomeoboxPROSITE-ProRule annotationAdd BLAST60

GO - Molecular functioni

  • chromatin binding Source: ZFIN
  • sequence-specific DNA binding Source: InterPro
  • transcription regulatory region DNA binding Source: ZFIN

GO - Biological processi

  • axial mesoderm development Source: ZFIN
  • forebrain development Source: ZFIN
  • negative regulation of axial mesodermal cell fate specification Source: ZFIN
  • negative regulation of transcription, DNA-templated Source: ZFIN
  • neuron development Source: GO_Central
  • paraxial mesodermal cell fate specification Source: ZFIN
  • paraxial mesoderm development Source: ZFIN
  • prechordal plate formation Source: ZFIN
  • response to stimulus Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
  • visual perception Source: UniProtKB-KW

Keywordsi

Molecular functionDevelopmental protein, DNA-binding
Biological processSensory transduction, Transcription, Transcription regulation, Vision

Names & Taxonomyi

Protein namesi
Recommended name:
Visual system homeobox 1
Alternative name(s):
Transcription factor VSX1
Gene namesi
Name:vsx1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-990415-205 vsx1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000493581 – 344Visual system homeobox 1Add BLAST344

Proteomic databases

PaxDbiO42250

Expressioni

Tissue specificityi

Highly expressed in the central and outer tiers of the inner nuclear layer of the retina.

Developmental stagei

Significant levels were first detected at the 14-somite stage (16 hours post-fertization; hpf) and increased by the prim-11 stage (28 hpf). At 16 hpf expression is observed in a small subset of neurons in the spinal cord and at 18 hpf in the developing hindbrain. At 28-32 hpf, significant levels of expression is seen in presumptive neurons along the rostral-caudal axis of the hindbrain and the spinal cord. During later stages of development expression is restricted to the developing retina and no longer detected in the hindbrain or spinal cord.

Interactioni

Subunit structurei

Interacts with UBE2I.1 Publication

Protein-protein interaction databases

STRINGi7955.ENSDARP00000073224

Structurei

3D structure databases

ProteinModelPortaliO42250
SMRiO42250
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini211 – 268CVCPROSITE-ProRule annotationAdd BLAST58

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni37 – 44Octapeptide motif8

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi147 – 151Nuclear localization signal1 Publication5

Domaini

The NLS interacts with UBE2I.

Sequence similaritiesi

Belongs to the paired homeobox family.Curated

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiKOG0494 Eukaryota
ENOG410ZN24 LUCA
HOGENOMiHOG000115909
HOVERGENiHBG036251
InParanoidiO42250
KOiK09335
PhylomeDBiO42250

Family and domain databases

CDDicd00086 homeodomain, 1 hit
InterProiView protein in InterPro
IPR023339 CVC
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
PfamiView protein in Pfam
PF00046 Homeobox, 1 hit
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS51496 CVC, 1 hit
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit

Sequencei

Sequence statusi: Complete.

O42250-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTGREEATDE KPKVKLYPSF GIDKSRLNGS GFRSKGFAIT DLLGLESELQ
60 70 80 90 100
PHQSGPGAGP NGEGQSAAVG GFSFPGGSLP LGLGFLCSLA AQQPPGAPCF
110 120 130 140 150
LPSHIPLLQS RTESHFMQNL EQQRDVYSDD DCLSGDRNDG KNSGNSQKRK
160 170 180 190 200
KRRHRTVFTS HQLEELEKAF NEAHYPDVYA REMLAMKTEL PEDRIQVWFQ
210 220 230 240 250
NRRAKWRKRE KCWGRSSVMA EYGLYGAMVR HSIPLPESII NSAKSGMMGS
260 270 280 290 300
CAPWLLGEPA GMHKKSMEIV KKAPGTPEST HSDTYSEEHK GKDSDTTWSS
310 320 330 340
GANGADDSED MAIDLSSTSK QENKSTLKRS PPRTENSSDS ENES
Length:344
Mass (Da):37,872
Last modified:May 1, 2000 - v2
Checksum:i5CA3C631D2F8E7F6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF025348 mRNA Translation: AAB71611.2
RefSeqiNP_571408.1, NM_131333.1
UniGeneiDr.558

Genome annotation databases

GeneIDi30598
KEGGidre:30598

Similar proteinsi

Entry informationi

Entry nameiVSX1_DANRE
AccessioniPrimary (citable) accession number: O42250
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: May 1, 2000
Last modified: November 22, 2017
This is version 112 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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