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Protein

Visual system homeobox 1

Gene

vsx1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

  • Nucleus PROSITE-ProRule annotation1 Publication

GO - Cellular componenti

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

InterProiView protein in InterPro
IPR023339. CVC.
IPR009057. Homeobox-like.
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

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 one 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.

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: May 10, 2017
This is version 110 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