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ush2a Usher syndrome 2A (autosomal recessive, mild) [ Danio rerio (zebrafish) ]

Gene ID: 568982, updated on 25-Apr-2024

Summary

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Official Symbol
ush2aprovided by ZNC
Official Full Name
Usher syndrome 2A (autosomal recessive, mild)provided by ZNC
Primary source
ZFIN:ZDB-GENE-060503-794
See related
Ensembl:ENSDARG00000029482 AllianceGenome:ZFIN:ZDB-GENE-060503-794
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
si:ch211-279e11.1
Summary
Acts upstream of or within eye photoreceptor cell development; response to auditory stimulus; and sensory perception of light stimulus. Predicted to be located in extracellular region and membrane. Predicted to be integral component of membrane. Predicted to be active in basement membrane. Is expressed in eye and photoreceptor cell. Used to study Usher syndrome type 2 and Usher syndrome type 2A. Human ortholog(s) of this gene implicated in Usher syndrome (multiple); nonsyndromic deafness; and retinitis pigmentosa (multiple). Orthologous to human USH2A (usherin). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 17
Exon count:
73
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (29374654..29774092, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (29358386..29757116, complement)

Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase receptor type Eb Neighboring gene potassium channel tetramerization domain containing 3 Neighboring gene estrogen-related receptor gamma a Neighboring gene uncharacterized LOC103909045

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Scrutinizing pathogenicity of the USH2A c.2276 G > T; p.(Cys759Phe) variant. Reurink J, et al. NPJ Genom Med, 2022 Jun 7. PMID 35672333, Free PMC Article
  2. Antisense oligonucleotide-based treatment of retinitis pigmentosa caused by USH2A exon 13 mutations. Dulla K, et al. Mol Ther, 2021 Aug 4. PMID 33895329, Free PMC Article
  3. Knockout of ush2a gene in zebrafish causes hearing impairment and late onset rod-cone dystrophy. Han S, et al. Hum Genet, 2018 Oct. PMID 30242501
  4. Usherin defects lead to early-onset retinal dysfunction in zebrafish. Dona M, et al. Exp Eye Res, 2018 Aug. PMID 29777677, Free PMC Article
  5. Poor Splice-Site Recognition in a Humanized Zebrafish Knockin Model for the Recurrent Deep-Intronic c.7595-2144A>G Mutation in USH2A. Slijkerman R, et al. Zebrafish, 2018 Dec. PMID 30281416

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The effects of ush2a gene knockout on vesicle transport in photoreceptors.
    Title: The effects of ush2a gene knockout on vesicle transport in photoreceptors.
  2. Clinical and preclinical therapeutic outcome metrics for USH2A-related disease.
    Title: Clinical and preclinical therapeutic outcome metrics for USH2A-related disease.
  3. This study shows that mutant ush2a zebrafish models present with early-onset retinal dysfunction that is exacerbated by light exposure. These models provide a better understanding of the pathophysiology underlying USH2A-associated RP and a unique opportunity to evaluate future therapeutic strategies.
    Title: Usherin defects lead to early-onset retinal dysfunction in zebrafish.
  4. The expression of Ush1b and Ush1c was up-regulated when Ush2a was null. We also found that disruption of fibronectin assembly at the retinal basement membrane weakened cell adhesion in ush2a(-/-) mutants.
    Title: Knockout of ush2a gene in zebrafish causes hearing impairment and late onset rod-cone dystrophy.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
involved_in animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within eye photoreceptor cell development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within inner ear development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within phototransduction, visible light IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within response to auditory stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within retinal cone cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within retinal rod cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in tissue development IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within visual perception IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
usherin
Names
novel Fibronectin type III domain containing protein

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007128.7 Reference GRCz11 Primary Assembly

    Range
    29374654..29774092 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009293147.3 → XP_009291422.1  usherin

    UniProtKB/TrEMBL
    A0A8M3ARH7
    Related
    ENSDARP00000080636.3, ENSDART00000086201.5
    Conserved Domains (9) summary
    smart00060
    Location:1386 → 1469
    FN3; Fibronectin type 3 domain
    smart00180
    Location:759 → 797
    EGF_Lam; Laminin-type epidermal growth factor-like domai
    cd00055
    Location:1015 → 1064
    EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
    cd00063
    Location:2635 → 2733
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    cd00110
    Location:1537 → 1699
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    pfam00041
    Location:2939 → 3014
    fn3; Fibronectin type III domain
    pfam00053
    Location:808 → 857
    Laminin_EGF; Laminin EGF domain
    pfam13385
    Location:160 → 297
    Laminin_G_3; Concanavalin A-like lectin/glucanases superfamily
    cl02806
    Location:307 → 528
    Laminin_N; Laminin N-terminal (Domain VI)
Nucleotide Protein Strain
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