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Clrn1 Gene Detail
Summary
  • Symbol
    Clrn1
  • Name
    clarin 1
  • Synonyms
    A130002D11Rik, clarin-1, USH3, Ush3a
  • Feature Type
    protein coding gene
  • IDs
    MGI:2388124
    NCBI Gene: 229320
  • Gene Overview
    MyGene.info: CLRN1
Location & Maps
more
  • Sequence Map
    Chr3:58844028-58885340 bp, - strand
  • From VEGA annotation of GRCm38

    Mouse Genome Browser

  • Download
    Sequence
      41313 bp   ±  kb flank

  • Genome Browsers
  • Genetic Map
    Chromosome 3, 28.78 cM
  • Mapping Data
    3 experiments
Homology
more
  • Human Ortholog
    CLRN1, clarin 1
  • Vertebrate Orthologs
    10
  • Human Ortholog
    CLRN1, clarin 1
    Orthology source: HomoloGene, HGNC
  • Synonyms
    RP61, USH3, USH3A
  • Links
    NCBI Gene ID: 7401
    neXtProt AC: NX_P58418

  • Chr Location
    3q25; chr3:150918911-150973020 (-)  GRCh38.p2

  • HomoloGene
    Vertebrate Homology Class 17738
    1 human;1 mouse;1 rat;1 chimpanzee;1 rhesus macaque;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed
  • HCOP
    human homology predictions: CLRN1
  • Gene Tree
Human Diseases
more
  • Diseases
    1 with Clrn1 mouse models; 3 with human CLRN1 associations

Human Disease Mouse Models
       Usher Syndrome, Type IIIA; USH3A   OMIM: 276902 View 2 models
       Retinitis Pigmentosa 61; RP61   OMIM: 614180
Retinitis Pigmentosa; RP   OMIM: 268000
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    3 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    22 phenotypes from 3 alleles in 3 genetic backgrounds
    13 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
  • All Mutations and Alleles
    7
  • Radiation induced
    1
  • Targeted
    6
  • Genomic Mutations
    1 involving Clrn1
  • Incidental Mutations
Mice homozygous for a null allele exhibit progressive hearing loss and loss of balance associated with defects in outer hair cells and supporting cells.
Gene Ontology
(GO)
Classifications
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  • All GO Annotations
  • GO References
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
receptor
receptor binding
RNA binding
transcription
transferase
transporter
Biological Process

nucleic acid-templated transcription
carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
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Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
  • Tissues
  • cDNA Data
  • Literature Summary
Interactions
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Sequences &
Gene Models
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Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000031611 VEGA Gene Model | MGI Sequence Detail 41313 C57BL/6J ±  kb
transcript OTTMUST00000078294 VEGA | MGI Sequence Detail 3083 Not Applicable  
polypeptide OTTMUSP00000041625 VEGA | MGI Sequence Detail 250 Not Applicable  
For the selected sequence
Polymorphisms
less
  • SNPs within 2kb
    346 from dbSNP Build 142
Protein
Information
less
Molecular
Reagents
less
  • All nucleic 8
    cDNA 7
    Primer pair 1

    Microarray probesets 2
Other
Accession IDs
less
MGI:2442622
References
more
  • Summaries
    All 33
    Developmental Gene Expression 4
    Diseases 3
    Gene Ontology 5
    Phenotypes 13
  • Earliest
    J:78872 Fields RR, et al., Usher Syndrome Type III: Revised Genomic Structure of the USH3 Gene and Identification of Novel Mutations. Am J Hum Genet. 2002 Sep;71(3):607-17
  • Latest
    J:218725 Cosgrove D, et al., Usher protein functions in hair cells and photoreceptors. Int J Biochem Cell Biol. 2014 Jan;46:80-9

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources
Funding Information
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last database update
09/27/2016
MGI 6.05
The Jackson Laboratory