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Clrn1
Gene Detail
Symbol

Name
ID
Clrn1
clarin 1
MGI:2388124
Synonyms
A130002D11Rik, clarin-1, USH3, Ush3a
Feature Type
protein coding gene
Genetic Map
Chromosome 3
28.78 cM
Detailed Genetic Map ± 1 cM


Mapping data(3)
Sequence Map
Chr3:58844028-58885340 bp, - strand
From VEGA annotation of GRCm38

  41313 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer


Mouse Genome Browser
Vertebrate
homology
HomoloGene:17738  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 rhesus macaque; 1 cattle; 1 dog; 1 chicken; 1 western clawed frog; 1 zebrafish

HCOP human homology predictions: CLRN1
Gene Tree: Clrn1

Human
homologs
CLRN1, clarin 1
Orthology source: HGNC, HomoloGene

IDs:
NCBI Gene ID: 7401
neXtProt AC: NX_P58418

Human Synonyms: RP61, USH3, USH3A

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

Disease Associations: (3) Diseases Associated with Human CLRN1

Mutations,
alleles, and
phenotypes
All mutations/alleles(6) : Targeted(6)
Incidental mutations (data from Mutagenetix , APF , CvDC )
 
Mice homozygous for a null allele exhibit progressive hearing loss and loss of balance associated with defects in outer hair cells and supporting cells.
 
Human Diseases Modeled in Mice Using Clrn1 (1)    Mutations Annotated to Human Diseases (2)   
Interactions
Clrn1 interacts with 278 markers (Mir7-1, Mir7-2, Mir7b, ...)
Gene Ontology
(GO)
classifications
All GO classifications: (23 annotations)
Process actin filament organization, auditory receptor cell development, ...
Component basal part of cell, integral component of membrane, ...
This is a GO Consortium Reference Genome Project gene.
External Resources: FuncBase
Expression
Literature Summary: (4 records)
Data Summary: Results (18)    Tissues (9)    Tissue x Stage Matrix (view)
Assay TypeResults
Immunohistochemistry 13
Western blot 3
RT-PCR 2
cDNA source data(7)
Other mouse links: Allen Institute   GEO   Expression Atlas
Other vertebrate links: Xenbase clrn1 ; ZFIN clrn1    NEW 
Molecular
reagents
All nucleic(8) cDNA(7) Primer pair(1)
Microarray probesets(2)
Other database
links
VEGA Gene Model OTTMUSG00000031611 (Evidence)
Ensembl Gene Model ENSMUSG00000043850 (Evidence)
Entrez Gene 229320 (Evidence)
UniGene 131502
DFCI TC1594654, TC1594172, TC1587887, TC1731237
DoTS DT.99839684, DT.94254507, DT.91446623, DT.101368696
NIA Mouse Gene Index U024083
Consensus CDS Project CCDS17369.1, CCDS38438.1, CCDS38439.1
International Mouse Phenotyping Consortium Status Clrn1
Sequences
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 sequences
All sequences(47) RefSeq(6) UniProt(4)
Polymorphisms
SNPs within 2kb(349 from dbSNP Build 137)
Protein-related
information
ResourceIDDescription
InterPro IPR026748 Clarin
InterPro IPR004031 PMP-22/EMP/MP20/Claudin
Protein Ontology PR:000005605 clarin-1
References
(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:219988 Zallocchi M, et al., Role for a novel Usher protein complex in hair cell synaptic maturation. PLoS One. 2012;7(2):e30573
All references(35)
Disease annotation references (2)
Other
accession IDs
MGI:2442622

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
07/21/2015
MGI 5.22
The Jackson Laboratory