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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 zebrafish

Gene Tree: Clrn1

Human
homologs
Human Homolog CLRN1, clarin 1
NCBI Gene ID 7401
neXtProt AC  NX_P58418
Human Synonyms  RP61, USH3, USH3A
Human Chr (Location)  3q25; chr3:150926163-150972999 (-)  GRCh38
Disease Associations  (3) Diseases Associated with Human CLRN1
Mutations,
alleles, and
phenotypes
All mutations/alleles(5) : Targeted(5)
Incidental mutations (data from Mutagenetix , APF )
 
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 Using Mouse Clrn1 (1)    Alleles Annotated to Human Diseases(2)   
Interactions
Clrn1 interacts with 279 markers (Mir7-1, Mir7-2, Mir7b, ...)
Gene Ontology
(GO)
classifications
All GO classifications: (19 annotations)
Process actin filament organization, auditory receptor cell development, ...
Component integral component of membrane, lamellipodium, ...
This is a GO Consortium Reference Genome Project gene.
External Resources: FuncBase
Expression
Literature Summary: (4 records)
Data Summary: Results (18)    Tissues (8)   
Theiler Stages: 26, 28
Assay TypeResults
Immunohistochemistry 13
Western blot 3
RT-PCR 2
cDNA source data(7)
External Resources: Allen Institute   GEO   Expression Atlas
Molecular
reagents
All nucleic(8) cDNA(7) Primer pair(1)
Microarray probesets(2)
Other database
links
VEGA Gene ModelOTTMUSG00000031611 (Evidence)
Ensembl Gene ModelENSMUSG00000043850 (Evidence)
Entrez Gene229320 (Evidence)
UniGene131502
DFCITC1587887, TC1594172, TC1594654, TC1731237
DoTSDT.101368696, DT.91446623, DT.94254507, DT.99839684
NIA Mouse Gene IndexU024083
Consensus CDS ProjectCCDS17369.1, CCDS38438.1, CCDS38439.1
International Mouse Knockout Project StatusClrn1
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:186316 Geng R, et al., The Mechanosensory Structure of the Hair Cell Requires Clarin-1, a Protein Encoded by Usher Syndrome III Causative Gene. J Neurosci. 2012 Jul 11;32(28):9485-9498
All references(34)
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
07/23/2014
MGI 5.19
The Jackson Laboratory