Clrn1 clarin 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clrn1provided by MGI
Official Full Name: clarin 1provided by MGI
Primary source: MGI:MGI:2388124
See related: Ensembl:ENSMUSG00000043850 AllianceGenome:MGI:2388124
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: USH3; Ush3a; clarin-1; A130002D11Rik
Summary: Acts upstream of or within auditory receptor cell stereocilium organization; neuromuscular process controlling balance; and sensory perception of sound. Located in several cellular components, including basal part of cell; stereocilium; and trans-Golgi network transport vesicle. Is expressed in gut; male reproductive gland or organ; nervous system; sensory organ; and skin. Used to study Usher syndrome type 3 and Usher syndrome type 3A. Human ortholog(s) of this gene implicated in Usher syndrome type 3A and retinitis pigmentosa 61. Orthologous to human CLRN1 (clarin 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

Location:: 3 D; 3 28.78 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (58751449..58792633, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (58844028..58885212, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

results identify clarin-1 as a key organizer of IHC ribbon synapses, and suggest new treatment possibilities for USH3A patients.
Title: Clarin-1 gene transfer rescues auditory synaptopathy in model of Usher syndrome.
CLRN1 expression is potentially supported by a variety of retinal cells, and the right combination of AAV vector dose, promoter, and delivery method needs to be selected to develop safe therapies for USH3 disorder.
Title: AAV-Mediated Clarin-1 Expression in the Mouse Retina: Implications for USH3A Gene Therapy.
Mutations that are Clrn1-/- biallelic cause visual defects when placed under A/J background.
Title: Impairment of Vision in a Mouse Model of Usher Syndrome Type III.
A novel synaptic Usher complex comprised of clarin-1 and specific isoforms of CDH23, PCDH15 and VLGR1, was identified.
Title: Role for a novel Usher protein complex in hair cell synaptic maturation.
The subcellular localization of clarin-1 in hair cells and photoreceptors suggests it functions at both the basal and apical poles of neurosensoriepithelia.
Title: Localization and expression of clarin-1, the Clrn1 gene product, in auditory hair cells and photoreceptors.
CLRN1 is unnecessary in the murine retina but essential for normal cochlear development and function.
Title: CLRN1 is nonessential in the mouse retina but is required for cochlear hair cell development.
Clrn1 is necessary for hair cell function and associated neural activation.
Title: Usher syndrome IIIA gene clarin-1 is essential for hair cell function and associated neural activation.
clarin-1 has a role in the regulation and homeostasis of actin filaments
Title: Clarin-1, encoded by the Usher Syndrome III causative gene, forms a membranous microdomain: possible role of clarin-1 in organizing the actin cytoskeleton.
Clarin-1 ribozyme induced apoptosis of cochlear hair cells and cells of stria vascularis. Suggest role for apoptosis in progressin of Usher syndrome type 3.
Title: Anti-clarin-1 AAV-delivered ribozyme induced apoptosis in the mouse cochlea.
a role for clarin-1 in hair cell and photoreceptor cell synapses, as well as a common pathophysiological pathway for different Usher syndromes
Title: USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (7) 1 citation

General gene information

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Markers

Clrn1 (e-PCR), detects polymorphism
- UniSTS:532266

D3Nds33 (e-PCR), detects polymorphism
- UniSTS:142410

Gene Ontology Provided by MGI

Process	Evidence Code	Pubs
acts_upstream_of_or_within actin filament organization	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within auditory receptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within auditory receptor cell stereocilium organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell motility	ISO Inferred from Sequence Orthology more info	PubMed
involved_in equilibrioception	IBA Inferred from Biological aspect of Ancestor more info
involved_in equilibrioception	IEA Inferred from Electronic Annotation more info
involved_in equilibrioception	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuromuscular process controlling balance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of lamellipodium assembly	ISO Inferred from Sequence Orthology more info	PubMed
involved_in sensory perception of light stimulus	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	IBA Inferred from Biological aspect of Ancestor more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in basal part of cell	IDA Inferred from Direct Assay more info	PubMed
located_in lamellipodium	ISO Inferred from Sequence Orthology more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in microtubule cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in microvillus	ISO Inferred from Sequence Orthology more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info	PubMed
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network transport vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: clarin-1

Names: Usher syndrome 3A homolog; usher syndrome type-3 protein homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_153384.3 → NP_700433.1 clarin-1 isoform 1

See identical proteins and their annotated locations for NP_700433.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC112998, AF495718, AK037267

Consensus CDS

CCDS38439.1

UniProtKB/Swiss-Prot

Q8K445

UniProtKB/TrEMBL

Q8BYX9

Related

ENSMUSP00000052254.7, ENSMUST00000055636.13
NM_153385.3 → NP_700434.1 clarin-1 isoform 2

See identical proteins and their annotated locations for NP_700434.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region compared to isoform 1. The encoded protein (isoform 2) is shorter than isoform 1.

Source sequence(s)

AC112998, AF495719, AK037267

Consensus CDS

CCDS38438.1

UniProtKB/Swiss-Prot

Q8K445, Q8K446

UniProtKB/TrEMBL

B7ZNE8

Related

ENSMUSP00000051738.8, ENSMUST00000051408.8
NM_153386.3 → NP_700435.1 clarin-1 isoform 3

See identical proteins and their annotated locations for NP_700435.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two in-frame exons in the coding region compared to variant 1. The encoded protein (isoform 3) is shorter than isoform 1.

Source sequence(s)

AC112998, AF495718, AK037267, AK041623

Consensus CDS

CCDS17369.1

UniProtKB/TrEMBL

Q8K444

Related

ENSMUSP00000072363.7, ENSMUST00000072551.7