Clrn1 clarin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clrn1provided by RGD
Official Full Name: clarin 1provided by RGD
Primary source: RGD:628779
See related: EnsemblRapid:ENSRNOG00000042477 AllianceGenome:RGD:628779
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ush3; Ush3a
Summary: Predicted to be involved in several processes, including equilibrioception; photoreceptor cell maintenance; and sensory perception of sound. Predicted to act upstream of or within several processes, including auditory receptor cell stereocilium organization; neuromuscular process controlling balance; and positive regulation of lamellipodium assembly. Predicted to be located in several cellular components, including lamellipodium; microvillus; and trans-Golgi network transport vesicle. Used to study retinitis pigmentosa. 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, Dec 2024]
Expression: Restricted expression toward (RPKM 7.0) See more
Orthologs: human mouse all
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Genomic context

Location:: 2q26

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (145233941..145280855, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (143084030..143130948, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (149049925..149088787, complement)

Chromosome 2 - NC_086020.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

First description of German family with Usher syndrome(USH) due to USH3A mutations, including one novel. Also in Central European population, USH3A mutations should be considered in cases of USH.
Title: Two truncating USH3A mutations, including one novel, in a German family with Usher syndrome.

Submit: New GeneRIF Correction

General gene information

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Markers

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

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in actin filament organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within actin filament organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within auditory receptor cell development	ISO Inferred from Sequence Orthology more info
involved_in auditory receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within auditory receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in cell motility	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell motility	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lamellipodium assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of lamellipodium assembly	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of light stimulus	IEA Inferred from Electronic Annotation more info
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	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
located_in basal part of cell	ISO Inferred from Sequence Orthology more info
located_in lamellipodium	IEA Inferred from Electronic Annotation more info
located_in lamellipodium	ISO Inferred from Sequence Orthology more info
located_in microtubule cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in microtubule cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in microvillus	IEA Inferred from Electronic Annotation more info
located_in microvillus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in stereocilium	IEA Inferred from Electronic Annotation more info
located_in stereocilium	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network transport vesicle	IEA Inferred from Electronic Annotation more info
located_in trans-Golgi network transport vesicle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: clarin-1

Names: Usher syndrome 3A homolog; Usher syndrome type III A; 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.