ZFIN is now using GRCz12tu for Genomic Data

Gene

clrn1

ID

ZDB-GENE-040718-420

Name

clarin 1

Symbol

clrn1 Nomenclature History

Previous Names

zgc:91933

Type

protein_coding_gene

Location

Chr: 15 Mapping Details/Browsers

Genome Assembly

GRCz12tu

Annotation Status

Current

Description

Acts upstream of or within several processes, including plasma membrane bounded cell projection organization; sensory perception of sound; and synaptic vesicle recycling via endosome. Located in ciliary transition zone and stereocilium bundle. Is expressed in auditory epithelial support cell; brain; hair cell; and sensory system. Used to study Usher syndrome 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).

Genome Resources

Note

None

Comparative Information

Expression

All Expression Data

11 figures from 4 publications

Cross-Species Comparison

High Throughput Data

Expression Atlas

UO scRNA-seq (UCSC browser)

Single Cell Expression Atlas

Daniocell

Thisse Expression Data

MGC:91933 (1 image)

Wild Type Expression Summary

Phenotype

All Phenotype Data: 11 figures from 3 publications
Cross-Species Comparison: Alliance

Phenotype Summary

Mutations

Mutants

Sequence Targeting Reagents

Human Disease

Associated With clrn1 Human Ortholog

Disease Ontology Term	Multi-Species Data	OMIM Term	OMIM Phenotype ID
retinitis pigmentosa 61	Alliance	Retinitis pigmentosa 61	614180
Usher syndrome type 3A	Alliance	Usher syndrome, type 3A	276902

Associated With clrn1 Via Experimental Models

Human Disease	Fish	Conditions	Citations
Usher syndrome	clrn1^{cwr1001/cwr1001}	control	Gopal et al., 2015
Usher syndrome	clrn1^{cwr1004/cwr1004}	control	Gopal et al., 2015
Usher syndrome	clrn1^{cwr1003/cwr1003}	control	Gopal et al., 2015
Usher syndrome	clrn1^{cwr1002/cwr1002}	control	Gopal et al., 2015

Gene Ontology

Protein Domains

Domain, Family, and Site Summary

Type	InterPro ID	Name
Family	IPR026748	Clarin

Domain Details Per Protein

Protein	Additional Resources	Length	Clarin
UniProtKB:Q6DGA8	InterPro	232

Transcripts

Genome Browsers

ZFIN

Type	Name	Annotation Method	Has Havana Data	Length (nt)	Analysis
mRNA	clrn1-201 (1) Ensembl	Ensembl		1,429 nt	Select Tool ZFIN BLAST

Interactions and Pathways

No data available

Antibodies

Name	Type	Antigen Genes	Isotype	Host Organism	Assay	Source	Citations
Ab2-clrn1	polyclonal	clrn1		Rabbit	IHC	Proteintech	2
Ab1-clrn1	polyclonal	clrn1		Rabbit	IHC WB	Novus Biologicals, LLC	4

Plasmids

No data available

Constructs

Marker Relationships

Sequences

Genome Browsers

NCBI Map Viewer

ZFIN

Orthology

Comparative Orthology: Alliance
Gene Tree: Ensembl

Citations