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CLRN1 clarin 1 [ Homo sapiens (human) ]

Gene ID: 7401, updated on 8-Dec-2018

Summary

Official Symbol
CLRN1provided by HGNC
Official Full Name
clarin 1provided by HGNC
Primary source
HGNC:HGNC:12605
See related
Ensembl:ENSG00000163646 MIM:606397
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RP61; USH3; USH3A
Summary
This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in adrenal (RPKM 2.0), duodenum (RPKM 0.5) and 1 other tissue See more
Orthologs

Genomic context

See CLRN1 in Genome Data Viewer
Location:
3q25.1
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (150926163..150972999, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (150643950..150690786, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986144 Neighboring gene MINDY family member 4B Neighboring gene CLRN1 antisense RNA 1 Neighboring gene mediator complex subunit 12 like Neighboring gene RNA, 5S ribosomal pseudogene 145 Neighboring gene G protein-coupled receptor 171

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
actin filament organization IDA
Inferred from Direct Assay
more info
PubMed 
auditory receptor cell stereocilium organization IEA
Inferred from Electronic Annotation
more info
 
cell motility IDA
Inferred from Direct Assay
more info
PubMed 
equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of lamellipodium assembly IDA
Inferred from Direct Assay
more info
PubMed 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basal part of cell IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
microtubule IEA
Inferred from Electronic Annotation
more info
 
microvillus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
stereocilium IEA
Inferred from Electronic Annotation
more info
 
trans-Golgi network transport vesicle IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
clarin-1
Names
Usher syndrome type-3 protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_009168.1 RefSeqGene

    Range
    5001..51837
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_700

mRNA and Protein(s)

  1. NM_001195794.1NP_001182723.1  clarin-1 isoform d

    See identical proteins and their annotated locations for NP_001182723.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) encodes the longest isoform (d).
    Source sequence(s)
    AF482697, AF495717, HM626132
    Consensus CDS
    CCDS56285.1
    UniProtKB/Swiss-Prot
    P58418
    Related
    ENSP00000329158.4, ENST00000328863.8
  2. NM_001256819.1NP_001243748.1  clarin-1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple differences in the coding region, compared to variant 5, one of which results in a translational frameshift. The resulting isoform (e) has a distinct C-terminus and is shorter than isoform d.
    Source sequence(s)
    AC020636, BM666773
    Related
    ENSP00000419892.2, ENST00000468836.2
  3. NM_052995.2NP_443721.1  clarin-1 isoform c

    See identical proteins and their annotated locations for NP_443721.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains multiple differences in the UTRs and coding region compared to variant 5. The resulting isoform (c) contains shorter and distinct N- and C-termini, compared to isoform d.
    Source sequence(s)
    AF388366
    Consensus CDS
    CCDS35492.1
    UniProtKB/Swiss-Prot
    P58418
    Related
    ENSP00000295911.2, ENST00000295911.6
  4. NM_174878.2NP_777367.1  clarin-1 isoform a

    See identical proteins and their annotated locations for NP_777367.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 3' coding region, compared to variant 5. The resulting isoform (a) is shorter than isoform d.
    Source sequence(s)
    AF482697, AF495717
    Consensus CDS
    CCDS3153.1
    UniProtKB/Swiss-Prot
    P58418
    Related
    ENSP00000322280.1, ENST00000327047.5

RNA

  1. NR_046380.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) has an additional exon in the 5' region, compared to variant 5. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC020636, AF482697, AF495717, BC074970, HM626132

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    150926163..150972999 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_174880.1: Suppressed sequence

    Description
    NM_174880.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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