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Entry version 120 (11 Dec 2019)
Sequence version 1 (01 Oct 2002)
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Protein

Clarin-3

Gene

CLRN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Protein family/group databases

Transport Classification Database

More...
TCDBi
9.A.46.1.3 the clarin (clrn) family

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Clarin-3
Alternative name(s):
Transmembrane protein 12
Usher syndrome type-3A-like protein 1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:CLRN3
Synonyms:TMEM12, USH3AL1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHomo sapiens (Human)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri9606 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 10

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
HostDB:ENSG00000180745.4

Human Gene Nomenclature Database

More...
HGNCi
HGNC:20795 CLRN3

neXtProt; the human protein knowledge platform

More...
neXtProti
NX_Q8NCR9

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei8 – 28HelicalSequence analysisAdd BLAST21
Transmembranei92 – 112HelicalSequence analysisAdd BLAST21
Transmembranei129 – 149HelicalSequence analysisAdd BLAST21
Transmembranei181 – 201HelicalSequence analysisAdd BLAST21

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywords - Cellular componenti

Membrane

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Organism-specific databases

Open Targets

More...
OpenTargetsi
ENSG00000180745

The Pharmacogenetics and Pharmacogenomics Knowledge Base

More...
PharmGKBi
PA162382510

Miscellaneous databases

Pharos NIH Druggable Genome Knowledgebase

More...
Pharosi
Q8NCR9 Tdark

Polymorphism and mutation databases

BioMuta curated single-nucleotide variation and disease association database

More...
BioMutai
CLRN3

Domain mapping of disease mutations (DMDM)

More...
DMDMi
74751198

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002746981 – 226Clarin-3Add BLAST226

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section specifies the position and type of each covalently attached glycan group (mono-, di-, or polysaccharide).<p><a href='/help/carbohyd' target='_top'>More...</a></p>Glycosylationi83N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
Q8NCR9

MassIVE - Mass Spectrometry Interactive Virtual Environment

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MassIVEi
Q8NCR9

MaxQB - The MaxQuant DataBase

More...
MaxQBi
Q8NCR9

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q8NCR9

PeptideAtlas

More...
PeptideAtlasi
Q8NCR9

PRoteomics IDEntifications database

More...
PRIDEi
Q8NCR9

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
72933 [Q8NCR9-1]
72934 [Q8NCR9-2]

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q8NCR9

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...
PhosphoSitePlusi
Q8NCR9

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSG00000180745 Expressed in 61 organ(s), highest expression level in colonic mucosa

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q8NCR9 HS

Organism-specific databases

Human Protein Atlas

More...
HPAi
HPA014482

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
125642, 2 interactors

Protein interaction database and analysis system

More...
IntActi
Q8NCR9, 2 interactors

STRING: functional protein association networks

More...
STRINGi
9606.ENSP00000357660

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
Q8NCR9 protein

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the clarin family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG410IXPT Eukaryota
ENOG4112478 LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00850000132319

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000111796

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q8NCR9

Identification of Orthologs from Complete Genome Data

More...
OMAi
PTGVYTW

Database of Orthologous Groups

More...
OrthoDBi
1309543at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q8NCR9

TreeFam database of animal gene trees

More...
TreeFami
TF331875

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR026748 Clarin

The PANTHER Classification System

More...
PANTHERi
PTHR31548 PTHR31548, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (2)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

This entry describes 2 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q8NCR9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MPTTKKTLMF LSSFFTSLGS FIVICSILGT QAWITSTIAV RDSASNGSIF
60 70 80 90 100
ITYGLFRGES SEELSHGLAE PKKKFAVLEI LNNSSQKTLH SVTILFLVLS
110 120 130 140 150
LITSLLSSGF TFYNSISNPY QTFLGPTGVY TWNGLGASFV FVTMILFVAN
160 170 180 190 200
TQSNQLSEEL FQMLYPATTS KGTTHSYGYS FWLILLVILL NIVTVTIIIF
210 220
YQKARYQRKQ EQRKPMEYAP RDGILF
Length:226
Mass (Da):25,321
Last modified:October 1, 2002 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i3139127324A08CF1
GO
Isoform 2 (identifier: Q8NCR9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-68: Missing.
     69-76: AEPKKKFA → MHSQNIVL

Show »
Length:158
Mass (Da):18,007
Checksum:i4D493CC716CC9F9C
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence CAE45899 differs from that shown. Reason: Erroneous initiation.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural variantiVAR_06939922I → N1 Publication1
Natural variantiVAR_05382875F → I. Corresponds to variant dbSNP:rs35070529Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_0228711 – 68Missing in isoform 2. 1 PublicationAdd BLAST68
Alternative sequenceiVSP_02287269 – 76AEPKKKFA → MHSQNIVL in isoform 2. 1 Publication8

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
BX640823 mRNA Translation: CAE45899.1 Different initiation.
AL158166 Genomic DNA No translation available.
BC029478 mRNA Translation: AAH29478.1

The Consensus CDS (CCDS) project

More...
CCDSi
CCDS7656.1 [Q8NCR9-1]

NCBI Reference Sequences

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RefSeqi
NP_689524.1, NM_152311.4 [Q8NCR9-1]

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENST00000368671; ENSP00000357660; ENSG00000180745 [Q8NCR9-1]

Database of genes from NCBI RefSeq genomes

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GeneIDi
119467

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
hsa:119467

UCSC genome browser

More...
UCSCi
uc001lka.2 human [Q8NCR9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX640823 mRNA Translation: CAE45899.1 Different initiation.
AL158166 Genomic DNA No translation available.
BC029478 mRNA Translation: AAH29478.1
CCDSiCCDS7656.1 [Q8NCR9-1]
RefSeqiNP_689524.1, NM_152311.4 [Q8NCR9-1]

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

BioGridi125642, 2 interactors
IntActiQ8NCR9, 2 interactors
STRINGi9606.ENSP00000357660

Protein family/group databases

TCDBi9.A.46.1.3 the clarin (clrn) family

PTM databases

iPTMnetiQ8NCR9
PhosphoSitePlusiQ8NCR9

Polymorphism and mutation databases

BioMutaiCLRN3
DMDMi74751198

Proteomic databases

jPOSTiQ8NCR9
MassIVEiQ8NCR9
MaxQBiQ8NCR9
PaxDbiQ8NCR9
PeptideAtlasiQ8NCR9
PRIDEiQ8NCR9
ProteomicsDBi72933 [Q8NCR9-1]
72934 [Q8NCR9-2]

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
119467

Genome annotation databases

EnsembliENST00000368671; ENSP00000357660; ENSG00000180745 [Q8NCR9-1]
GeneIDi119467
KEGGihsa:119467
UCSCiuc001lka.2 human [Q8NCR9-1]

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
119467
EuPathDBiHostDB:ENSG00000180745.4

GeneCards: human genes, protein and diseases

More...
GeneCardsi
CLRN3
HGNCiHGNC:20795 CLRN3
HPAiHPA014482
neXtProtiNX_Q8NCR9
OpenTargetsiENSG00000180745
PharmGKBiPA162382510

GenAtlas: human gene database

More...
GenAtlasi
Search...

Phylogenomic databases

eggNOGiENOG410IXPT Eukaryota
ENOG4112478 LUCA
GeneTreeiENSGT00850000132319
HOGENOMiHOG000111796
InParanoidiQ8NCR9
OMAiPTGVYTW
OrthoDBi1309543at2759
PhylomeDBiQ8NCR9
TreeFamiTF331875

Miscellaneous databases

Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens

More...
GenomeRNAii
119467
PharosiQ8NCR9 Tdark

Protein Ontology

More...
PROi
PR:Q8NCR9
RNActiQ8NCR9 protein

Gene expression databases

BgeeiENSG00000180745 Expressed in 61 organ(s), highest expression level in colonic mucosa
GenevisibleiQ8NCR9 HS

Family and domain databases

InterProiView protein in InterPro
IPR026748 Clarin
PANTHERiPTHR31548 PTHR31548, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCLRN3_HUMAN
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q8NCR9
Secondary accession number(s): Q6MZX8
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 6, 2007
Last sequence update: October 1, 2002
Last modified: December 11, 2019
This is version 120 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
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