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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CLRN3 Gene

protein-coding   GIFtS: 44
GCID: GC10M129676

clarin 3

(Previous name: transmembrane protein 12 )
(Previous symbol: TMEM12)
 Explore 4 diseases affiliated with
CLRN3 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for CLRN3    

Aliases
for CLRN3 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Clarin 31 2     Usher Syndrome Type-3A-Like Protein 12 3
Transmembrane Protein 121 2 3     MGC328711
TMEM121 2 3     Clarin-31
USH3AL11 2 3     

External Ids:    HGNC: 207951   Entrez Gene: 1194672   Ensembl: ENSG000001807457   UniProtKB: Q8NCR93   

Export aliases for CLRN3 gene to outside databases

Previous GC identifers: GC10M129568 GC10M123250


Summaries
for CLRN3 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
  --

Genomic Views
for CLRN3 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.1  NT_008818.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CLRN3 gene promoter:
         E2F-3a   E2F-4   E2F-5   Tal-1   E2F-2   E47   CBF-B   E2F   E2F-1   CBF-A   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CLRN3 promoter sequence
   Search SABiosciences Chromatin IP Primers for CLRN3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLRN3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10q26.2   Ensembl cytogenetic band:  10q26.2   HGNC cytogenetic band: 10q26.2

CLRN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLRN3 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M129676:  view genomic region     (about GC identifiers)

Start:
 129,676,105 bp from pter      End:
 129,691,211 bp from pter
Size:
 15,107 bases      Orientation:
 minus strand

Proteins
for CLRN3 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: CLRN3_HUMAN, Q8NCR9 (See protein sequence)
Recommended Name: Clarin-3  
Size: 226 amino acids; 25321 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Sequence caution: Sequence=CAE45899.1; Type=Erroneous initiation;
Secondary accessions: Q6MZX8
Alternative splicing: 2 isoforms:  Q8NCR9-1   Q8NCR9-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CLRN3: NX_Q8NCR9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8NCR9

    • CLRN3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_689524.1  
    ENSEMBL proteins: 
     ENSP00000357660  

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    Uscn Proteins for CLRN3

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--


    CLRN3 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for CLRN3 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    CLRN3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR026748 Clarin

    Graphical View of Domain Structure for InterPro Entry Q8NCR9

    ProtoNet protein and cluster: Q8NCR9

    UniProtKB/Swiss-Prot: CLRN3_HUMAN, Q8NCR9
    Similarity: Belongs to the clarin family


    Function
    for CLRN3 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate CLRN3:
    hsa-miR-198
    SwitchGear 3'UTR luciferase reporter plasmid: CLRN3 3' UTR sequence
    Inhib. RNA
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    3 GenomeRNAi human phenotypes for CLRN3:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 


    Pathways & Interactions
    for CLRN3 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CLRN3

    Drugs & Compounds
    for CLRN3 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CLRN3
    Search CenterWatch for drugs/clinical trials and news about CLRN3 

    Transcripts
    for CLRN3 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for CLRN3 gene: 
    NM_152311.3  

    Unigene Cluster for CLRN3:

    Clarin 3
    Hs.242014  [show with all ESTs]
    Unigene Representative Sequence: BX640823
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000368671(uc001ljz.1 uc001lka.1)

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    hsa-miR-198
    SwitchGear 3'UTR luciferase reporter plasmid: CLRN3 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLRN3
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLRN3

    Additional cDNA sequence: 

    BC029478.1 BX640823.1 

    3 DOTS entries:

    DT.453290  DT.40208297  DT.92060001 

    24/47 AceView cDNA sequences (see all 47):

    CB128909 BM827295 AA741216 AA877523 BX640823 BG618618 BM789465 BM797186 
    BM830163 CB159007 AA887896 AA515094 BX283220 CB128395 AA577173 AA314510 
    CB147597 CB129557 BG616657 NM_152311 AW024392 BC029478 AW961147 CB144639 

    GeneLoc Exon Structure


    Expression
    for CLRN3 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CLRN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATACTGTTTG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    CLRN3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Gut TubeHindgutHindgut Endoderm CellsEndoderm
    Gut TubeMidgutMidgut Endoderm CellsEndoderm
    Gut TubeHindgutGut Tube
    Gut TubeMidgutGut Tube
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CLRN3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLRN3

    SOURCE GeneReport for Unigene cluster: Hs.242014
        SABiosciences Custom PCR Arrays for CLRN3
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLRN3

    Orthologs
    for CLRN3 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of chordates.

    Orthologs for CLRN3 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Clrn31 , 5 clarin 31, 5 76.4(n)1
    73.01(a)1    		   7 (81.27 cM)5
    2120701  NM_178669.51  NP_848784.11 
     1355114665 
    chicken
    (Gallus gallus)    		 Aves CLRN31 clarin 3 55.62(n)
    43.12(a)    		   423961  XM_421820.3  XP_421820.3 
    lizard
    (Anolis carolinensis)    		 Reptilia CLRN36
    		 --
    		 56(a)
    		 1 ↔ 1
    		 3(53790086-53790247)
    zebrafish
    (Danio rerio)    		 Actinopterygii LOC1000005021 clarin-3-like 45.33(n)
    32.44(a)    		   100000502  XM_001340649.1  XP_001340685.1 


    ENSEMBL Gene Tree for CLRN3 (if available)
    TreeFam Gene Tree for CLRN3 (if available) 

    Paralogs
    for CLRN3 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CLRN3 gene
    CLRN12  CLRN22  

    CLRN3 for paralogs           About GeneDecksing



    Genomic Variants
    for CLRN3 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/322 NCBI SNPs in CLRN3 are shown (see all 322)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 10 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs618757731,2
    		C,--129675634(+) CCCAGG/CTCTAC 1 -- int14Minor allele frequency- C:0.13NA WA EA 360
    rs1178137641,2
    		F,--129675756(+) GTTTAG/ACCTCT 1 -- int11Minor allele frequency- A:0.03EA 120
    rs733743501,2
    		C,--129675767(+) TTAGCA/GTATAG 1 -- int13Minor allele frequency- G:0.08WA CSA 121
    rs1855175971,2
    		--129675816(+) CATTTA/CTATTC 1 -- int10--------
    rs1893318101,2
    		--129675818(+) TTTCTA/TTTCTC 1 -- int10--------
    rs79123031,2
    		C,F,A,H--129676027(+) CATGCA/GTAGAG 1 -- int110Minor allele frequency- G:0.00NS EA NA 848
    rs560711081,2
    		C,--129676046(+) AAATAC/TCCAGT 1 -- int13Minor allele frequency- T:0.22WA CSA 123
    rs1140367581,2
    		--129676121(+) TGACAC/GAGCCT 1 -- ut311Minor allele frequency- G:0.01WA 118
    rs22967851,2
    		C,F,H,--129676169(+) CGTTAC/TGCTCA 1 -- ut31 ese325Minor allele frequency- T:0.12EA NA NS WA 4452
    rs1415575381,2
    		--129676182(+) ATGATA/GCTACT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for CLRN3 (129676105 - 129691211 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for CLRN3: --

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    Disorders / Diseases
    for CLRN3 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    CLRN3 for disorders           About GeneDecksing

    4 diseases for CLRN3:    About MalaCards
    usher syndrome type 3a    usher syndrome type 3    usher syndrome    alzheimer's disease

    Human Genome Epidemiology (HuGE) Navigator: CLRN3 (2 documents)

    Export disorders for CLRN3 gene to outside databases

    Publications
    for CLRN3 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CLRN3 gene, integrated from 9 sources (see all 16):
    (articles sorted by number of sources associating them with CLRN3)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (2004)
    3. Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. (PubMed id 12145752)1, 3 Fields R.R.... Sumegi J. (2002)
    4. USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. (PubMed id 12080385)1, 3 Adato A.... Lancet D. (2002)
    5. Genomic determinants of motor and cognitive outcomes i n Parkinson's disease. (PubMed id 22658654)1 Chung S.J....Maraganore D.M. (2012)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    8. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    9. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1 Grupe A....Goate A. (2006)
    10. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)

    External Searches for CLRN3 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing CLRN3 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 119467 HGNC: 20795 AceView: MGC32871 Ensembl:ENSG00000180745 euGenes: HUgn119467
    ECgene: CLRN3 H-InvDB: CLRN3

    Other Databases showing CLRN3 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing CLRN3 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CLRN3 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for CLRN3 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for CLRN3 gene:
    Search GeneIP for patents involving CLRN3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for CLRN3 gene

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    Advanced Cell Diagnostics
    About This Section

     
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