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CLRN2 Gene

protein-coding   GIFtS: 34
GCID: GC04P017516

Clarin 2

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Clarin 21 2
clarin-22

External Ids:    HGNC: 339391   Entrez Gene: 6451042   Ensembl: ENSG000002495817   UniProtKB: A0PK113   

Export aliases for CLRN2 gene to outside databases

Previous GC identifers: GC04P017126 GC04P016871


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CLRN2 Gene:
This gene belongs to the clarin family of genes. The clarins appear to belong to a large superfamily of small
integral membrane glycoproteins with four transmembrane domains. The exact function of this gene is unknown.
(provided by RefSeq, Oct 2008)

GeneCards Summary for CLRN2 Gene:
CLRN2 (clarin 2) is a protein-coding gene. An important paralog of this gene is ENSG00000260234.




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000004.11  NC_018915.2  NT_006316.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLRN2 gene promoter:
         RFX1   NF-1   NF-1/L   AML1a   Olf-1   FOXD3   Ik-2   FOXJ2 (long isoform)   FOXJ2   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLRN2


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

Entrez Gene cytogenetic band: 4p15.32   Ensembl cytogenetic band:  4p15.32   HGNC cytogenetic band: 4p15.32

CLRN2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLRN2 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P017516:  view genomic region     (about GC identifiers)

Start:
17,516,788 bp from pter      End:
17,528,727 bp from pter
Size:
11,940 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CLRN2_HUMAN, A0PK11 (See protein sequence)
Recommended Name: Clarin-2  
Size: 232 amino acids; 25446 Da

Explore the universe of human proteins at neXtProt for CLRN2: NX_A0PK11

Explore proteomics data for CLRN2 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn48

  • See CLRN2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001073296.1  
    ENSEMBL proteins: 
     ENSP00000424711  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR004031 PMP22/EMP/MP20/Claudin
     IPR026748 Clarin

    Graphical View of Domain Structure for InterPro Entry A0PK11

    ProtoNet protein and cluster: A0PK11

    UniProtKB/Swiss-Prot: CLRN2_HUMAN, A0PK11
    Similarity: Belongs to the clarin family


    Find genes that share domains with CLRN2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for CLRN2

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CLRN2_HUMAN, A0PK11: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    extracellular2
    cytoskeleton1
    cytosol1
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with CLRN2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CLRN2
    Interactions:

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    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CLRN2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CLRN2 gene: 
    NM_001079827.2  

    Unigene Cluster for CLRN2:

    Clarin 2
    Hs.631526  [show with all ESTs]
    Unigene Representative Sequence: BC127863
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000511148(uc003gpg.1)
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    Additional mRNA sequence: BC127863.1 

    1 DOTS entry:

    DT.121217503 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CLRN2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGCAAACTT
    CLRN2 Expression
    About this image

    CLRN2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLRN2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631526
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    In Situ
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    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CLRN2 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clrn21 , 5 clarin 21, 5 85.78(n)1
    94.4(a)1
      5 (24.93 cM)5
    6242241  NM_001163317.11  NP_001156789.11 
     454537515 
    chicken
    (Gallus gallus)
    Aves CLRN21 clarin 2 70.83(n)
    68.53(a)
      100858515  XM_003641249.2  XP_003641297.1 
    lizard
    (Anolis carolinensis)
    Reptilia CLRN26
    clarin 2
    63(a)
    1 ↔ 1
    4(125383015-125392596)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia clrn21 clarin 2 65.95(n)
    62.5(a)
      100491228  XM_002938635.1  XP_002938681.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7958071 novel protein similar to vertebrate Usher syndrome more 57.9(n)
    50(a)
      795807  NM_001114690.1  NP_001108162.1 


    ENSEMBL Gene Tree for CLRN2 (if available)
    TreeFam Gene Tree for CLRN2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLRN2 gene
    ENSG000002602342  CLRN32  CLRN12  
    1 SIMAP similar gene for CLRN2 using alignment to 1 protein entry:     CLRN2_HUMAN:
    CLRN1

    Find genes that share paralogs with CLRN2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CLRN2 (see all 295)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs778227151,2
    F--17516304(+) ACCGGG/AGTCAT 1 -- us2k11Minor allele frequency- A:0.01WA 118
    rs117275311,2
    H--17516331(+) CAGTCC/TTAAAG 1 -- us2k10--------
    rs1921626971,2
    --17516413(+) TACTGC/TGCATT 1 -- us2k10--------
    rs1839395301,2
    --17516467(+) TCTAAC/TACATG 1 -- us2k10--------
    rs1391077791,2
    --17516470(+) AACACA/GTGCAT 1 -- us2k10--------
    rs1886627941,2
    --17516485(+) TGAGAC/TTGGTT 1 -- us2k10--------
    rs25977831,2
    C,F,A,H--17516691(+) CTCTGT/CAGAGG 1 -- us2k118Minor allele frequency- C:0.34NS EA NA WA CSA 2160
    rs1499038061,2
    --17516732(+) TGTGCA/TAGCTT 1 -- us2k10--------
    rs1449130161,2
    C--17516765(+) TGGACC/TTACAA 1 -- us2k10--------
    rs25977841,2
    C,H--17516771(+) TACAAT/CCTTGA 1 -- us2k112Minor allele frequency- C:0.02NA WA CSA EA 374

    HapMap Linkage Disequilibrium report for CLRN2 (17516788 - 17528727 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for CLRN2: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing CLRN2
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    (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.)
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      --

    (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)
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    PubMed articles for CLRN2 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CLRN2)
        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. (Genome Res. 2004)
    2. 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. (Eur. J. Hum. Genet. 2002)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 645104 HGNC: 33939 Ensembl:ENSG00000249581 euGenes: HUgn645104 ECgene: CLRN2
    H-InvDB: CLRN2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CLRN2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLRN2 gene:
    Search GeneIP for patents involving CLRN2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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     Browse SwitchGear Promoter luciferase reporter plasmids for CLRN2
     Search ThermoFisher Antibodies for CLRN2
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLRN2
     Browse compounds at ApexBio
     Search Addgene for plasmids for CLRN2
      Search eBioscience for proteins for CLRN2
      Search eBioscience for elisas for CLRN2
      eBioscience FlowRNA Probe Sets
     genOway: Develop your customized and physiologically relevant rodent model for CLRN2
      Search antibodies-online for antibodies for CLRN2
     antibodies-online kits for CLRN2 (2 products)
      Search antibodies-online for peptides for CLRN2
      Search antibodies-online for proteins for CLRN2
           
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