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Aliases for CLRN2 Gene

Aliases for CLRN2 Gene

  • Clarin 2 2 3 5
  • Clarin-2 3

External Ids for CLRN2 Gene

Previous GeneCards Identifiers for CLRN2 Gene

  • GC04P017126
  • GC04P016871

Summaries for CLRN2 Gene

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 CLRN1.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN2 Gene

Genomics for CLRN2 Gene

Regulatory Elements for CLRN2 Gene

Enhancers for CLRN2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04F017492 0.6 FANTOM5 ENCODE 11.2 -20.9 -20887 3.0 INSM2 KLF17 ZEB1 GLIS2 ZNF366 FOS CREM SP3 TSHZ1 ZEB2 CLRN2 ENSG00000206780 MED28 LAP3 GC04M017492 GC04P017443
GH04F017490 0.6 ENCODE 11.2 -24.7 -24701 0.9 ELF3 PKNOX1 ARID4B THRB RAD21 RARA YY1 GATA4 GATA2 CREM QDPR CLRN2 ENSG00000206780 GC04M017492 GC04P017443
GH04F017543 1.2 FANTOM5 Ensembl ENCODE 11.1 +29.4 29411 1.3 ELF3 PKNOX1 ATF1 MLX ARID4B ZSCAN9 RARA CREM MIXL1 THAP11 CLRN2 QDPR DCAF16 NCAPG GC04M017552
GH04F017481 0.4 FANTOM5 5.5 -33.0 -33002 0.4 QDPR CLRN2 GC04M017492 GC04P017443
GH04F017978 0.3 FANTOM5 4.6 +463.2 463247 0.4 LCORL CLRN2 KRT18P63
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CLRN2 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLRN2 Gene

Chromosome:
4
Start:
17,515,165 bp from pter
End:
17,527,104 bp from pter
Size:
11,940 bases
Orientation:
Plus strand

Genomic View for CLRN2 Gene

Genes around CLRN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLRN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLRN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN2 Gene

Proteins for CLRN2 Gene

  • Protein details for CLRN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A0PK11-CLRN2_HUMAN
    Recommended name:
    Clarin-2
    Protein Accession:
    A0PK11

    Protein attributes for CLRN2 Gene

    Size:
    232 amino acids
    Molecular mass:
    25446 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLRN2 Gene

Post-translational modifications for CLRN2 Gene

Other Protein References for CLRN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLRN2 Gene

Domains & Families for CLRN2 Gene

Protein Domains for CLRN2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLRN2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A0PK11

UniProtKB/Swiss-Prot:

CLRN2_HUMAN :
  • Belongs to the clarin family.
Family:
  • Belongs to the clarin family.
genes like me logo Genes that share domains with CLRN2: view

No data available for Gene Families for CLRN2 Gene

Function for CLRN2 Gene

Phenotypes for CLRN2 Gene

GenomeRNAi human phenotypes for CLRN2:
genes like me logo Genes that share phenotypes with CLRN2: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN2 Gene

Localization for CLRN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLRN2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLRN2 Gene COMPARTMENTS Subcellular localization image for CLRN2 gene
Compartment Confidence
plasma membrane 3
extracellular 2

Gene Ontology (GO) - Cellular Components for CLRN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CLRN2: view

Pathways & Interactions for CLRN2 Gene

SuperPathways for CLRN2 Gene

No Data Available

Interacting Proteins for CLRN2 Gene

Gene Ontology (GO) - Biological Process for CLRN2 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CLRN2 Gene

Transcripts for CLRN2 Gene

mRNA/cDNA for CLRN2 Gene

(1) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLRN2 Gene

Clarin 2:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN2 Gene

No ASD Table

Relevant External Links for CLRN2 Gene

GeneLoc Exon Structure for
CLRN2
ECgene alternative splicing isoforms for
CLRN2

Expression for CLRN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLRN2 Gene

mRNA differential expression in normal tissues according to GTEx for CLRN2 Gene

This gene is overexpressed in Testis (x8.4), Brain - Hypothalamus (x5.9), Brain - Spinal cord (cervical c-1) (x5.7), and Brain - Hippocampus (x4.7).

Protein differential expression in normal tissues from HIPED for CLRN2 Gene

This gene is overexpressed in Rectum (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLRN2 Gene



Protein tissue co-expression partners for CLRN2 Gene

NURSA nuclear receptor signaling pathways regulating expression of CLRN2 Gene:

CLRN2

SOURCE GeneReport for Unigene cluster for CLRN2 Gene:

Hs.631526
genes like me logo Genes that share expression patterns with CLRN2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for CLRN2 Gene

Orthologs for CLRN2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLRN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLRN2 34 35
  • 98.99 (n)
dog
(Canis familiaris)
Mammalia CLRN2 34 35
  • 90.09 (n)
cow
(Bos Taurus)
Mammalia CLRN2 34 35
  • 87.21 (n)
mouse
(Mus musculus)
Mammalia Clrn2 34 16 35
  • 85.78 (n)
rat
(Rattus norvegicus)
Mammalia Clrn2 34
  • 85.63 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLRN2 35
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLRN2 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLRN2 34 35
  • 70.83 (n)
lizard
(Anolis carolinensis)
Reptilia CLRN2 35
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn2 34
  • 65.95 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC795807 34
  • 57.9 (n)
CLRN2 35
  • 49 (a)
OneToOne
Species where no ortholog for CLRN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLRN2 Gene

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

Paralogs for CLRN2 Gene

Paralogs for CLRN2 Gene

(1) SIMAP similar genes for CLRN2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CLRN2: view

Variants for CLRN2 Gene

Sequence variations from dbSNP and Humsavar for CLRN2 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs10020740 -- 17,514,065(+) TTTCA(C/T)TGTGG upstream-variant-2KB
rs10020773 -- 17,525,059(+) AGGTG(A/C)ATAGC intron-variant
rs10026004 -- 17,513,701(+) GCACT(A/G)ACATC upstream-variant-2KB
rs10031707 -- 17,515,187(+) GAGCA(A/G)AGCAT utr-variant-5-prime
rs10527873 -- 17,524,236(+) GTGTG(-/TGGGTGTGTG/TGTG/TGTGAGTG)CGCGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLRN2 Gene

Variant ID Type Subtype PubMed ID
nsv1003127 CNV gain 25217958
nsv593781 CNV gain 21841781

Variation tolerance for CLRN2 Gene

Residual Variation Intolerance Score: 71.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.00; 74.89% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLRN2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLRN2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLRN2 Gene

Disorders for CLRN2 Gene

Relevant External Links for CLRN2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLRN2

No disorders were found for CLRN2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLRN2 Gene

Publications for CLRN2 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  2. USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. (PMID: 12080385) Adato A. … Lancet D. (Eur. J. Hum. Genet. 2002) 2 3 64
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 64

Products for CLRN2 Gene

Sources for CLRN2 Gene

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