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Aliases for CLCN3 Gene

Aliases for CLCN3 Gene

  • Chloride Channel, Voltage-Sensitive 3 2 3
  • Chloride Channel Protein 3 3 4
  • Chloride Transporter ClC-3 3 4
  • Chloride Channel 3 2 3
  • ClC-3 3 4
  • H(+)/Cl(-) Exchange Transporter 3 3
  • CLC3 3

External Ids for CLCN3 Gene

Previous GeneCards Identifiers for CLCN3 Gene

  • GC04P171346
  • GC04P170970
  • GC04P171126
  • GC04P171237
  • GC04P170916
  • GC04P170778
  • GC04P170541
  • GC04P166296

Summaries for CLCN3 Gene

Entrez Gene Summary for CLCN3 Gene

  • This gene encodes a member of the voltage-gated chloride channel (ClC) family. The encoded protein is present in all cell types and localized in plasma membranes and in intracellular vesicles. It is a multi-pass membrane protein which contains a ClC domain and two additional C-terminal CBS (cystathionine beta-synthase) domains. The ClC domain catalyzes the selective flow of Cl- ions across cell membranes, and the CBS domain may have a regulatory function. This protein plays a role in both acidification and transmitter loading of GABAergic synaptic vesicles, and in smooth muscle cell activation and neointima formation. This protein is required for lysophosphatidic acid (LPA)-activated Cl- current activity and fibroblast-to-myofibroblast differentiation. The protein activity is regulated by Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) in glioma cells. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]

GeneCards Summary for CLCN3 Gene

CLCN3 (Chloride Channel, Voltage-Sensitive 3) is a Protein Coding gene. Among its related pathways are Activation of cAMP-Dependent PKA and Activation of cAMP-Dependent PKA. GO annotations related to this gene include protein homodimerization activity and PDZ domain binding. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCN3 Gene

  • Mediates the exchange of chloride ions against protons. Functions as antiporter and contributes to the acidification of the endosome and synaptic vesicle lumen, and may thereby affect vesicle trafficking and exocytosis. May play an important role in neuronal cell function through regulation of membrane excitability by protein kinase C. It could help neuronal cells to establish short-term memory.

Gene Wiki entry for CLCN3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN3 Gene

Genomics for CLCN3 Gene

Regulatory Elements for CLCN3 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CLCN3 Gene

Start:
169,612,633 bp from pter
End:
169,723,673 bp from pter
Size:
111,041 bases
Orientation:
Plus strand

Genomic View for CLCN3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCN3 Gene

Proteins for CLCN3 Gene

  • Protein details for CLCN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51790-CLCN3_HUMAN
    Recommended name:
    H(+)/Cl(-) exchange transporter 3
    Protein Accession:
    P51790
    Secondary Accessions:
    • B7Z932
    • B9EGJ9
    • D3DP34
    • E9PB97
    • O14918
    • Q86Z21

    Protein attributes for CLCN3 Gene

    Size:
    818 amino acids
    Molecular mass:
    90966 Da
    Quaternary structure:
    • Homo- or heterodimer. Isoform 2 interacts with GOPC, PDZK1 and SLC9A3R1/EBP50.
    Miscellaneous:
    • The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The presence of conserved gating glutamate residues is typical for family members that function as antiporters (By similarity).
    SequenceCaution:
    • Sequence=BAC54560.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAA55281.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for CLCN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLCN3 Gene

Proteomics data for CLCN3 Gene at MOPED

Post-translational modifications for CLCN3 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for CLCN3 (CLCN3)

No data available for DME Specific Peptides for CLCN3 Gene

Domains for CLCN3 Gene

Gene Families for CLCN3 Gene

HGNC:
  • CLCN :Ion channels / Chloride channels : Voltage-sensitive
IUPHAR :

Suggested Antigen Peptide Sequences for CLCN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P51790

UniProtKB/Swiss-Prot:

CLCN3_HUMAN :
  • P51790
Domain:
  • Isoform 2 contains a C-terminal PDZ-binding motif mediating the interaction with GOPC.
  • Contains 2 CBS domains.
Family:
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-3/CLCN3 subfamily.
genes like me logo Genes that share domains with CLCN3: view

Function for CLCN3 Gene

Molecular function for CLCN3 Gene

GENATLAS Biochemistry: chloride voltage-gated channel 3,expressed in tissues derived from neuroectoderm
UniProtKB/Swiss-Prot Function: Mediates the exchange of chloride ions against protons. Functions as antiporter and contributes to the acidification of the endosome and synaptic vesicle lumen, and may thereby affect vesicle trafficking and exocytosis. May play an important role in neuronal cell function through regulation of membrane excitability by protein kinase C. It could help neuronal cells to establish short-term memory.

Gene Ontology (GO) - Molecular Function for CLCN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005244 voltage-gated ion channel activity --
GO:0005247 voltage-gated chloride channel activity IEA --
GO:0005254 chloride channel activity TAS 12471024
GO:0005515 protein binding IPI 12471024
genes like me logo Genes that share ontologies with CLCN3: view
genes like me logo Genes that share phenotypes with CLCN3: view

Animal Models for CLCN3 Gene

MGI Knock Outs for CLCN3:

Animal Model Products

CRISPR Products

miRNA for CLCN3 Gene

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CLCN3 Gene

Localization for CLCN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN3 Gene

Isoform 1: Membrane; Multi-pass membrane protein. Early endosome membrane; Multi-pass membrane protein. Late endosome membrane; Multi-pass membrane protein. Cytoplasmic vesicle, secretory vesicle membrane; Multi-pass membrane protein. Note=Isoform 1 is localized mainly in early and late endosomes.
Isoform 2: Membrane; Multi-pass membrane protein. Early endosome membrane; Multi-pass membrane protein. Late endosome membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein. Note=Isoform 2 partially colocalized with isoform 1 but is mainly enriched in the Golgi.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLCN3 Gene COMPARTMENTS Subcellular localization image for CLCN3 gene
Compartment Confidence
endosome 5
golgi apparatus 5
plasma membrane 3
cytosol 1
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLCN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005622 intracellular --
GO:0005769 early endosome IDA 12471024
GO:0005770 late endosome IDA 12471024
GO:0005794 Golgi apparatus IDA 12471024
genes like me logo Genes that share ontologies with CLCN3: view

Pathways for CLCN3 Gene

genes like me logo Genes that share pathways with CLCN3: view

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for CLCN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS 7665160
GO:0006811 ion transport --
GO:0006821 chloride transport --
GO:0006885 regulation of pH TAS 12471024
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCN3: view

Compounds for CLCN3 Gene

(1) HMDB Compounds for CLCN3 Gene

Compound Synonyms Cas Number PubMed IDs
Chlorine
  • Cl2
16887-00-6

(1) IUPHAR Ligand for CLCN3 Gene

Ligand Type Action Affinity Pubmed IDs
phloretin Inhibitor Inhibition

(6) Novoseek inferred chemical compound relationships for CLCN3 Gene

Compound -log(P) Hits PubMed IDs
chloride 78.3 31
dids 68 1
thapsigargin 41.1 2
nadph 33.8 1
calcium 0 2
genes like me logo Genes that share compounds with CLCN3: view

Transcripts for CLCN3 Gene

Unigene Clusters for CLCN3 Gene

Chloride channel, voltage-sensitive 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN3

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for CLCN3

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLCN3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b
SP1: - - - -
SP2: - - - - -
SP3: -
SP4:
SP5:
SP6:
SP7:

Relevant External Links for CLCN3 Gene

GeneLoc Exon Structure for
CLCN3
ECgene alternative splicing isoforms for
CLCN3

Expression for CLCN3 Gene

mRNA expression in normal human tissues for CLCN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLCN3 Gene

SOURCE GeneReport for Unigene cluster for CLCN3 Gene Hs.481186

mRNA Expression by UniProt/SwissProt for CLCN3 Gene

P51790-CLCN3_HUMAN
Tissue specificity: Expressed primarily in tissues derived from neuroectoderm. Within the brain, its expression is particularly evident in the hippocampus, olfactory cortex, and olfactory bulb. Highly expressed in aortic and coronary vascular smooth muscle cells, and aortic endothelial cells. Also expressed in tracheal and alveolar epithelial cells, and intima and media of the pulmonary vessels. Expressed in bronchus and colon (at protein level).
genes like me logo Genes that share expressions with CLCN3: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for CLCN3 Gene

Orthologs for CLCN3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CLCN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLCN3 35
  • 99.85 (n)
  • 100 (a)
CLCN3 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLCN3 35
  • 83.83 (n)
  • 95.15 (a)
CLCN3 36
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLCN3 35
  • 94.07 (n)
  • 98.67 (a)
CLCN3 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clcn3 35
  • 92.3 (n)
  • 98.61 (a)
Clcn3 16
Clcn3 36
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLCN3 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLCN3 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clcn3 35
  • 91.56 (n)
  • 98.64 (a)
chicken
(Gallus gallus)
Aves CLCN3 35
  • 87.3 (n)
  • 98.04 (a)
CLCN3 36
  • 98 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLCN3 36
  • 95 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Clcn3 35
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn3 35
  • 79.01 (n)
  • 93.33 (a)
Str.5054 35
zebrafish
(Danio rerio)
Actinopterygii clcn3 35
  • 74.84 (n)
  • 89.34 (a)
clcn3 36
  • 87 (a)
OneToOne
Dr.10303 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005777 35
  • 59.81 (n)
  • 66.12 (a)
fruit fly
(Drosophila melanogaster)
Insecta ClC-c 35
  • 60.65 (n)
  • 63.47 (a)
ClC-c 36
  • 53 (a)
OneToMany
CG5284 37
  • 59 (a)
worm
(Caenorhabditis elegans)
Secernentea clh-5 35
  • 57.24 (n)
  • 55.51 (a)
clh-5 36
  • 52 (a)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL071C 35
  • 46.27 (n)
  • 36.27 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEF1 35
  • 47.35 (n)
  • 35.51 (a)
GEF1 36
  • 31 (a)
OneToMany
GEF1 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E22507g 35
  • 47.47 (n)
  • 35.31 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06624 35
  • 50.68 (n)
  • 43.74 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC19C7.11 35
  • 47.01 (n)
  • 34.63 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 59 (a)
OneToMany
Species with no ortholog for CLCN3:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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)

Evolution for CLCN3 Gene

ENSEMBL:
Gene Tree for CLCN3 (if available)
TreeFam:
Gene Tree for CLCN3 (if available)

Paralogs for CLCN3 Gene

Paralogs for CLCN3 Gene

Selected SIMAP similar genes for CLCN3 Gene using alignment to 7 proteins:

Pseudogenes.org Pseudogenes for CLCN3 Gene

genes like me logo Genes that share paralogs with CLCN3: view

Variants for CLCN3 Gene

Sequence variations from dbSNP and Humsavar for CLCN3 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type MAF
rs7438 -- 169,721,095(+) AAGAT(A/G)TCTCA utr-variant-3-prime
rs9602 -- 169,721,268(-) TTATT(C/T)TATAA utr-variant-3-prime
rs13550 -- 169,721,630(+) GGTTA(C/T)GTCCA utr-variant-3-prime
rs1010713 -- 169,713,257(-) AGCTT(C/T)CGGAA reference, synonymous-codon
rs1014368 -- 169,722,671(-) AAATG(C/T)CAGTC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for CLCN3 Gene

Variant ID Type Subtype PubMed ID
nsv518832 CNV Loss 19592680
nsv4600 CNV Insertion 18451855

Relevant External Links for CLCN3 Gene

HapMap Linkage Disequilibrium report
CLCN3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCN3 Gene

Disorders for CLCN3 Gene

(5) Novoseek inferred disease relationships for CLCN3 Gene

Disease -log(P) Hits PubMed IDs
cystic fibrosis 42.7 2
glioma 23.6 5
carcinoma 0 1
prostate cancer 0 1
cancer 0 2

Relevant External Links for CLCN3

Genetic Association Database (GAD)
CLCN3
genes like me logo Genes that share disorders with CLCN3: view

No data available for UniProtKB/Swiss-Prot for CLCN3 Gene

Publications for CLCN3 Gene

  1. The PDZ-binding chloride channel ClC-3B localizes to the Golgi and associates with cystic fibrosis transmembrane conductance regulator- interacting PDZ proteins. (PMID: 12471024) Gentzsch M. … Riordan J.R. (J. Biol. Chem. 2003) 3 4 23
  2. Molecular interaction and functional regulation of ClC-3 by Ca2+/calmodulin-dependent protein kinase II (CaMKII) in human malignant glioma. (PMID: 20139089) Cuddapah V.A. … Sontheimer H. (J. Biol. Chem. 2010) 3 23
  3. Characterization of a human and murine gene (CLCN3) sharing similarities to voltage-gated chloride channels and to a yeast integral membrane protein. (PMID: 7665160) Borsani G. … Ballabio A. (Genomics 1995) 3 4
  4. Cardiac-specific overexpression of the human short CLC-3 chloride channel isoform in mice. (PMID: 18986326) Xiong D. … Hume J.R. (Clin. Exp. Pharmacol. Physiol. 2009) 3 23
  5. Anion channels, including ClC-3, are required for normal neutrophil oxidative function, phagocytosis, and transendothelial migration. (PMID: 16522634) Moreland J.G. … Lamb F.S. (J. Biol. Chem. 2006) 3 23

Products for CLCN3 Gene

Sources for CLCN3 Gene

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