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    Clcn3 chloride channel, voltage-sensitive 3 [ Mus musculus (house mouse) ]

    Gene ID: 12725, updated on 6-Feb-2017
    Official Symbol
    Clcn3provided by MGI
    Official Full Name
    chloride channel, voltage-sensitive 3provided by MGI
    Primary source
    MGI:MGI:103555
    See related
    Ensembl:ENSMUSG00000004319 Vega:OTTMUSG00000022342
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Clc3
    Orthologs
    Location:
    8 B3.1; 8 30.9 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 8 NC_000074.6 (60910389..60983311, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (63389186..63462108, complement)

    Chromosome 8 - NC_000074.6Genomic Context describing neighboring genes Neighboring gene STAM binding protein, pseudogene 1 Neighboring gene histone PARylation factor 1 Neighboring gene RIKEN cDNA B230317F23 gene Neighboring gene predicted gene, 18394 Neighboring gene NIMA (never in mitosis gene a)-related expressed kinase 1 Neighboring gene RIKEN cDNA 1700001D01 gene Neighboring gene SH3 domain containing ring finger 1

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    antiporter activity IEA
    Inferred from Electronic Annotation
    more info
     
    chloride channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    ion channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    voltage-gated chloride channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    voltage-gated chloride channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    voltage-gated ion channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    NOT volume-sensitive chloride channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    adult locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    chloride transmembrane transport ISO
    Inferred from Sequence Orthology
    more info
     
    chloride transport ISO
    Inferred from Sequence Orthology
    more info
     
    ion transport ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of cell volume ISO
    Inferred from Sequence Orthology
    more info
     
    neuron cellular homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    phagocytosis, engulfment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of reactive oxygen species biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    synaptic transmission, GABAergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    synaptic transmission, glutamatergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    synaptic vesicle lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    apical plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    axon terminus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic vesicle ISO
    Inferred from Sequence Orthology
    more info
     
    early endosome ISO
    Inferred from Sequence Orthology
    more info
     
    endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    external side of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    inhibitory synapse ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    integral component of membrane ISO
    Inferred from Sequence Orthology
    more info
     
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    intracellular ISO
    Inferred from Sequence Orthology
    more info
     
    late endosome ISO
    Inferred from Sequence Orthology
    more info
     
    membrane ISO
    Inferred from Sequence Orthology
    more info
     
    phagocytic vesicle ISO
    Inferred from Sequence Orthology
    more info
     
    plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    secretory granule ISO
    Inferred from Sequence Orthology
    more info
     
    specific granule ISO
    Inferred from Sequence Orthology
    more info
     
    synapse ISO
    Inferred from Sequence Orthology
    more info
     
    synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    synaptic vesicle ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
     
    Preferred Names
    H(+)/Cl(-) exchange transporter 3
    Names
    chloride channel 3
    chloride channel protein 3
    chloride transporter ClC-3
    clC-3

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_007711.3NP_031737.1  H(+)/Cl(-) exchange transporter 3 isoform a

      See identical proteins and their annotated locations for NP_031737.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (a) has multiple differences in the coding region and uses a downstream start codon, compared to variant b. It encodes isoform a, which is shorter than isoform b.
      Source sequence(s)
      AC114920
      Consensus CDS
      CCDS22323.1
      UniProtKB/Swiss-Prot
      P51791
      UniProtKB/TrEMBL
      Q790S0
      Related
      ENSMUSP00000091202, OTTMUSP00000025333, ENSMUST00000093490, OTTMUST00000053282
      Conserved Domains (4) summary
      COG0517
      Location:598743
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:78584
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:607745
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:163564
      Voltage_CLC; Voltage gated chloride channel
    2. NM_173873.1NP_776298.1  H(+)/Cl(-) exchange transporter 3 isoform b

      See identical proteins and their annotated locations for NP_776298.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (b) represents the predominant transcript and encodes isoform b.
      Source sequence(s)
      AC114920
      Consensus CDS
      CCDS52554.1
      UniProtKB/Swiss-Prot
      P51791
      Related
      ENSMUSP00000105930, OTTMUSP00000025336, ENSMUST00000110301, OTTMUST00000053285
      Conserved Domains (4) summary
      COG0517
      Location:656801
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:136642
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:665803
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:221622
      Voltage_CLC; Voltage gated chloride channel
    3. NM_173874.1NP_776299.1  H(+)/Cl(-) exchange transporter 3 isoform e

      See identical proteins and their annotated locations for NP_776299.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (e) includes an alternate exon in the 3' coding region that causes a frameshift, compared to variant b. It encodes isoform e which is longer and has a distinct C-terminus, compared to isoform b.
      Source sequence(s)
      AC114920
      Consensus CDS
      CCDS52555.1
      UniProtKB/TrEMBL
      Q3TF45
      Related
      ENSMUSP00000004430, OTTMUSP00000025334, ENSMUST00000004430, OTTMUST00000053283
      Conserved Domains (4) summary
      COG0517
      Location:656801
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:136642
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:665803
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:221622
      Voltage_CLC; Voltage gated chloride channel
    4. NM_173876.3NP_776301.1  H(+)/Cl(-) exchange transporter 3 isoform c

      See identical proteins and their annotated locations for NP_776301.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (c) uses an alternate in-frame exon in the 5' coding region, compared to variant b. It encodes isoform c, which is shorter and has a distinct N-terminus compared to isoform b.
      Source sequence(s)
      AC114920
      Consensus CDS
      CCDS22322.1
      UniProtKB/TrEMBL
      Q8K4W8
      Related
      ENSMUSP00000058648, OTTMUSP00000025335, ENSMUST00000056508, OTTMUST00000053284
      Conserved Domains (4) summary
      COG0517
      Location:629774
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:109615
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:638776
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:194595
      Voltage_CLC; Voltage gated chloride channel

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000074.6 Reference GRCm38.p4 C57BL/6J

      Range
      60910389..60983311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006509260.2XP_006509323.1  H(+)/Cl(-) exchange transporter 3 isoform X2

      Conserved Domains (4) summary
      COG0517
      Location:598743
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:78584
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:607745
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:163564
      Voltage_CLC; Voltage gated chloride channel
    2. XM_006509259.2XP_006509322.1  H(+)/Cl(-) exchange transporter 3 isoform X1

      UniProtKB/TrEMBL
      E9Q2I1
      Related
      ENSMUSP00000105931, OTTMUSP00000025337, ENSMUST00000110302, OTTMUST00000053287
      Conserved Domains (4) summary
      COG0517
      Location:629774
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:109615
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:638776
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:194595
      Voltage_CLC; Voltage gated chloride channel
    3. XM_017312552.1XP_017168041.1  H(+)/Cl(-) exchange transporter 3 isoform X2

      Conserved Domains (4) summary
      COG0517
      Location:598743
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:78584
      ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
      cd04591
      Location:607745
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:163564
      Voltage_CLC; Voltage gated chloride channel
    4. XM_017312553.1XP_017168042.1  H(+)/Cl(-) exchange transporter 3 isoform X3

    RNA

    1. XR_001778397.1 RNA Sequence

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