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

    Gene ID: 12725, updated on 3-Dec-2024

    Summary

    Official Symbol
    Clcn3provided by MGI
    Official Full Name
    chloride channel, voltage-sensitive 3provided by MGI
    Primary source
    MGI:MGI:103555
    See related
    Ensembl:ENSMUSG00000004319 AllianceGenome:MGI:103555
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Clc3
    Summary
    Enables antiporter activity. Involved in synaptic vesicle lumen acidification. Acts upstream of or within several processes, including chemical synaptic transmission; photoreceptor cell maintenance; and positive regulation of reactive oxygen species biosynthetic process. Located in several cellular components, including endosome membrane; lysosomal membrane; and synaptic vesicle. Is active in glutamatergic synapse. Is expressed in several structures, including central nervous system; dorsal root ganglion; early conceptus; genitourinary system; and heart. Used to study neuronal ceroid lipofuscinosis 3. Orthologous to human CLCN3 (chloride voltage-gated channel 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in cerebellum adult (RPKM 11.4), frontal lobe adult (RPKM 10.6) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Clcn3 in Genome Data Viewer
    Location:
    8 B3.1; 8 30.9 cM
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (61363423..61436351, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (60910389..60983317, complement)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_21566 Neighboring gene STARR-seq mESC enhancer starr_21571 Neighboring gene predicted gene, 23329 Neighboring gene STARR-seq mESC enhancer starr_21573 Neighboring gene STARR-positive B cell enhancer mm9_chr8:63369016-63369317 Neighboring gene histone PARylation factor 1 Neighboring gene STARR-seq mESC enhancer starr_21578 Neighboring gene predicted gene, 18394 Neighboring gene STARR-positive B cell enhancer ABC_E10500 Neighboring gene STARR-positive B cell enhancer ABC_E6639 Neighboring gene STARR-positive B cell enhancer ABC_E11383 Neighboring gene NIMA (never in mitosis gene a)-related expressed kinase 1 Neighboring gene STARR-seq mESC enhancer starr_21581 Neighboring gene RIKEN cDNA 1700001D01 gene Neighboring gene SH3 domain containing ring finger 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 
    • Targeted (9)  1 citation

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables PDZ domain binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables antiporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables antiporter activity TAS
    Traceable Author Statement
    more info
     
    enables chloride channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables monoatomic ion channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables voltage-gated chloride channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables voltage-gated chloride channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables voltage-gated chloride channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables voltage-gated monoatomic ion channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables volume-sensitive chloride channel activity IEA
    Inferred from Electronic Annotation
    more info
     
    NOT enables volume-sensitive chloride channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chloride transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in monoatomic ion transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell volume IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within neuron cellular homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within phagocytosis, engulfment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of reactive oxygen species biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within synaptic transmission, GABAergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within synaptic transmission, glutamatergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic vesicle lumen acidification IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within synaptic vesicle lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic vesicle lumen acidification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in GABA-ergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in apical plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in axon terminus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in early endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in inhibitory synapse ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in phagocytic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in postsynaptic membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in specific granule IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in synaptic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic vesicle ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in synaptic vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    H(+)/Cl(-) exchange transporter 3
    Names
    chloride channel 3
    chloride channel protein 3
    chloride transporter ClC-3
    clC-3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001416732.1NP_001403661.1  H(+)/Cl(-) exchange transporter 3 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC114920
      UniProtKB/TrEMBL
      E9Q2I1, Q8K4W9
      Related
      ENSMUSP00000105931.2, ENSMUST00000110302.8
    2. NM_001416733.1NP_001403662.1  H(+)/Cl(-) exchange transporter 3 isoform h

      Status: VALIDATED

      Source sequence(s)
      AC114920
      UniProtKB/TrEMBL
      Q8K4W7
    3. NM_001416734.1NP_001403663.1  H(+)/Cl(-) exchange transporter 3 isoform i

      Status: VALIDATED

      Source sequence(s)
      AC114920
      UniProtKB/TrEMBL
      Q6PGA5, Q790S0
    4. NM_007711.4NP_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/TrEMBL
      Q6PGA5, Q790S0
      Related
      ENSMUSP00000091202.3, ENSMUST00000093490.9
      Conserved Domains (2) summary
      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:595745
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    5. NM_173873.2NP_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, Q3TF45, Q8K4X0, Q8K4X1
      UniProtKB/TrEMBL
      A0A6Q6Q7B9
      Related
      ENSMUSP00000105930.2, ENSMUST00000110301.2
      Conserved Domains (2) summary
      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:653803
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    6. NM_173874.2NP_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
      Q3TTK0
      Related
      ENSMUSP00000004430.8, ENSMUST00000004430.14
      Conserved Domains (2) summary
      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:653803
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    7. NM_173876.4NP_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
      Q6PGA5, Q8K4W8
      Related
      ENSMUSP00000058648.6, ENSMUST00000056508.12
      Conserved Domains (2) summary
      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:626776
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria

    RNA

    1. NR_184390.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC114920

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000074.7 Reference GRCm39 C57BL/6J

      Range
      61363423..61436351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036153740.1XP_036009633.1  H(+)/Cl(-) exchange transporter 3 isoform X2

      UniProtKB/TrEMBL
      Q8K4W7
      Conserved Domains (2) summary
      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:595745
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    2. XM_017312552.3XP_017168041.1  H(+)/Cl(-) exchange transporter 3 isoform X2

      UniProtKB/TrEMBL
      Q8K4W7
      Conserved Domains (2) summary
      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:595745
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    3. XM_017312553.2XP_017168042.1  H(+)/Cl(-) exchange transporter 3 isoform X4

      UniProtKB/TrEMBL
      Q3UEX5
      Conserved Domains (1) summary
      cd03684
      Location:136588
      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 ...

    RNA

    1. XR_001778397.2 RNA Sequence