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    Clcn3 chloride voltage-gated channel 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84360, updated on 9-Dec-2024

    Summary

    Official Symbol
    Clcn3provided by RGD
    Official Full Name
    chloride voltage-gated channel 3provided by RGD
    Primary source
    RGD:621219
    See related
    EnsemblRapid:ENSRNOG00000010682 AllianceGenome:RGD:621219
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    ClC-3
    Summary
    Enables voltage-gated chloride channel activity. Involved in chloride transport. Located in apical plasma membrane; inhibitory synapse; and synaptic vesicle. Is active in glutamatergic synapse and postsynaptic membrane. Orthologous to human CLCN3 (chloride voltage-gated channel 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 191.4), Heart (RPKM 105.9) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Clcn3 in Genome Data Viewer
    Location:
    16p12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 16 NC_086034.1 (34138004..34210984)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (29127152..29200133)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (32448821..32520649)

    Chromosome 16 - NC_086034.1Genomic Context describing neighboring genes Neighboring gene SH3 domain containing ring finger 1 Neighboring gene NIMA-related kinase 1 Neighboring gene ATP synthase subunit g, mitochondrial pseudogene Neighboring gene chromobox 3 like 1 Neighboring gene histone PARylation factor 1 Neighboring gene Stam binding protein, pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding  
    enables PDZ domain binding  
    enables PDZ domain binding  
    enables PDZ domain binding  
    enables antiporter activity  
    enables antiporter activity  
    enables antiporter activity  
    enables chloride channel activity PubMed 
    enables chloride channel activity  
    enables monoatomic ion channel activity PubMed 
    enables voltage-gated chloride channel activity  
    enables voltage-gated chloride channel activity PubMed 
    enables voltage-gated chloride channel activity  
    enables voltage-gated monoatomic ion channel activity PubMed 
    enables volume-sensitive chloride channel activity  
    NOT enables volume-sensitive chloride channel activity  
    enables volume-sensitive chloride channel activity  
    Process Evidence Code Pubs
    involved_in adult locomotory behavior  
    acts_upstream_of_or_within adult locomotory behavior  
    involved_in chloride transmembrane transport  
    involved_in chloride transmembrane transport  
    involved_in chloride transport PubMed 
    involved_in monoatomic ion transport PubMed 
    involved_in negative regulation of cell volume  
    involved_in negative regulation of cell volume  
    acts_upstream_of_or_within neuron cellular homeostasis  
    involved_in phagocytosis, engulfment  
    acts_upstream_of_or_within phagocytosis, engulfment  
    involved_in photoreceptor cell maintenance  
    acts_upstream_of_or_within photoreceptor cell maintenance  
    involved_in positive regulation of reactive oxygen species biosynthetic process  
    acts_upstream_of_or_within positive regulation of reactive oxygen species biosynthetic process  
    involved_in synaptic transmission, GABAergic  
    acts_upstream_of_or_within synaptic transmission, GABAergic  
    involved_in synaptic transmission, glutamatergic  
    acts_upstream_of_or_within synaptic transmission, glutamatergic  
    involved_in synaptic vesicle lumen acidification  
    acts_upstream_of_or_within synaptic vesicle lumen acidification  
    involved_in synaptic vesicle lumen acidification  
    Items 1 - 20 of 54
    Component Evidence Code Pubs
    located_in GABA-ergic synapse  
    is_active_in GABA-ergic synapse  
    is_active_in Golgi apparatus  
    located_in Golgi apparatus  
    located_in Golgi apparatus  
    located_in Golgi apparatus  
    located_in apical plasma membrane PubMed 
    located_in axon terminus  
    located_in axon terminus  
    located_in cytoplasmic vesicle  
    is_active_in early endosome  
    located_in early endosome  
    located_in early endosome  
    located_in early endosome membrane  
    located_in early endosome membrane  
    located_in endosome  
    located_in endosome membrane  
    located_in endosome membrane  
    located_in external side of plasma membrane  
    located_in external side of plasma membrane  
    is_active_in glutamatergic synapse PubMed 
    located_in glutamatergic synapse  
    is_active_in glutamatergic synapse  
    located_in inhibitory synapse PubMed 
    located_in intracellular membrane-bounded organelle  
    located_in late endosome  
    located_in late endosome  
    located_in late endosome membrane  
    located_in late endosome membrane  
    located_in lysosomal membrane  
    located_in lysosomal membrane  
    located_in lysosomal membrane  
    located_in phagocytic vesicle  
    located_in phagocytic vesicle  
    is_active_in plasma membrane  
    located_in plasma membrane PubMed 
    located_in plasma membrane  
    located_in plasma membrane  
    is_active_in postsynaptic membrane PubMed 
    located_in recycling endosome  
    located_in recycling endosome  
    located_in recycling endosome  
    located_in recycling endosome membrane  
    located_in secretory granule  
    located_in specific granule  
    located_in specific granule  
    located_in synapse PubMed 
    is_active_in synaptic vesicle  
    located_in synaptic vesicle PubMed 
    located_in synaptic vesicle  
    located_in synaptic vesicle membrane  
    is_active_in synaptic vesicle membrane  
    located_in vesicle membrane  
    located_in vesicle membrane  
    Items 1 - 20 of 54

    General protein information

    Preferred Names
    H(+)/Cl(-) exchange transporter 3
    Names
    chloride channel 3
    chloride channel protein 3
    chloride channel, voltage-sensitive 3
    chloride transporter ClC-3
    protein kinase C-regulated chloride channel

    NCBI Reference Sequences (RefSeq)

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    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_001413712.1NP_001400641.1  H(+)/Cl(-) exchange transporter 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000016
      UniProtKB/TrEMBL
      A0A0G2K2K6
    2. NM_053363.3NP_445815.2  H(+)/Cl(-) exchange transporter 3 isoform 1

      See identical proteins and their annotated locations for NP_445815.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000016
      UniProtKB/Swiss-Prot
      P51792, Q9R287
      UniProtKB/TrEMBL
      A6KIS2
      Related
      ENSRNOP00000045523.6, ENSRNOT00000050549.7
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086034.1 Reference GRCr8

      Range
      34138004..34210984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039094870.2XP_038950798.1  H(+)/Cl(-) exchange transporter 3 isoform X3

      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_039094868.2XP_038950796.1  H(+)/Cl(-) exchange transporter 3 isoform X1

      UniProtKB/TrEMBL
      A0A8L2ULZ0
      Related
      ENSRNOP00000101815.1, ENSRNOT00000163967.1
      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
    3. XM_039094875.2XP_038950803.1  H(+)/Cl(-) exchange transporter 3 isoform X3

      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
    4. XM_063275789.1XP_063131859.1  H(+)/Cl(-) exchange transporter 3 isoform X4

      UniProtKB/TrEMBL
      A6KIS3
    5. XM_039094869.2XP_038950797.1  H(+)/Cl(-) exchange transporter 3 isoform X2

      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
    6. XM_039094871.2XP_038950799.1  H(+)/Cl(-) exchange transporter 3 isoform X3

      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
    7. XM_039094873.2XP_038950801.1  H(+)/Cl(-) exchange transporter 3 isoform X3

      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
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