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

Gene ID: 12725, updated on 18-Apr-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, Apr 2022]
Expression
Ubiquitous expression in cerebellum adult (RPKM 11.4), frontal lobe adult (RPKM 10.6) and 28 other tissues See more
Orthologs
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Genomic context

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 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 nucleotide binding IEA
Inferred from Electronic Annotation
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 monoatomic ion channel activity ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
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
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 apical plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in axon terminus IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasmic vesicle ISO
Inferred from Sequence Orthology
more info
 
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 membrane IDA
Inferred from Direct Assay
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
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 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 lysosome IEA
Inferred from Electronic Annotation
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in phagocytic vesicle ISO
Inferred from Sequence Orthology
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 secretory granule ISO
Inferred from Sequence Orthology
more info
 
located_in specific granule ISO
Inferred from Sequence Orthology
more info
 
located_in synapse ISO
Inferred from Sequence Orthology
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 
is_active_in synaptic vesicle membrane ISO
Inferred from Sequence Orthology
more info
 
located_in vesicle membrane ISO
Inferred from Sequence Orthology
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
    Related
    ENSMUSP00000105931.2, ENSMUST00000110302.8
  2. NM_001416733.1NP_001403662.1  H(+)/Cl(-) exchange transporter 3 isoform h

    Status: VALIDATED

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

    Status: VALIDATED

    Source sequence(s)
    AC114920
    UniProtKB/TrEMBL
    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