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

Gene ID: 84360, updated on 22-Aug-2021

Summary

Official Symbol
Clcn3provided by RGD
Official Full Name
chloride voltage-gated channel 3provided by RGD
Primary source
RGD:621219
See related
Ensembl:ENSRNOG00000010682
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
mediates transepithelial chloride transport [RGD, Feb 2006]
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:
19
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (29127419..29200133)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (32448821..32520649)

Chromosome 16 - NC_051351.1Genomic Context describing neighboring genes Neighboring gene SH3 domain containing ring finger 1 Neighboring gene uncharacterized LOC102547442 Neighboring gene NIMA-related kinase 1 Neighboring gene ATP synthase subunit g, mitochondrial pseudogene Neighboring gene chromobox homolog 3-like Neighboring gene histone PARylation factor 1 Neighboring gene Stam binding protein-like

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

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables PDZ domain 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 IEA
Inferred from Electronic Annotation
more info
 
enables antiporter activity ISO
Inferred from Sequence Orthology
more info
 
enables antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables chloride channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables chloride channel activity ISO
Inferred from Sequence Orthology
more info
 
enables ion channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables solute:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables voltage-gated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables voltage-gated chloride channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables voltage-gated chloride channel activity IEA
Inferred from Electronic Annotation
more info
 
enables voltage-gated ion channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables volume-sensitive chloride channel activity IEA
Inferred from Electronic Annotation
more info
 
NOT enables volume-sensitive chloride channel activity ISO
Inferred from Sequence Orthology
more info
 
enables volume-sensitive chloride channel activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within adult locomotory behavior ISO
Inferred from Sequence Orthology
more info
 
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
involved_in chloride transmembrane transport ISO
Inferred from Sequence Orthology
more info
 
involved_in chloride transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in ion transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of cell volume IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cell volume ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within neuron cellular homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in phagocytosis, engulfment IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within phagocytosis, engulfment ISO
Inferred from Sequence Orthology
more info
 
involved_in photoreceptor cell maintenance IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within photoreceptor cell maintenance ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of reactive oxygen species biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of reactive oxygen species biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in synaptic transmission, GABAergic IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within synaptic transmission, GABAergic ISO
Inferred from Sequence Orthology
more info
 
involved_in synaptic transmission, glutamatergic IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within synaptic transmission, glutamatergic ISO
Inferred from Sequence Orthology
more info
 
involved_in synaptic vesicle lumen acidification IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within synaptic vesicle lumen acidification ISO
Inferred from Sequence Orthology
more info
 
involved_in synaptic vesicle lumen acidification ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in GABA-ergic synapse ISO
Inferred from Sequence Orthology
more info
 
located_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
PubMed 
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
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 IDA
Inferred from Direct Assay
more info
PubMed 
located_in axon terminus IEA
Inferred from Electronic Annotation
more info
 
located_in axon terminus ISO
Inferred from Sequence Orthology
more info
 
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
PubMed 
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 IEA
Inferred from Electronic Annotation
more info
 
located_in early endosome membrane ISO
Inferred from Sequence Orthology
more info
 
located_in endosome ISO
Inferred from Sequence Orthology
more info
 
located_in endosome membrane ISO
Inferred from Sequence Orthology
more info
 
located_in endosome membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
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 
located_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
 
located_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
 
located_in inhibitory synapse IDA
Inferred from Direct Assay
more info
PubMed 
located_in integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in integral component of postsynaptic membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in integral component of postsynaptic membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in integral component of synaptic vesicle membrane ISO
Inferred from Sequence Orthology
more info
 
located_in integral component of synaptic vesicle membrane ISO
Inferred from Sequence Orthology
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
located_in late endosome membrane ISO
Inferred from Sequence Orthology
more info
 
located_in lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
located_in lysosomal membrane ISO
Inferred from Sequence Orthology
more info
 
located_in lysosomal membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in phagocytic vesicle IEA
Inferred from Electronic Annotation
more info
 
located_in phagocytic vesicle ISO
Inferred from Sequence Orthology
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
 
located_in recycling endosome IEA
Inferred from Electronic Annotation
more info
 
located_in recycling endosome ISO
Inferred from Sequence Orthology
more info
 
located_in recycling endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in recycling endosome membrane ISO
Inferred from Sequence Orthology
more info
 
located_in secretory granule ISO
Inferred from Sequence Orthology
more info
 
located_in specific granule IEA
Inferred from Electronic Annotation
more info
 
located_in specific granule ISO
Inferred from Sequence Orthology
more info
 
located_in synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in synaptic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in synaptic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
located_in synaptic vesicle IEA
Inferred from Electronic Annotation
more info
 
located_in synaptic vesicle 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 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_053363.3NP_445815.2  H(+)/Cl(-) exchange transporter 3

    See identical proteins and their annotated locations for NP_445815.2

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000279
    UniProtKB/Swiss-Prot
    P51792
    Related
    ENSRNOP00000045523.4, ENSRNOT00000050549.5
    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: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051351.1 Reference mRatBN7.2 Primary Assembly

    Range
    29127419..29200133
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039094868.1XP_038950796.1  H(+)/Cl(-) exchange transporter 3 isoform X1

    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
  2. XM_039094870.1XP_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
  3. XM_039094875.1XP_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_039094869.1XP_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
  5. XM_039094876.1XP_038950804.1  H(+)/Cl(-) exchange transporter 3 isoform X4

    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_039094873.1XP_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
  7. XM_039094872.1XP_038950800.1  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
  8. XM_039094871.1XP_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
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