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Clcn4 chloride voltage-gated channel 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 60586, updated on 17-Aug-2024

Summary

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Official Symbol
Clcn4provided by RGD
Official Full Name
chloride voltage-gated channel 4provided by RGD
Primary source
RGD:708381
See related
EnsemblRapid:ENSRNOG00000003533 AllianceGenome:RGD:708381
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
Clcn4-2
Summary
Predicted to enable solute:proton antiporter activity and voltage-gated chloride channel activity. Predicted to be involved in chloride transport and non-motile cilium assembly. Predicted to be located in endoplasmic reticulum membrane; endosome; and lysosomal membrane. Predicted to be active in Golgi apparatus; ciliary base; and cytoplasmic vesicle. Predicted to be integral component of plasma membrane. Human ortholog(s) of this gene implicated in Raynaud-Claes syndrome. Orthologous to human CLCN4 (chloride voltage-gated channel 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Liver (RPKM 206.1), Brain (RPKM 175.6) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Clcn4 in Genome Data Viewer
Location:
Xq13
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (27290769..27356967)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (23729194..23795391)
106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (25016177..25082563)

Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated multipass transmembrane protein 2 Neighboring gene WWC family member 3 Neighboring gene uncharacterized LOC120099331 Neighboring gene midline 1 Neighboring gene capping actin protein of muscle Z-line subunit alpha 1, pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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Related articles in PubMed

  1. Properties of voltage-gated chloride channels of the ClC gene family. Jentsch TJ, et al. J Physiol, 1995 Jan. PMID 7730971, Free PMC Article
  2. De novo and inherited mutations in the X-linked gene CLCN4 are associated with syndromic intellectual disability and behavior and seizure disorders in males and females. Palmer EE, et al. Mol Psychiatry, 2018 Feb. PMID 27550844, Free PMC Article
  3. The human ClC-4 protein, a member of the CLC chloride channel/transporter family, is localized to the endoplasmic reticulum by its N-terminus. Okkenhaug H, et al. FASEB J, 2006 Nov. PMID 17023393
  4. Identification of an acid-activated Cl(-) channel from human skeletal muscles. Kawasaki M, et al. Am J Physiol, 1999 Nov. PMID 10564087
  5. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Hu H, et al. Mol Psychiatry, 2016 Jan. PMID 25644381, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Clone Names

  • MGC105433

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATP binding 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 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 IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within chloride transport ISO
Inferred from Sequence Orthology
more info
  
involved_in chloride transport ISO
Inferred from Sequence Orthology
more info
  
involved_in chloride transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in non-motile cilium assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in non-motile cilium assembly ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary base IEA
Inferred from Electronic Annotation
more info
  
is_active_in ciliary base 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 membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endosome membrane IEA
Inferred from Electronic Annotation
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 intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
located_in late endosome 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
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
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 IEA
Inferred from Electronic Annotation
more info
  
is_active_in synaptic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
H(+)/Cl(-) exchange transporter 4
Names
chloride channel 4
chloride channel 4-2
chloride channel protein 4
chloride channel, voltage-sensitive 4
chloride transporter ClC-4
clC-4
putative chloride channel (similar to Mm Clcn4-2)
putative chloride channel 4-2

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_022198.2 → NP_071534.2  H(+)/Cl(-) exchange transporter 4

    See identical proteins and their annotated locations for NP_071534.2

    Status: VALIDATED

    Source sequence(s)
    BC092209
    UniProtKB/Swiss-Prot
    P51794
    UniProtKB/TrEMBL
    Q56A19
    Related
    ENSRNOP00000056037.4, ENSRNOT00000059270.4
    Conserved Domains (2) summary
    cd03684
    Location:72 → 578
    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:589 → 739
    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

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_086039.1 Reference GRCr8

    Range
    27290769..27356967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006256828.5 → XP_006256890.1  H(+)/Cl(-) exchange transporter 4 isoform X1

    UniProtKB/Swiss-Prot
    P51794
    UniProtKB/TrEMBL
    F7F9W4
    Conserved Domains (4) summary
    COG0517
    Location:612 → 757
    CBS; CBS domain [Signal transduction mechanisms]
    cd03684
    Location:92 → 598
    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:621 → 759
    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:176 → 578
    Voltage_CLC; Voltage gated chloride channel
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51794.1 GenPept UniProtKB/Swiss-Prot:P51794

Gene LinkOut

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