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

    Gene ID: 60586, updated on 11-Apr-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
    Ensembl: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
    • 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
      ENSRNOP00000080147.1, ENSRNOT00000100086.1
      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
      Related
      ENSRNOP00000056037.3
      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

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