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    Clcn1 chloride voltage-gated channel 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25688, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Clcn1provided by RGD
    Official Full Name
    chloride voltage-gated channel 1provided by RGD
    Primary source
    RGD:2360
    See related
    EnsemblRapid:ENSRNOG00000016917 AllianceGenome:RGD:2360
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    SMCC
    Summary
    Enables voltage-gated chloride channel activity. Involved in chloride transport. Predicted to be located in sarcolemma. Predicted to be part of chloride channel complex. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in Becker disease; Thomsen disease; and myotonia congenita. Orthologous to human CLCN1 (chloride voltage-gated channel 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 334.9), Heart (RPKM 18.3) and 1 other tissue See more
    Orthologs
    human mouse all
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    Genomic context

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    See Clcn1 in Genome Data Viewer
    Location:
    4q24
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (72138739..72168113)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (71171949..71201483)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (71674218..71704318)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 139 Neighboring gene small nucleolar RNA SNORD88 Neighboring gene caspase 2 Neighboring gene family with sequence similarity 131, member B Neighboring gene uncharacterized LOC120102260 Neighboring gene zyxin Neighboring gene Eph receptor A1

    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. Regulation of ClC-1 and KATP channels in action potential-firing fast-twitch muscle fibers. Pedersen TH, et al. J Gen Physiol, 2009 Oct. PMID 19786584, Free PMC Article
    2. Expression of novel isoforms of the CIC-1 chloride channel in astrocytic glial cells in vitro. Zhang XD, et al. Glia, 2004 Jul. PMID 15139012
    3. Impaired surface membrane insertion of homo- and heterodimeric human muscle chloride channels carrying amino-terminal myotonia-causing mutations. Ronstedt K, et al. Sci Rep, 2015 Oct 27. PMID 26502825, Free PMC Article
    4. Clinical, Molecular, and Functional Characterization of CLCN1 Mutations in Three Families with Recessive Myotonia Congenita. Portaro S, et al. Neuromolecular Med, 2015 Sep. PMID 26007199, Free PMC Article
    5. Myotonia congenita: novel mutations in CLCN1 gene and functional characterizations in Italian patients. Ulzi G, et al. J Neurol Sci, 2012 Jul 15. PMID 22521272

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Regulation of ClC-1 in action potential-firing fast-twitch muscle fibers
      Title: Regulation of ClC-1 and KATP channels in action potential-firing fast-twitch muscle fibers.
    2. Statins and fenofibrate affect skeletal muscle chloride conductance in rats by differently impairing ClC-1 channel regulation and expression.
      Title: Statins and fenofibrate affect skeletal muscle chloride conductance in rats by differently impairing ClC-1 channel regulation and expression.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables voltage-gated chloride channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 chloride channel activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chloride transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within chloride transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in muscle contraction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in muscle contraction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in muscle contraction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuronal action potential propagation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within neuronal action potential propagation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in T-tubule IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of chloride channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in sarcolemma IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sarcolemma ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    chloride channel protein 1
    Names
    chloride channel 1, skeletal muscle
    chloride channel protein, skeletal muscle
    chloride channel, voltage-sensitive 1
    clC-1

    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_013147.1 → NP_037279.1  chloride channel protein 1

      See identical proteins and their annotated locations for NP_037279.1

      Status: PROVISIONAL

      Source sequence(s)
      X62894
      UniProtKB/Swiss-Prot
      P35524
      UniProtKB/TrEMBL
      F1LPY4
      Related
      ENSRNOP00000043372.3, ENSRNOT00000051265.5
      Conserved Domains (3) summary
      cd03683
      Location:117 → 592
      ClC_1_like; ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is ...
      cd02205
      Location:610 → 826
      CBS_pair_SF; CBS repeat [structural motif]
      cl15354
      Location:605 → 875
      CBS_pair_SF; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily

    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_086022.1 Reference GRCr8

      Range
      72138739..72168113
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008762873.4 → XP_008761095.1  chloride channel protein 1 isoform X2

      UniProtKB/TrEMBL
      F1LPY4
      Related
      ENSRNOP00000103689.1, ENSRNOT00000144769.1
      Conserved Domains (4) summary
      cd03683
      Location:117 → 558
      ClC_1_like; ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is ...
      cd04591
      Location:793 → 841
      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:170 → 537
      Voltage_CLC; Voltage gated chloride channel
      cl15354
      Location:576 → 631
      CBS_pair; The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called ...

    2. XM_039107135.2 → XP_038963063.1  chloride channel protein 1 isoform X1

      UniProtKB/TrEMBL
      F1LPY4
      Related
      ENSRNOP00000087495.1, ENSRNOT00000104906.2
      Conserved Domains (3) summary
      cd03683
      Location:117 → 573
      ClC_1_like; ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is ...
      cd02205
      Location:591 → 807
      CBS_pair_SF; CBS repeat [structural motif]
      cl15354
      Location:586 → 856
      CBS_pair_SF; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P35524.1 GenPept UniProtKB/Swiss-Prot:P35524

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