U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Clcn5 chloride voltage-gated channel 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25749, updated on 13-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Clcn5provided by RGD
    Official Full Name
    chloride voltage-gated channel 5provided by RGD
    Primary source
    RGD:2362
    See related
    Ensembl:ENSRNOG00000002862 AllianceGenome:RGD:2362
    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
    CLC5
    Summary
    Enables voltage-gated chloride channel activity. Involved in chloride transport. Located in endosome and membrane. Used to study renal tubular transport disease. Human ortholog(s) of this gene implicated in Dent disease; X-linked nephrolithiasis type I; X-linked recessive hypophosphatemic rickets; and low molecular weight proteinuria with hypercalciuric nephrocalcinosis. Orthologous to human CLCN5 (chloride voltage-gated channel 5). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 249.7), Adrenal (RPKM 69.6) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    Xq12
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (17857260..18011844)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (15185380..15339977)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (16170585..16196691)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene Fus RNA binding protein like 1 Neighboring gene ubiquitin specific peptidase 27, X-linked Neighboring gene small nucleolar RNA SNORA40 Neighboring gene microRNA 532 Neighboring gene microRNA 188 Neighboring gene microRNA 3560 Neighboring gene microRNA 362 Neighboring gene microRNA 501 Neighboring gene microRNA 500 Neighboring gene U6 spliceosomal RNA Neighboring gene A-kinase anchoring protein 4

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Intrarenal and subcellular localization of rat CLC5. Luyckx VA, et al. Am J Physiol, 1998 Nov. PMID 9815133
    2. Identification of a new outwardly rectifying Cl- channel that belongs to a subfamily of the ClC Cl- channels. Sakamoto H, et al. J Biol Chem, 1996 Apr 26. PMID 8626585
    3. Chloride channel ClC-5 binds to aspartyl aminopeptidase to regulate renal albumin endocytosis. Lee A, et al. Am J Physiol Renal Physiol, 2015 Apr 1. PMID 25587118
    4. Role of CFTR and ClC-5 in modulating vacuolar H+-ATPase activity in kidney proximal tubule. Carraro-Lacroix LR, et al. Cell Physiol Biochem, 2010. PMID 21063094
    5. Nucleotide recognition by the cytoplasmic domain of the human chloride transporter ClC-5. Meyer S, et al. Nat Struct Mol Biol, 2007 Jan. PMID 17195847

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. identified another key molecular component of the albumin endocytic machinery in the renal proximal tubule and describe a new role for aspartyl aminopeptidase in stabilizing the actin cytoskeleton
      Title: Chloride channel ClC-5 binds to aspartyl aminopeptidase to regulate renal albumin endocytosis.
    2. ClC-5 chloride-proton exchangers by siRNA-mediated silencing are important modulators of H+-ATPase function in immortalized rat renal proximal tubule cells.
      Title: Role of CFTR and ClC-5 in modulating vacuolar H+-ATPase activity in kidney proximal tubule.
    3. ClC-5 is expressed exclusively in H(+)-ATPase-rich cells (narrow and clear cells). ClC-5 also partially colocalizes with the H(+)-ATPase in the subapical pole of clear cells in the epididymis.
      Title: Detection of ClC-3 and ClC-5 in epididymal epithelium: immunofluorescence and RT-PCR after LCM.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables antiporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding 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 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 transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chloride transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in renal system process 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 Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in apical part of cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in apical part of cell ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in synaptic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    H(+)/Cl(-) exchange transporter 5
    Names
    chloride channel 5
    chloride channel protein 5
    chloride channel, voltage-sensitive 5
    chloride transporter ClC-5
    clC-5

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001414393.1 → NP_001401322.1  H(+)/Cl(-) exchange transporter 5 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/Swiss-Prot
      A0A0G2K839, P51796, P70642
      Related
      ENSRNOP00000074459.1, ENSRNOT00000079054.2

    2. NM_017106.2 → NP_058802.2  H(+)/Cl(-) exchange transporter 5 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A8I5ZVV0, A6KPB2
      Related
      ENSRNOP00000003895.5, ENSRNOT00000003895.7
      Conserved Domains (2) summary
      cd03684
      Location:72 → 570
      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:581 → 731
      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
      17857260..18011844
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039099512.2 → XP_038955440.1  H(+)/Cl(-) exchange transporter 5 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZVV0
      Conserved Domains (2) summary
      cd03684
      Location:135 → 633
      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:644 → 794
      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
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51796.2 GenPept UniProtKB/Swiss-Prot:P51796

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous