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    Clcn5 chloride channel, voltage-sensitive 5 [ Mus musculus (house mouse) ]

    Gene ID: 12728, updated on 24-Jul-2021

    Summary

    Official Symbol
    Clcn5provided by MGI
    Official Full Name
    chloride channel, voltage-sensitive 5provided by MGI
    Primary source
    MGI:MGI:99486
    See related
    Ensembl:ENSMUSG00000004317
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Clc; ClC-; Clc5; Sfc1; ClC-5; Clc4-; Clcn4; Sfc13; Clc4-1; T25545; Clcn4-1; DXImx42; DXImx42e; 5430408K11Rik; D930009B12Rik
    Expression
    Broad expression in limb E14.5 (RPKM 8.4), placenta adult (RPKM 7.7) and 26 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Clcn5 in Genome Data Viewer
    Location:
    X A1.1; X 3.21 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) X NC_000086.8 (7020049..7185597, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (7153810..7319358, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (6735945..6765840, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene A kinase (PRKA) anchor protein 4 Neighboring gene ribosomal protein L23a pseudogene Neighboring gene predicted gene, 26401 Neighboring gene microRNA 500 Neighboring gene microRNA 501 Neighboring gene microRNA 362 Neighboring gene microRNA 188 Neighboring gene microRNA 532 Neighboring gene predicted gene 14379 Neighboring gene ubiquitin specific peptidase 27, X chromosome

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    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 chloride channel activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    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
     
    acts_upstream_of_or_within endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in apical part of cell ISO
    Inferred from Sequence Orthology
    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
    PubMed 
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
     
    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 
    located_in membrane ISO
    Inferred from Sequence Orthology
    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
    PubMed 

    General protein information

    Preferred Names
    H(+)/Cl(-) exchange transporter 5
    Names
    chloride channel 4-1
    chloride channel 5
    chloride channel protein 5
    chloride transporter ClC-5

    NCBI Reference Sequences (RefSeq)

    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_001243762.1NP_001230691.1  H(+)/Cl(-) exchange transporter 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes two alternate exons in the 5' UTR and 5' CDS, compared to variant 1. It encodes isoform 2, which is longer and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AL663104, AL808124
      Consensus CDS
      CCDS57727.1
      UniProtKB/TrEMBL
      B1ATV0
      Related
      ENSMUSP00000111412.2, ENSMUST00000115746.8
      Conserved Domains (2) summary
      cd03684
      Location:142640
      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:651801
      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. NM_016691.4NP_057900.3  H(+)/Cl(-) exchange transporter 5 isoform 1

      See identical proteins and their annotated locations for NP_057900.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AF134117, AK052990, AK145763, AL808124
      Consensus CDS
      CCDS29963.1
      UniProtKB/Swiss-Prot
      Q9WVD4
      UniProtKB/TrEMBL
      Q3UL16, Q8C6W8
      Related
      ENSMUSP00000004428.8, ENSMUST00000004428.14
      Conserved Domains (4) summary
      COG0517
      Location:583729
      CBS; CBS domain [Signal transduction mechanisms]
      cd03684
      Location:72570
      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:595731
      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:149550
      Voltage_CLC; Voltage gated chloride channel

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000086.8 Reference GRCm39 C57BL/6J

      Range
      7020049..7185597 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527562.5XP_006527625.1  H(+)/Cl(-) exchange transporter 5 isoform X3

      Conserved Domains (2) summary
      cd03684
      Location:154652
      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:663813
      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_011247445.4XP_011245747.1  H(+)/Cl(-) exchange transporter 5 isoform X2

      Conserved Domains (2) summary
      cd03684
      Location:165663
      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:674824
      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_011247442.3XP_011245744.1  H(+)/Cl(-) exchange transporter 5 isoform X1

      See identical proteins and their annotated locations for XP_011245744.1

      Conserved Domains (2) summary
      cd03684
      Location:177675
      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:686836
      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_011247443.4XP_011245745.1  H(+)/Cl(-) exchange transporter 5 isoform X1

      See identical proteins and their annotated locations for XP_011245745.1

      Conserved Domains (2) summary
      cd03684
      Location:177675
      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:686836
      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_011247444.4XP_011245746.1  H(+)/Cl(-) exchange transporter 5 isoform X1

      See identical proteins and their annotated locations for XP_011245746.1

      Conserved Domains (2) summary
      cd03684
      Location:177675
      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:686836
      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_036161803.1XP_036017696.1  H(+)/Cl(-) exchange transporter 5 isoform X4

      Conserved Domains (2) summary
      cd03684
      Location:142640
      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:651801
      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_011247446.4XP_011245748.1  H(+)/Cl(-) exchange transporter 5 isoform X5

      Conserved Domains (2) summary
      cd03684
      Location:138636
      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:647797
      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

    RNA

    1. XR_004940325.1 RNA Sequence

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