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CLCNKA chloride voltage-gated channel Ka [ Homo sapiens (human) ]

Gene ID: 1187, updated on 29-Mar-2020

Summary

Official Symbol
CLCNKAprovided by HGNC
Official Full Name
chloride voltage-gated channel Kaprovided by HGNC
Primary source
HGNC:HGNC:2026
See related
Ensembl:ENSG00000186510 MIM:602024
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLCK1; ClC-K1; hClC-Ka
Summary
This gene is a member of the CLC family of voltage-gated chloride channels. The encoded protein is predicted to have 12 transmembrane domains, and requires a beta subunit called barttin to form a functional channel. It is thought to function in salt reabsorption in the kidney and potassium recycling in the inner ear. The gene is highly similar to CLCNKB, which is located 10 kb downstream from this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in kidney (RPKM 55.9), salivary gland (RPKM 4.5) and 1 other tissue See more
Orthologs

Genomic context

See CLCNKA in Genome Data Viewer
Location:
1p36.13
Exon count:
20
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (16022036..16034050)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16348486..16360548)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene steroid receptor associated and regulated protein Neighboring gene heat shock protein family B (small) member 7 Neighboring gene CLCNKA recombination region Neighboring gene family with sequence similarity 131 member C pseudogene Neighboring gene CLCNKB recombination region Neighboring gene chloride voltage-gated channel Kb

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: SPEN

Homology

Clone Names

  • MGC61490

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
voltage-gated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
chloride transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
excretion TAS
Traceable Author Statement
more info
PubMed 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chloride channel complex IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
chloride channel protein ClC-Ka
Names
chloride channel Ka
chloride channel, kidney, A
chloride channel, voltage-sensitive Ka

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_009359.1 RefSeqGene

    Range
    5046..17060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042704.2NP_001036169.1  chloride channel protein ClC-Ka isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a protein (isoform 2) that is one amino acid shorter than isoform 1.
    Source sequence(s)
    AK225550, BC053869
    Consensus CDS
    CCDS41269.1
    UniProtKB/Swiss-Prot
    P51800
    Related
    ENSP00000364844.1, ENST00000375692.5
    Conserved Domains (3) summary
    cd03683
    Location:49534
    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:555675
    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:106513
    Voltage_CLC; Voltage gated chloride channel
  2. NM_001257139.2NP_001244068.1  chloride channel protein ClC-Ka isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein is shorter compared to isoform 1.
    Source sequence(s)
    AI821546, AK298285, AL355994
    Consensus CDS
    CCDS57973.1
    UniProtKB/Swiss-Prot
    P51800
    Related
    ENSP00000414445.2, ENST00000439316.6
    Conserved Domains (3) summary
    cd03683
    Location:49491
    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:512633
    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:59470
    Voltage_CLC; Voltage gated chloride channel
  3. NM_004070.4NP_004061.3  chloride channel protein ClC-Ka isoform 1

    See identical proteins and their annotated locations for NP_004061.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC053869, Z30643
    Consensus CDS
    CCDS167.1
    UniProtKB/Swiss-Prot
    P51800
    Related
    ENSP00000332771.4, ENST00000331433.5
    Conserved Domains (3) summary
    cd03683
    Location:49534
    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:555676
    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:106513
    Voltage_CLC; Voltage gated chloride channel

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    16022036..16034050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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