Clcnka chloride voltage-gated channel Ka [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clcnkaprovided by RGD
Official Full Name: chloride voltage-gated channel Kaprovided by RGD
Primary source: RGD:68435
See related: Ensembl:ENSRNOG00000052368 AllianceGenome:RGD:68435
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: Clcnk1
Summary: This gene is a member of the CLC family of voltage-gated chloride channels. The gene is located adjacent to a highly similar chloride channel gene on chromosome 5. This gene is syntenic with human CLCNKB (geneID:1188).[provided by RefSeq, Sep 2009]
Expression: Restricted expression toward (RPKM 136.4) See more
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Genomic context

Location:: 5q36

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (158974190..158989275, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (153691208..153706295, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (159931497..159946483, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Changes in CLC-K1, UT-A1, UT-A3, and TonEBP play important roles in the renal response to osmotic diuresis in an attempt to minimize changes in plasma osmolality and maintain water homeostasis.
Title: Urea and NaCl regulate UT-A1 urea transporter in opposing directions via TonEBP pathway during osmotic diuresis.

Submit: New GeneRIF Correction

General gene information

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Markers

C75963 (e-PCR)
- UniSTS:159322

BE115105 (e-PCR)
- UniSTS:261368

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chloride channel activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation 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
enables voltage-gated chloride channel activity	TAS Traceable Author Statement more info	PubMed
enables voltage-gated monoatomic ion channel activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in body fluid secretion	IEP Inferred from Expression Pattern more info	PubMed
involved_in chloride transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in chloride transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney development	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of body fluid levels	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of body fluid levels	ISO Inferred from Sequence Orthology more info
involved_in renal absorption	TAS Traceable Author Statement more info	PubMed
involved_in renal inner medulla development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within renal inner medulla development	ISO Inferred from Sequence Orthology more info
involved_in response to calcium ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to pH	IEP Inferred from Expression Pattern more info	PubMed
involved_in transepithelial chloride transport	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
part_of chloride channel complex	IEA Inferred from Electronic Annotation more info
part_of monoatomic ion channel complex	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: chloride channel protein ClC-Ka

Names: chloride channel K1; chloride channel Ka; chloride channel, voltage-sensitive Ka; clC-K1

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)

NM_053327.2 → NP_445779.2 chloride channel protein ClC-Ka

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

P97709, Q06393

UniProtKB/TrEMBL

Q66HN9

Related

ENSRNOP00000097659.1, ENSRNOT00000108320.1

Conserved Domains (2) summary

cd03683
Location:49 → 533

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:546 → 676

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

NC_086023.1 Reference GRCr8

Range

158974190..158989275 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063288464.1 → XP_063144534.1 chloride channel protein ClC-Ka isoform X1

UniProtKB/TrEMBL

Q66HN9
XM_008764292.4 → XP_008762514.1 chloride channel protein ClC-Ka isoform X1

See identical proteins and their annotated locations for XP_008762514.1

UniProtKB/Swiss-Prot

P97709, Q06393

UniProtKB/TrEMBL

Q66HN9

Related

ENSRNOP00000072591.1

Conserved Domains (2) summary

cd03683
Location:49 → 533

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:546 → 676

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