Clcn6 chloride voltage-gated channel 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clcn6provided by RGD
Official Full Name: chloride voltage-gated channel 6provided by RGD
Primary source: RGD:1305379
See related: EnsemblRapid:ENSRNOG00000008345 AllianceGenome:RGD:1305379
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
Summary: Predicted to enable voltage-gated chloride channel activity. Involved in response to mechanical stimulus. Predicted to be located in membrane. Predicted to be active in intracellular membrane-bounded organelle. Human ortholog(s) of this gene implicated in coronary artery disease. Orthologous to human CLCN6 (chloride voltage-gated channel 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 103.6), Brain (RPKM 59.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (163715593..163748301, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (158434299..158465174, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (164811815..164844554, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Modulation of blood pressure regulatory genes in the Agtrap-Plod1 locus associated with a deletion in Clcn6.
Title: Modulation of blood pressure regulatory genes in the Agtrap-Plod1 locus associated with a deletion in Clcn6.
Loss of Chloride Channel 6 (CLC-6) Affects Vascular Smooth Muscle Contractility and Arterial Stiffness via Alterations to Golgi Calcium Stores.
Title: Loss of Chloride Channel 6 (CLC-6) Affects Vascular Smooth Muscle Contractility and Arterial Stiffness via Alterations to Golgi Calcium Stores.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables antiporter activity	IEA Inferred from Electronic Annotation more info
enables chloride transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor 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	ISO Inferred from Sequence Orthology more info
involved_in response to mechanical stimulus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: H(+)/Cl(-) exchange transporter 6

Names: chloride channel 6; chloride channel, voltage-sensitive 6; chloride transport protein 6

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_001106479.1 → NP_001099949.1 H(+)/Cl(-) exchange transporter 6

See identical proteins and their annotated locations for NP_001099949.1

Status: PROVISIONAL

Source sequence(s)

CH473968

UniProtKB/TrEMBL

A6IU39, D4A3H5

Related

ENSRNOP00000011287.6, ENSRNOT00000011287.8

Conserved Domains (5) summary

smart00116
Location:609 → 656

CBS; Domain in cystathionine beta-synthase and other proteins

COG0517
Location:804 → 854

CBS; CBS domain [Signal transduction mechanisms]

cd03685
Location:49 → 589

ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...

cd04591
Location:801 → 854

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:140 → 571

Voltage_CLC; Voltage gated chloride channel

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

163715593..163748301 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006239378.5 → XP_006239440.1 H(+)/Cl(-) exchange transporter 6 isoform X1

See identical proteins and their annotated locations for XP_006239440.1

UniProtKB/TrEMBL

D4A3H5

Conserved Domains (2) summary

cd03685
Location:1 → 522

ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...

cd04591
Location:534 → 787

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
XM_039109377.2 → XP_038965305.1 H(+)/Cl(-) exchange transporter 6 isoform X3

Conserved Domains (2) summary

cl02915
Location:70 → 196

Voltage_gated_ClC; CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This ...

cd04591
Location:208 → 461

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
XM_039109375.2 → XP_038965303.1 H(+)/Cl(-) exchange transporter 6 isoform X2

Conserved Domains (3) summary

cd03685
Location:49 → 589

ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...

cd02205
Location:607 → 655

CBS_pair_SF; CBS repeat [structural motif]

cl15354
Location:601 → 655

CBS_pair_SF; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily