Clcn1 chloride voltage-gated channel 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clcn1provided by RGD
Official Full Name: chloride voltage-gated channel 1provided by RGD
Primary source: RGD:2360
See related: EnsemblRapid:ENSRNOG00000016917 AllianceGenome:RGD:2360
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: SMCC
Summary: Enables voltage-gated chloride channel activity. Involved in chloride transport. Predicted to be located in sarcolemma. Predicted to be part of chloride channel complex. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in Becker disease; Thomsen disease; and myotonia congenita. Orthologous to human CLCN1 (chloride voltage-gated channel 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Muscle (RPKM 334.9), Heart (RPKM 18.3) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 4q24

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (72138739..72168113)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (71171949..71201483)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (71674218..71704318)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Regulation of ClC-1 in action potential-firing fast-twitch muscle fibers
Title: Regulation of ClC-1 and KATP channels in action potential-firing fast-twitch muscle fibers.
Statins and fenofibrate affect skeletal muscle chloride conductance in rats by differently impairing ClC-1 channel regulation and expression.
Title: Statins and fenofibrate affect skeletal muscle chloride conductance in rats by differently impairing ClC-1 channel regulation and expression.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity 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 transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in chloride transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in chloride transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within chloride transport	ISO Inferred from Sequence Orthology more info
involved_in muscle contraction	IEA Inferred from Electronic Annotation more info
involved_in muscle contraction	ISO Inferred from Sequence Orthology more info
involved_in muscle contraction	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuronal action potential propagation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuronal action potential propagation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in T-tubule	IEA Inferred from Electronic Annotation more info
part_of chloride channel complex	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in sarcolemma	IEA Inferred from Electronic Annotation more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: chloride channel protein 1

Names: chloride channel 1, skeletal muscle; chloride channel protein, skeletal muscle; chloride channel, voltage-sensitive 1; clC-1

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_013147.1 → NP_037279.1 chloride channel protein 1

See identical proteins and their annotated locations for NP_037279.1

Status: PROVISIONAL

Source sequence(s)

X62894

UniProtKB/Swiss-Prot

P35524

UniProtKB/TrEMBL

F1LPY4

Related

ENSRNOP00000043372.3, ENSRNOT00000051265.5

Conserved Domains (3) summary

cd03683
Location:117 → 592

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 ...

cd02205
Location:610 → 826

CBS_pair_SF; CBS repeat [structural motif]

cl15354
Location:605 → 875

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

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_086022.1 Reference GRCr8

Range

72138739..72168113

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008762873.4 → XP_008761095.1 chloride channel protein 1 isoform X2

UniProtKB/TrEMBL

F1LPY4

Related

ENSRNOP00000103689.1, ENSRNOT00000144769.1

Conserved Domains (4) summary

cd03683
Location:117 → 558

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:793 → 841

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:170 → 537

Voltage_CLC; Voltage gated chloride channel

cl15354
Location:576 → 631

CBS_pair; The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called ...
XM_039107135.2 → XP_038963063.1 chloride channel protein 1 isoform X1

UniProtKB/TrEMBL

F1LPY4

Related

ENSRNOP00000087495.1, ENSRNOT00000104906.2

Conserved Domains (3) summary

cd03683
Location:117 → 573

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 ...

cd02205
Location:591 → 807

CBS_pair_SF; CBS repeat [structural motif]

cl15354
Location:586 → 856

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