Clcn4 chloride channel, voltage-sensitive 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clcn4provided by MGI
Official Full Name: chloride channel, voltage-sensitive 4provided by MGI
Primary source: MGI:MGI:104571
See related: Ensembl:ENSMUSG00000000605 AllianceGenome:MGI:104571
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-4; Clc4-2; Clcn4-2
Summary: Predicted to enable antiporter activity and voltage-gated chloride channel activity. Involved in non-motile cilium assembly. Is active in ciliary base. Is expressed in cortical plate; early conceptus; heart; heart ventricle; and oocyte. Human ortholog(s) of this gene implicated in Raynaud-Claes syndrome. Orthologous to human CLCN4 (chloride voltage-gated channel 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E18 (RPKM 21.6), frontal lobe adult (RPKM 18.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 A1; 7 4.23 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (7285308..7303837, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (7282309..7300916, complement)

Chromosome 7 - NC_000073.7 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration.
Title: Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration.
In Mus spretus, the chloride channel 4 gene Clcn4-2 is X-linked and dosage compensated by X up-regulation and X inactivation, while in the closely related mouse species Mus musculus, Clcn4-2 has been translocated to chromosome 7.
Title: Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Clcn4-1 (e-PCR), detects polymorphism
- UniSTS:141349

STS-AA018252 (e-PCR)
- UniSTS:72946

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables antiporter activity	ISO Inferred from Sequence Orthology more info
enables antiporter 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	IEA Inferred from Electronic Annotation 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 chloride transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in non-motile cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in ciliary base	IDA Inferred from Direct Assay more info	PubMed
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in recycling endosome	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: H(+)/Cl(-) exchange transporter 4

Names: chloride channel 4-2; chloride channel protein 4; chloride transporter ClC-4; voltage-gated chloride channel ClC-4A

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_001302386.2 → NP_001289315.1 H(+)/Cl(-) exchange transporter 4 isoform 2 precursor

See identical proteins and their annotated locations for NP_001289315.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) is shorter at the 5' end, lacks an alternate exon in the 5' coding region and uses a downstream start codon, compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC149056

Consensus CDS

CCDS85212.1

UniProtKB/TrEMBL

Q3LRV6, Q8CBL5

Related

ENSMUSP00000147562.2, ENSMUST00000210594.2

Conserved Domains (2) summary

cd03684
Location:5 → 511

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:522 → 672

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
NM_001302387.3 → NP_001289316.1 H(+)/Cl(-) exchange transporter 4 isoform 3

See identical proteins and their annotated locations for NP_001289316.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, compared to variant 1. It encodes isoform 3 which is shorter compared to isoform 1. Variants 3 and 13 both encode the same isoform (3).

Source sequence(s)

AC149056

Consensus CDS

CCDS85213.1

UniProtKB/TrEMBL

A0A1B0GT29, Q8CBL5

Conserved Domains (2) summary

cd03684
Location:65 → 540

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:551 → 701

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
NM_001357102.2 → NP_001344031.1 H(+)/Cl(-) exchange transporter 4 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1, 6, 7, and 9-11 all encode the same isoform (1).

Source sequence(s)

AC149056

Consensus CDS

CCDS20786.1

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5

Conserved Domains (2) summary

cd03684
Location:65 → 571

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:582 → 732

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
NM_001357103.2 → NP_001344032.1 H(+)/Cl(-) exchange transporter 4 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1, 6, 7, and 9-11 all encode the same isoform (1).

Source sequence(s)

AC149056

Consensus CDS

CCDS20786.1

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5

Conserved Domains (2) summary

cd03684
Location:65 → 571

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:582 → 732

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
NM_001357104.2 → NP_001344033.1 H(+)/Cl(-) exchange transporter 4 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (8) lacks two alternate exon in the 5' coding region and uses a downstream start codon, compared to variant 1. It encodes isoform 4. Variants 8, 14, and 15 all encode the same isoform (4).

Source sequence(s)

AC149056

UniProtKB/TrEMBL

Q8CBL5

Conserved Domains (2) summary

cd03684
Location:58 → 490

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:501 → 651

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
NM_001412259.1 → NP_001399188.1 H(+)/Cl(-) exchange transporter 4 isoform 1

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5
NM_001412260.1 → NP_001399189.1 H(+)/Cl(-) exchange transporter 4 isoform 1

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5
NM_001412261.1 → NP_001399190.1 H(+)/Cl(-) exchange transporter 4 isoform 1

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5
NM_001412262.1 → NP_001399191.1 H(+)/Cl(-) exchange transporter 4 isoform 5

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/TrEMBL

Q8CBL5
NM_001412263.1 → NP_001399192.1 H(+)/Cl(-) exchange transporter 4 isoform 3

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/TrEMBL

A0A1B0GT29, Q8CBL5
NM_001412264.1 → NP_001399193.1 H(+)/Cl(-) exchange transporter 4 isoform 4

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/TrEMBL

Q8CBL5
NM_001412265.1 → NP_001399194.1 H(+)/Cl(-) exchange transporter 4 isoform 4

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/TrEMBL

Q8CBL5
NM_001412266.1 → NP_001399195.1 H(+)/Cl(-) exchange transporter 4 isoform 6 precursor

Status: VALIDATED

Source sequence(s)

AC149056

UniProtKB/TrEMBL

Q8CBL5
NM_011334.5 → NP_035464.3 H(+)/Cl(-) exchange transporter 4 isoform 1

See identical proteins and their annotated locations for NP_035464.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 6, 7, and 9-11 all encode the same isoform (1).

Source sequence(s)

AC149056

Consensus CDS

CCDS20786.1

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5

Related

ENSMUSP00000000619.7, ENSMUST00000000619.8

Conserved Domains (2) summary

cd03684
Location:65 → 571

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:582 → 732

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

NR_126156.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AC149056

Related

ENSMUST00000210989.2
NR_126157.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an upstream alternate 5'-terminal exon, lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AC149056

Related

ENSMUST00000210809.2
NR_178086.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC149056
NR_178087.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC149056

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000073.7 Reference GRCm39 C57BL/6J

Range

7285308..7303837 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036152617.1 → XP_036008510.1 H(+)/Cl(-) exchange transporter 4 isoform X1

UniProtKB/Swiss-Prot

Q2TAX6, Q61418

UniProtKB/TrEMBL

Q8CBL5

Conserved Domains (2) summary

cd03684
Location:65 → 571

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:582 → 732

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_030242051.2 → XP_030097911.1 H(+)/Cl(-) exchange transporter 4 isoform X3

UniProtKB/TrEMBL

A0A1B0GT29, Q8CBL5

Related

ENSMUSP00000148174.2, ENSMUST00000210061.2

Conserved Domains (2) summary

cd03684
Location:65 → 540

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:551 → 701

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_030242049.2 → XP_030097909.1 H(+)/Cl(-) exchange transporter 4 isoform X2

UniProtKB/TrEMBL

Q8CBL5

Conserved Domains (2) summary

cd03684
Location:41 → 547

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:558 → 708

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