clcn3 chloride channel 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: clcn3provided by ZNC
Official Full Name: chloride channel 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-1699
See related: Ensembl:ENSDARG00000003269 AllianceGenome:ZFIN:ZDB-GENE-030131-1699
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: fb78c02; wu:fb78c02
Summary: Predicted to enable voltage-gated chloride channel activity. Predicted to act upstream of or within chloride transport and transmembrane transport. Predicted to be located in early endosome membrane; late endosome membrane; and lysosomal membrane. Predicted to be active in Golgi apparatus; cytoplasmic vesicle; and plasma membrane. Is expressed in several structures, including eye; female organism; heart; liver; and pleuroperitoneal region. Orthologous to human CLCN3 (chloride voltage-gated channel 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 7

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (7511874..7643941)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (7278501..7408672)

Chromosome 7 - NC_007118.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

fk72e08.x1 (e-PCR)
- UniSTS:201476

fj05h11.y1 (e-PCR)
- UniSTS:198412

fb78c02.x1 (e-PCR)
- UniSTS:203437

fk70h07.x1 (e-PCR)
- UniSTS:201451

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
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
acts_upstream_of_or_within chloride transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
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 endosome	IEA Inferred from Electronic Annotation more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor 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 3

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007118.7 Reference GRCz11 Primary Assembly

Range

7511874..7643941

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021477691.2 → XP_021333366.1 H(+)/Cl(-) exchange transporter 3 isoform X3

UniProtKB/TrEMBL

A0A8M9PPD0

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_021477689.2 → XP_021333364.1 H(+)/Cl(-) exchange transporter 3 isoform X1

UniProtKB/TrEMBL

A0A140LGR0, A0A8M9Q887

Related

ENSDARP00000142439.1, ENSDART00000172848.2

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_021477693.2 → XP_021333368.1 H(+)/Cl(-) exchange transporter 3 isoform X4

UniProtKB/TrEMBL

A0A8M9Q239

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_021477692.2 → XP_021333367.1 H(+)/Cl(-) exchange transporter 3 isoform X3

UniProtKB/TrEMBL

A0A8M9PPD0

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_068222433.1 → XP_068078534.1 H(+)/Cl(-) exchange transporter 3 isoform X1

UniProtKB/TrEMBL

A0A140LGR0, A0A8M9Q887
XM_021477690.2 → XP_021333365.1 H(+)/Cl(-) exchange transporter 3 isoform X2

UniProtKB/TrEMBL

A0A8M9QHF3, F1R7J9

Related

ENSDARP00000049310.7, ENSDART00000049311.7

Conserved Domains (2) summary

cd03684
Location:115 → 623

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:646 → 784

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 ...
XM_021477694.2 → XP_021333369.1 H(+)/Cl(-) exchange transporter 3 isoform X5

UniProtKB/TrEMBL

A0A8M9Q891

Related

ENSDARP00000142496.1, ENSDART00000173018.2

Conserved Domains (2) summary

cd03684
Location:115 → 623

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:646 → 784

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 ...

Reference GRCz11 ALT_DRER_TU_1

Genomic

NW_018394672.1 Reference GRCz11 ALT_DRER_TU_1

Range

62646..173795

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005166349.5 → XP_005166406.1 H(+)/Cl(-) exchange transporter 3 isoform X3

See identical proteins and their annotated locations for XP_005166406.1

UniProtKB/TrEMBL

A0A8M9PPD0

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_001923468.8 → XP_001923503.1 H(+)/Cl(-) exchange transporter 3 isoform X1

See identical proteins and their annotated locations for XP_001923503.1

UniProtKB/TrEMBL

A0A140LGR0, A0A8M9Q887

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_005166348.5 → XP_005166405.1 H(+)/Cl(-) exchange transporter 3 isoform X4

UniProtKB/TrEMBL

A0A8M9Q239

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_009302926.4 → XP_009301201.1 H(+)/Cl(-) exchange transporter 3 isoform X3

See identical proteins and their annotated locations for XP_009301201.1

UniProtKB/TrEMBL

A0A8M9PPD0

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_005166345.5 → XP_005166402.1 H(+)/Cl(-) exchange transporter 3 isoform X1

See identical proteins and their annotated locations for XP_005166402.1

UniProtKB/TrEMBL

A0A140LGR0, A0A8M9Q887

Conserved Domains (2) summary

cd03684
Location:140 → 648

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:671 → 809

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 ...
XM_068218355.1 → XP_068074456.1 H(+)/Cl(-) exchange transporter 3 isoform X6
XM_003198891.6 → XP_003198939.1 H(+)/Cl(-) exchange transporter 3 isoform X2

UniProtKB/TrEMBL

A0A8M9QHF3, F1R7J9

Conserved Domains (2) summary

cd03684
Location:115 → 623

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:646 → 784

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 ...
XM_005166350.5 → XP_005166407.1 H(+)/Cl(-) exchange transporter 3 isoform X5

UniProtKB/TrEMBL

A0A8M9Q891

Conserved Domains (2) summary

cd03684
Location:115 → 623

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:646 → 784

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 ...