ClC-a Chloride channel-a [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: ClC-aprovided by FlyBase
Official Full Name: Chloride channel-aprovided by FlyBase
Primary source: FLYBASE:FBgn0051116
Locus tag: Dmel_CG31116
See related: AllianceGenome:FB:FBgn0051116
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: CG14726; CG31116; CG6942; CLC-2; Clc-a; DmClC-2; DmClC-a; DmClCa; Dmel\CG31116; FBgn0037951
Summary: Enables chloride channel activity. Involved in chloride transport and water transport. Located in apical plasma membrane and basal plasma membrane. Is expressed in several structures, including Malpighian tubule Type II cell; adult head; embryonic/larval midgut; ganglia; and glial cell. Used to study myopathy. Human ortholog(s) of this gene implicated in several diseases, including idiopathic generalized epilepsy 11; myotonia congenita (multiple); primary hyperaldosteronism; renal tubular transport disease (multiple); and sensorineural hearing loss. Orthologous to several human genes including CLCN2 (chloride voltage-gated channel 2). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 86F8-86F8; 3-51 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3R	NT_033777.3 (11797244..11813207, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3R	NT_033777.2 (7622966..7638929, complement)

Chromosome 3R - NT_033777.3 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ClC-a was expressed in the niche in cortex glia and loss-of-function mutations resulted in smaller brains and neural wiring defects.
Title: Drosophila ClC-a is required in glia of the stem cell niche for proper neurogenesis and wiring of neural circuits.

Submit: New GeneRIF Correction

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

mobile_element

Loc: c11807783-11807583 mobile_element_type = transposon:INE-1{}2915

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables chloride channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chloride transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in chloride transport	IEA Inferred from Electronic Annotation more info
involved_in chloride transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in renal water homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in renal water transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transepithelial chloride transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transepithelial water transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in actin cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basal plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	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	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: chloride channel-a

Names: CG31116-PA; CG31116-PC; CG31116-PD; CG31116-PF; CG31116-PG; CG31116-PH; CG31116-PI; ClC-a-PA; ClC-a-PC; ClC-a-PD; ClC-a-PF; ClC-a-PG; ClC-a-PH; ClC-a-PI

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NT_033777.3 Reference assembly

Range

11797244..11813207 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001104281.2 → NP_001097751.2 chloride channel-a, isoform G [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001097751.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9VGH7

Conserved Domains (3) summary

cd03683
Location:123 → 598

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:844 → 921

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:179 → 567

Voltage_CLC; Voltage gated chloride channel
NM_001170121.1 → NP_001163592.1 chloride channel-a, isoform H [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001163592.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9VGH7

Conserved Domains (3) summary

cd03683
Location:123 → 598

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:952 → 1048

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:179 → 567

Voltage_CLC; Voltage gated chloride channel
NM_001275558.1 → NP_001262487.1 chloride channel-a, isoform I [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001262487.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A0B4KGV4
NM_001104282.3 → NP_001097752.1 chloride channel-a, isoform F [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001097752.1

Status: REVIEWED

UniProtKB/TrEMBL

H1UUP0

Conserved Domains (3) summary

cd03683
Location:171 → 646

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:905 → 969

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

cl15354
Location:659 → 718

CBS_pair_SF; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily
NM_176462.2 → NP_788639.1 chloride channel-a, isoform D [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_788639.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4VCL3, A8JQX8, A8JQX9, E1JIJ0, Q7YU63, Q8INJ7, Q8MRL4, Q9VGH7, Q9VGH8

Related

FBpp0082002

Conserved Domains (3) summary

cd03683
Location:171 → 646

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:1000 → 1096

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:227 → 615

Voltage_CLC; Voltage gated chloride channel
NM_169431.3 → NP_731634.2 chloride channel-a, isoform C [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_731634.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9VGH7

Related

FBpp0082001

Conserved Domains (3) summary

cd03683
Location:154 → 629

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:875 → 952

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:210 → 598

Voltage_CLC; Voltage gated chloride channel
NM_169432.3 → NP_731635.2 chloride channel-a, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_731635.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9VGH7

Related

FBpp0082000

Conserved Domains (3) summary

cd03683
Location:154 → 629

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:983 → 1079

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:210 → 598

Voltage_CLC; Voltage gated chloride channel