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CLCA4 chloride channel accessory 4 [ Homo sapiens (human) ]

Gene ID: 22802, updated on 18-Jan-2020

Summary

Official Symbol
CLCA4provided by HGNC
Official Full Name
chloride channel accessory 4provided by HGNC
Primary source
HGNC:HGNC:2018
See related
Ensembl:ENSG00000016602 MIM:616857
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CaCC; CaCC2
Summary
The protein encoded by this gene belongs to the calcium sensitive chloride conductance protein family. To date, all members of this gene family map to the same site on chromosome 1p31-p22 and share high degrees of homology in size, sequence and predicted structure, but differ significantly in their tissue distributions. Alternative splicing results in multiple transcript variants, only one of which is thought to be protein coding. [provided by RefSeq, Dec 2008]
Expression
Biased expression in colon (RPKM 204.3), esophagus (RPKM 195.4) and 1 other tissue See more
Orthologs

Genomic context

See CLCA4 in Genome Data Viewer
Location:
1p22.3
Exon count:
15
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (86547078..86580758)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (87012759..87046437)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378827 Neighboring gene uncharacterized LOC105378826 Neighboring gene cell division cycle associated 4 pseudogene 2 Neighboring gene CLCA4 antisense RNA 1 Neighboring gene chloride channel accessory 3, pseudogene Neighboring gene SH3 domain containing GRB2 like, endophilin B1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of chloride channel accessory 4 (CLCA4) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 from both CCR5- and CXCR4-tropic HIV-1 strains opens calcium-activated potassium (K(Ca)), chloride, and calcium-permeant nonselective cation channels in macrophages; these signals are mediated by CCR5 and CXCR4 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • MGC142247, MGC142249

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chloride channel activity TAS
Traceable Author Statement
more info
PubMed 
intracellular calcium activated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
metallopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
calcium-activated chloride channel regulator 4
Names
caCC-2
calcium-activated chloride channel family member 4
calcium-activated chloride channel protein 2
chloride channel regulator 4
chloride channel, calcium activated, family member 4
hCLCA4
hCaCC-2

NCBI Reference Sequences (RefSeq)

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)

  1. NM_012128.4NP_036260.2  calcium-activated chloride channel regulator 4 precursor

    See identical proteins and their annotated locations for NP_036260.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AY358470, DA761219
    Consensus CDS
    CCDS41355.1
    UniProtKB/Swiss-Prot
    Q14CN2
    Related
    ENSP00000359594.3, ENST00000370563.3
    Conserved Domains (2) summary
    cd00198
    Location:305459
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam08434
    Location:24909
    CLCA; Calcium-activated chloride channel

RNA

  1. NR_024602.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK307785, CB851641, DA668017

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    86547078..86580758
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541015.2XP_011539317.1  calcium-activated chloride channel regulator 4 isoform X1

    Conserved Domains (2) summary
    cd00198
    Location:254408
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam08434
    Location:2858
    CLCA; Calcium-activated chloride channel
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