Human Gene CLCA4 (ENST00000370563.3) from GENCODE V41
  Description: Homo sapiens chloride channel accessory 4 (CLCA4), transcript variant 2, non-coding RNA. (from RefSeq NR_024602)
RefSeq Summary (NM_012128): 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].
Gencode Transcript: ENST00000370563.3
Gencode Gene: ENSG00000016602.9
Transcript (Including UTRs)
   Position: hg38 chr1:86,547,078-86,580,754 Size: 33,677 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg38 chr1:86,547,120-86,580,345 Size: 33,226 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2022-05-14 18:57:26

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:86,547,078-86,580,754)mRNA (may differ from genome)Protein (919 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Calcium-activated chloride channel regulator 4; AltName: Full=Calcium-activated chloride channel family member 4; Short=hCLCA4; AltName: Full=Calcium-activated chloride channel protein 2; Short=CaCC-2; Short=hCaCC-2; Contains: RecName: Full=Calcium-activated chloride channel regulator 4, 110 kDa form; Contains: RecName: Full=Calcium-activated chloride channel regulator 4, 30 kDa form; Flags: Precursor;
FUNCTION: May be involved in mediating calcium-activated chloride conductance.
SUBCELLULAR LOCATION: Cell membrane; Single-pass membrane protein (By similarity). Apical cell membrane (By similarity). Secreted (By similarity). Note=The C-terminus 30 kDa form is anchored to the membrane (By similarity). The N-terminus 110 kDa form is released from the membrane triggered by an unknown stimulus (By similarity).
TISSUE SPECIFICITY: Primarily expressed in the digestive tract, mainly in colon. Detected in smaller amounts in brain, urogenital organs, testis, and salivary and mammary glands. Highly expressed in the epithelial layer and submucosal gland of the inferior turbinate mucosa. Lower levels in the epithelial layer of nasal polyp.
INDUCTION: Down-regulated in oral tongue squamous cell carcinomas.
PTM: Processed at a monobasic residue to yield a larger N-terminal and a smaller C-terminal cleavage products of 90 to 110 and 30 to 35 kDa, respectively (By similarity).
SIMILARITY: Belongs to the CLCR family.
SIMILARITY: Contains 1 VWFA domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: CLCA4
Diseases sorted by gene-association score: cystic fibrosis* (13), bestrophinopathy (11), farber lipogranulomatosis (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 224.30 RPKM in Esophagus - Mucosa
Total median expression: 351.05 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00420.000 Picture PostScript Text
3' UTR -68.60409-0.168 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004727 - CaCC_prot
IPR013642 - Cl_channel_Ca
IPR015394 - DUF1973
IPR002035 - VWF_A

Pfam Domains:
PF08434 - Calcium-activated chloride channel N terminal
PF09315 - n/a

ModBase Predicted Comparative 3D Structure on Q14CN2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Protein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004222 metalloendopeptidase activity
GO:0005229 intracellular calcium activated chloride channel activity
GO:0005254 chloride channel activity
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006508 proteolysis
GO:0006821 chloride transport
GO:0034220 ion transmembrane transport
GO:1902476 chloride transmembrane transport

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane

-  Descriptions from all associated GenBank mRNAs
  AK314430 - Homo sapiens cDNA, FLJ95221.
AK000072 - Homo sapiens cDNA FLJ20065 fis, clone COL01613, highly similar to ECLC_BOVIN EPITHELIAL CHLORIDE CHANNEL PROTEIN.
BC113687 - Homo sapiens chloride channel accessory 4, mRNA (cDNA clone MGC:142247 IMAGE:8322739), complete cds.
BC113689 - Homo sapiens chloride channel accessory 4, mRNA (cDNA clone MGC:142249 IMAGE:8322741), complete cds.
AF127035 - Homo sapiens calcium-activated chloride channel protein 2 (CaCC2) mRNA, complete cds.
AY358470 - Homo sapiens clone DNA60629 CLCA4 (UNQ562) mRNA, complete cds.
KJ902232 - Synthetic construct Homo sapiens clone ccsbBroadEn_11626 CLCA4 gene, encodes complete protein.
HQ258531 - Synthetic construct Homo sapiens clone IMAGE:100072960 chloride channel accessory 4 (CLCA4) gene, encodes complete protein.
AK307785 - Homo sapiens cDNA, FLJ97733.
AK307898 - Homo sapiens cDNA, FLJ97846.
AK293766 - Homo sapiens cDNA FLJ54980 complete cds, highly similar to Homo sapiens chloride channel, calcium activated, family member 4 (CLCA4), mRNA.
AK000138 - Homo sapiens cDNA FLJ20131 fis, clone COL06357.
JD301585 - Sequence 282609 from Patent EP1572962.
JD245238 - Sequence 226262 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04740 - Olfactory transduction

Reactome (by CSHL, EBI, and GO)

Protein Q14CN2 (Reactome details) participates in the following event(s):

R-HSA-5333671 CLCAs self cleave
R-HSA-2672351 Stimuli-sensing channels
R-HSA-983712 Ion channel transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: CaCC2, CLCA4_HUMAN, ENST00000370563.1, ENST00000370563.2, NR_024602, Q14CN2, Q6UX81, Q9UNF7, uc009wcs.1, uc009wcs.2, uc009wcs.3, uc009wcs.4, UNQ562/PRO1124
UCSC ID: ENST00000370563.3
RefSeq Accession: NM_012128
Protein: Q14CN2 (aka CLCA4_HUMAN)
CCDS: CCDS41355.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.