This gene is a transcribed pseudogene belonging 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. This gene contains several nonsense codons compared... See more...

Aliases for CLCA3P Gene

Aliases for CLCA3P Gene

  • Chloride Channel Accessory 3, Pseudogene 2 3 5
  • Chloride Channel, Calcium Activated, Family Member 3 2 3
  • CLCA3 3 4
  • Calcium-Activated Chloride Channel Regulator Family Member 3 4
  • Calcium-Activated Chloride Channel Family Member 3 4
  • Chloride Channel Regulator 3 Pseudogene 3
  • Chloride Channel Regulator 3 2
  • HCLCA3 4

External Ids for CLCA3P Gene

Previous HGNC Symbols for CLCA3P Gene

  • CLCA3

Previous GeneCards Identifiers for CLCA3P Gene

  • GC01P086873
  • GC01P087099
  • GC01P085210

Summaries for CLCA3P Gene

Entrez Gene Summary for CLCA3P Gene

  • This gene is a transcribed pseudogene belonging 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. This gene contains several nonsense codons compared to other family members that render the transcript a candidate for nonsense-mediated mRNA decay (NMD). Therefore, this gene is unlikely to be protein-coding. [provided by RefSeq, Jan 2009]

GeneCards Summary for CLCA3P Gene

CLCA3P (Chloride Channel Accessory 3, Pseudogene) is a Pseudogene. Among its related pathways are Activation of cAMP-Dependent PKA and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include transporter activity and chloride channel activity.

Gene Wiki entry for CLCA3P Gene

Additional gene information for CLCA3P Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLCA3P Gene

Genomics for CLCA3P Gene

GeneHancer (GH) Regulatory Elements for CLCA3P Gene

Promoters and enhancers for CLCA3P Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J086542 Enhancer 0.3 Ensembl ENCODE 5.8 -91.2 -91234 1.5 CLCA3P piR-31936-004 piR-31470-022
GH01J086548 Enhancer 0.2 ENCODE 5.4 -85.4 -85376 1.1 CLCA4 CLCA3P CDCA4P2
GH01J086648 Enhancer 0.4 Ensembl 0.4 +14.1 14128 1.2 FOS FOSL1 JUN JUND ENSG00000261737 CLCA3P piR-55194-011 CLCA4-AS1
GH01J086636 Enhancer 0.2 ENCODE 0.6 +2.8 2760 0.2 CLCA3P piR-55194-011 CLCA4-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLCA3P on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLCA3P gene promoter:
  • Cart-1
  • HEN1
  • LCR-F1
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)

Genomic Locations for CLCA3P Gene

Genomic Locations for CLCA3P Gene
chr1:86,634,273-86,655,376
(GRCh38/hg38)
Size:
21,104 bases
Orientation:
Plus strand
chr1:87,099,956-87,121,059
(GRCh37/hg19)
Size:
21,104 bases
Orientation:
Plus strand

Genomic View for CLCA3P Gene

Genes around CLCA3P on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCA3P Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLCA3P Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCA3P Gene

Proteins for CLCA3P Gene

  • Protein details for CLCA3P Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y6N3-CLCA3_HUMAN
    Recommended name:
    Calcium-activated chloride channel regulator family member 3
    Protein Accession:
    Q9Y6N3

    Protein attributes for CLCA3P Gene

    Size:
    262 amino acids
    Molecular mass:
    29971 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLCA3P Gene

Post-translational modifications for CLCA3P Gene

No data available for DME Specific Peptides for CLCA3P Gene

Domains & Families for CLCA3P Gene

Gene Families for CLCA3P Gene

Protein Domains for CLCA3P Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLCA3P Gene

GenScript: Design optimal peptide antigens:
  • Calcium-activated chloride channel regulator family member 3 (CLCA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y6N3

UniProtKB/Swiss-Prot:

CLCA3_HUMAN :
  • Belongs to the CLCR family.
Family:
  • Belongs to the CLCR family.
genes like me logo Genes that share domains with CLCA3P: view

Function for CLCA3P Gene

Gene Ontology (GO) - Molecular Function for CLCA3P Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity TAS 10095065
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005254 chloride channel activity IEA --
GO:0005262 calcium channel activity IEA --
genes like me logo Genes that share ontologies with CLCA3P: view
genes like me logo Genes that share phenotypes with CLCA3P: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCA3P

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLCA3P Gene

Localization for CLCA3P Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCA3P Gene

Secreted.

Gene Ontology (GO) - Cellular Components for CLCA3P Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space TAS 10095065
GO:0005886 plasma membrane TAS --
GO:0034707 chloride channel complex IEA --
genes like me logo Genes that share ontologies with CLCA3P: view

No data available for Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for CLCA3P Gene

Pathways & Interactions for CLCA3P Gene

PathCards logo

SuperPathways for CLCA3P Gene

genes like me logo Genes that share pathways with CLCA3P: view

Pathways by source for CLCA3P Gene

5 Qiagen pathways for CLCA3P Gene
  • Activation of cAMP-Dependent PKA
  • cAMP Pathway
  • Cholera Infection
  • Hepatic ABC Transporters
  • PKA Signaling

Gene Ontology (GO) - Biological Process for CLCA3P Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034220 ion transmembrane transport TAS --
GO:0034765 regulation of ion transmembrane transport IEA --
GO:0070588 calcium ion transmembrane transport IEA --
GO:1902476 chloride transmembrane transport IEA --
genes like me logo Genes that share ontologies with CLCA3P: view

No data available for SIGNOR curated interactions for CLCA3P Gene

Drugs & Compounds for CLCA3P Gene

(3) Drugs for CLCA3P Gene - From: Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
CFTRinh 172 Pharma Voltage-independent, selective CFTR chloride channel blocker 0
DCEBIO Pharma Activates Cl- conductance and hKCa3.1 channels 0
PPQ 102 Pharma Potent, voltage-independent CFTR chloride channel inhibitor 0

(1) Additional Compounds for CLCA3P Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
GlyH 101
328541-79-3

(4) Tocris Compounds for CLCA3P Gene

Compound Action Cas Number
CFTRinh 172 Voltage-independent, selective CFTR chloride channel blocker 307510-92-5
DCEBIO Activates Cl- conductance and hKCa3.1 channels 60563-36-2
GlyH 101 Reversible, voltage-dependent CFTR chloride channel blocker 328541-79-3
PPQ 102 Potent, voltage-independent CFTR chloride channel inhibitor 931706-15-9
genes like me logo Genes that share compounds with CLCA3P: view

Transcripts for CLCA3P Gene

mRNA/cDNA for CLCA3P Gene

(1) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCA3P

Alternative Splicing Database (ASD) splice patterns (SP) for CLCA3P Gene

No ASD Table

Relevant External Links for CLCA3P Gene

GeneLoc Exon Structure for
CLCA3P
ECgene alternative splicing isoforms for
CLCA3P

Expression for CLCA3P Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLCA3P Gene

mRNA differential expression in normal tissues according to GTEx for CLCA3P Gene

This gene is overexpressed in Esophagus - Mucosa (x26.0) and Minor Salivary Gland (x7.7).

Protein differential expression in normal tissues from HIPED for CLCA3P Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLCA3P Gene



Protein tissue co-expression partners for CLCA3P Gene

NURSA nuclear receptor signaling pathways regulating expression of CLCA3P Gene:

CLCA3P

SOURCE GeneReport for Unigene cluster for CLCA3P Gene:

Hs.673847

mRNA Expression by UniProt/SwissProt for CLCA3P Gene:

Q9Y6N3-CLCA3_HUMAN
Tissue specificity: Expressed in the lung, trachea, spleen, thymus and mammary gland.
genes like me logo Genes that share expression patterns with CLCA3P: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLCA3P Gene

Orthologs for CLCA3P Gene

Evolution for CLCA3P Gene

ENSEMBL:
Gene Tree for CLCA3P (if available)
TreeFam:
Gene Tree for CLCA3P (if available)

No data available for Orthologs for CLCA3P Gene

Paralogs for CLCA3P Gene

(2) SIMAP similar genes for CLCA3P Gene using alignment to 1 proteins:

  • CLCA3_HUMAN
genes like me logo Genes that share paralogs with CLCA3P: view

No data available for Paralogs for CLCA3P Gene

Variants for CLCA3P Gene

Sequence variations from dbSNP and Humsavar for CLCA3P Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000248325 -- 86,652,826(+) T/C intron_variant
rs1000314091 -- 86,634,402(+) G/A non_coding_transcript_variant
rs1000509501 -- 86,640,939(+) T/C intron_variant
rs1000604377 -- 86,641,338(+) C/T intron_variant
rs1000825628 -- 86,654,299(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLCA3P Gene

Variant ID Type Subtype PubMed ID
esv2714407 CNV deletion 23290073
esv2761188 CNV gain+loss 21179565
esv3586705 CNV loss 21293372
esv3586706 CNV loss 21293372
nsv546760 CNV gain 21841781

Additional Variant Information for CLCA3P Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLCA3P

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for CLCA3P Gene

Disorders for CLCA3P Gene

Additional Disease Information for CLCA3P

No disorders were found for CLCA3P Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLCA3P Gene

Publications for CLCA3P Gene

  1. Molecular cloning and biochemical characterization of a truncated, secreted member of the human family of Ca2+-activated Cl- channels. (PMID: 10095065) Gruber AD … Pauli BU (Biochimica et biophysica acta 1999) 2 3 4 56
  2. A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells. (PMID: 23284306) Xie L … Green MR (PLoS genetics 2012) 3 56
  3. Talniflumate increases survival in a cystic fibrosis mouse model of distal intestinal obstructive syndrome. (PMID: 16354791) Walker NM … Clarke LL (The Journal of pharmacology and experimental therapeutics 2006) 23 56
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 56
  5. Molecular characteristics and functional diversity of CLCA family members. (PMID: 11071307) Pauli BU … Elble RC (Clinical and experimental pharmacology & physiology 2000) 3 56

Products for CLCA3P Gene

Sources for CLCA3P Gene