Free for academic non-profit institutions. Other users need a Commercial license
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
- CLCA3P 5
- HCLCA3 4
External Ids for CLCA3P Gene
- HGNC: 2017
- Entrez Gene: 9629
- Ensembl: ENSG00000153923
- OMIM: 604337
- UniProtKB: Q9Y6N3
Previous HGNC Symbols for CLCA3P Gene
- CLCA3
Previous GeneCards Identifiers for CLCA3P Gene
- GC01P086873
- GC01P087099
- GC01P085210
Summaries 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 Neuropathic Pain-Signaling in Dorsal Horn Neurons. Gene Ontology (GO) annotations related to this gene include transporter activity and chloride channel activity.
Additional gene information for CLCA3P Gene
- HGNC(2017)
- Entrez Gene(9629)
- Ensembl(ENSG00000153923)
- OMIM(604337)
- UniProtKB(Q9Y6N3)
- Open Targets Platform(ENSG00000153923)
- Search for CLCA3P at DataMed
- Search for CLCA3P at HumanCyc
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 Pubs
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 CLCA4 piR-31936-004 piR-31470-022 CLCA1 | ||
| GH01J086548 | Enhancer | 0.2 | ENCODE | 5.4 | -85.4 | -85376 | 1.1 | CLCA4 CLCA3P CDCA4P2 SH3GLB1 | ||
| GH01J086648 | Enhancer | 0.5 | Ensembl | 0.4 | +14.1 | 14128 | 1.2 | CEBPB FOS FOSL1 BHLHE40 JUN JUND | ENSG00000261737 CLCA3P piR-55194-011 CLCA4-AS1 SH3GLB1 CLCA4 | |
| GH01J086636 | Enhancer | 0.2 | ENCODE | 0.7 | +2.8 | 2760 | 0.2 | CLCA3P piR-55194-011 SH3GLB1 CLCA4-AS1 CLCA4 |
- 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 the GeneHancer Hub at the UCSC Golden Path
- 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:
-
- 1p22.3 by HGNC
- 1p22.3 by Entrez Gene
- 1p22.3 by Ensembl
CLCA3P Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
Protein Expression for CLCA3P Gene
Post-translational modifications for CLCA3P Gene
- N-glycosylated.
-
Glycosylation at Asn75 and Asn180
- NX_Q9Y6N3 (NX_Q9Y6N3-1)
- Modification sites at PhosphoSitePlus
Antibody Products
-
Abcam antibodies for CLCA3P
- Invitrogen Antibodies for CLCA3P (AFLGC-CLCA3P)
- antibodies-online: Show 9 available CLCA3P Antibodies ranked by validation data
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for CLCA3P
- Origene Custom Protein Services for CLCA3P
- Novus Biologicals proteins for CLCA3P
-
Abcam proteins for CLCA3P
No data available for DME Specific Peptides for CLCA3P Gene
Domains & Families for CLCA3P Gene
Gene Families for CLCA3P Gene
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- Family:
-
- Belongs to the CLCR family.
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 | -- |
Phenotypes for CLCA3P Gene
- GenomeRNAi human phenotypes for CLCA3P:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for CLCA3P - Select products 50% OFF >
- * CLCA3P CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Browse CRISPR knockouts for CLCA3P
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for CLCA3P
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for CLCA3P
- Browse OriGene Inhibitory RNA Products For CLCA3P
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCA3P
Clone Products
- Applied Biological Materials (abm): Clones for CLCA3P - Select products 50% OFF >
- * CLCA3P as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter 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.
| 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 | -- |
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
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Activation of cAMP-Dependent PKA |
Activation of cAMP-Dependent PKA
.77
cAMP Pathway
.77
|
PKA Signaling
.56
|
| 2 | Ion channel transport | ||
| 3 | Neuropathic Pain-Signaling in Dorsal Horn Neurons |
Cholera Infection
.40
|
|
| 4 | Hepatic ABC Transporters |
Hepatic ABC Transporters
.41
|
|
| 5 | Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds | ||
Pathways by source for CLCA3P Gene
3 Reactome pathways for CLCA3P Gene
5 Qiagen pathways for CLCA3P Gene
- Activation of cAMP-Dependent PKA
- cAMP Pathway
- Cholera Infection
- Hepatic ABC Transporters
- PKA Signaling
| 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 | -- |
No data available for Interacting Proteins and SIGNOR curated interactions for CLCA3P Gene
Drugs & Compounds for CLCA3P Gene
| 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 |
Transcripts for CLCA3P Gene
mRNA/cDNA for CLCA3P Gene
- 1 REFSEQ mRNAs :
- 1 NCBI additional mRNA sequence :
- 3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000284054 2407 nts (view in UCSC)
- ENST00000490028 2781 nts (view in UCSC)
- ENST00000466454 3412 nts (view in UCSC)
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for CLCA3P - Select products 50% OFF >
- * CLCA3P CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Browse CRISPR knockouts for CLCA3P
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for CLCA3P
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for CLCA3P
- Browse OriGene Inhibitory RNA Products For CLCA3P
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCA3P
Clone Products
- Applied Biological Materials (abm): Clones for CLCA3P - Select products 50% OFF >
- * CLCA3P as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for CLCA3P
Relevant External Links for CLCA3P Gene
- GeneLoc Exon Structure for
- CLCA3P
Expression 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).
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
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLCA3P
SOURCE GeneReport for Unigene cluster for CLCA3P Gene:
Hs.673847mRNA Expression by UniProt/SwissProt for CLCA3P Gene:
Q9Y6N3-CLCA3_HUMAN
Tissue specificity:
Expressed in the lung, trachea, spleen, thymus and mammary gland.
Primer Products
-
OriGene qPCR primer pairs for CLCA3P
Gene Expression Assay Products
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
No data available for Orthologs for CLCA3P Gene
Paralogs for CLCA3P Gene
No data available for Paralogs for CLCA3P Gene
Variants 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
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Additional dbSNP identifiers (rs#s) 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
- 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
- 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
- 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
- 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
- Molecular characteristics and functional diversity of CLCA family members. (PMID: 11071307) Pauli BU … Elble RC (Clinical and experimental pharmacology & physiology 2000) 3
ExternalLinks
Products for CLCA3P Gene
- Browse OriGene Antibodies
- Custom Antibody Services
- Browse OriGene ELISA Kits
- Custom Assay Services
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for CLCA3P
- Origene Custom Protein Services for CLCA3P
- Origene shrna, sirna, and RNAi products in human, mouse, rat for CLCA3P
- Browse OriGene Inhibitory RNA Products For CLCA3P
- OriGene qPCR primer pairs for CLCA3P
- Browse CRISPR knockouts for CLCA3P
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For CLCA3P
- Browse Sino Biological cDNA Clones
- Browse Sino Biological Recombinant Proteins
- Browse Sino Biological Cell Lysates
- Browse Sino Biological Antibodies
- Browse Sino Biological Assays
- Browse ELISA Kits
- Browse CRO Services
- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Novus Biologicals proteins for CLCA3P
- Browse Antibodies
- Browse Peptides and Proteins
- Browse Lysates
- Browse ELISA Kits
- Abcam antibodies for CLCA3P
- Abcam proteins for CLCA3P
- Find your target
- Browse Primary Antibodies
- Browse Conjugated Primary Antibodies
- Browse Secondary Antibodies
- Browse ELISA Kits
- Browse Matched Antibody Pairs
- Browse Proteins and Peptides
- Search Knockout (KO) Validated Antibodies
- Browse Monoclonal Antibodies
- Browse Recombinant Antibodies
- Invitrogen Antibodies for CLCA3P (AFLGC-CLCA3P)
- VectorBuilder Custom and pre-made DNA vectors for CLCA3P (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for CLCA3P (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for CLCA3P (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for CLCA3P CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for CLCA3P
- antibodies-online: Show 9 available CLCA3P Antibodies ranked by validation data
- antibodies-online: Search results for available CLCA3P related products ranked by validation data
- antibodies-online: Search results for available CLCA3P related products ranked by validation data
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for CLCA3P
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for CLCA3P
- Search GeneCopoeia for miRNA 3'UTR Target clone products for CLCA3P
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCA3P
Sources for CLCA3P Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) Genetics Home Reference
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNACentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Signalway Antibody
- (175) Open Targets Platform
- (176) 5SRRNADB
- (177) snoDB
- (178) MirGeneDB