CLCA3P Gene
pseudogene GIFtS: 40
GCID: GC01P087099
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chloride channel accessory 3, pseudogene(Previous names: chloride channel, calcium activated, family member 3, chloride...)
(Previous symbol: CLCA3)
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Aliases
for CLCA3P gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA
Quality score for the ORGUL clustered with this gene is 3
| Aliases |
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| Chloride Channel Accessory 3, Pseudogene1 2 | | CLCA31 2 3 5 | | Chloride Channel Regulator 31 | | Chloride Channel, Calcium Activated, Family Member 31 | | Calcium-Activated Chloride Channel Family Member 33 | | HCLCA31 |
| External Ids: | HGNC: 20171 | Entrez Gene: 96292 | Ensembl: ENSG000001539237 | OMIM: 6043375 | UniProtKB: Q9Y6N33 |
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| | ORGUL members: | |
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| NONCODE:n386575 | |
Export aliases for CLCA3P gene to outside databasesPrevious GC identifers: GC01P086873 GC01P085210
Summaries
for CLCA3P gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for CLCA3P:
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 insize, sequence and predicted structure, but differ significantly in their tissue distributions. This gene containsseveral nonsense codons compared to other family members that render the transcript a candidate for nonsense-mediatedmRNA decay (NMD). Therefore, this gene is unlikely to be protein-coding. (provided by RefSeq, Jan 2009)
Gene Wiki entry for CLCA3P (CLCA3)
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Genomic Views
for CLCA3P gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000001.10 NC_018912.1 NT_032977.9
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the CLCA3P gene promoter:
POU3F2 (N-Oct-5a) POU3F2 (N-Oct-5b) LCR-F1 POU3F2 HEN1 POU2F1 POU2F1b POU2F1a Cart-1 POU2F1c
Other transcription factors
Search SABiosciences Chromatin IP Primers for CLCA3P
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLCA3P |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 1p31-p22 Ensembl cytogenetic band: 1p22.3 HGNC cytogenetic band: 1p31-p22CLCA3P Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01P087099: view genomic region
(about GC identifiers)
Start:
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87,099,956 bp from pter |
End:
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87,121,059 bp from pter |
Size:
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21,104 bases |
Orientation:
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plus strand |
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Proteins
for CLCA3P gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
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UniProtKB/Swiss-Prot: CLCA3_HUMAN, Q9Y6N3 (See
protein sequence)Recommended Name: Calcium-activated chloride channel regulator family member 3 precursor Size: 262 amino acids; 29971 Da
Subcellular location: Secreted
Caution: In contrast to other members of the family, this protein is much shorter and lacks the VWFA domain. Defined asa pseudogene by HGNC. PubMed:10095065 reports that it is expressed and glycosylated in mammalian cellsExplore the universe of human proteins at neXtProt for CLCA3P: NX_Q9Y6N3
Post-translational modifications:
N-glycosylated1
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9Y6N3
CLCA3P Protein expression data from MOPED and PaxDb: About this image 
Human Recombinant Protein Products for CLCA3P:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
CLCA3P for ontologies About GeneDecksing
CLCA3P Antibody Products:
Assay Products for CLCA3P: |
Protein
Domains /
Families
for CLCA3P gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
CLCA3P for domains About GeneDecksing
1 InterPro domain/family:Graphical View of Domain Structure for InterPro Entry Q9Y6N3ProtoNet protein and cluster: Q9Y6N3 UniProtKB/Swiss-Prot: CLCA3_HUMAN, Q9Y6N3Similarity: Belongs to the CLCR family |
Function
for CLCA3P gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
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Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view): About this table
CLCA3P for ontologies About GeneDecksing
Phenotypes:
1 GenomeRNAi human phenotype for CLCA3P:
Animal Models:
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCA3P |
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Pathways & Interactions
for CLCA3P gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
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Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CLCA3P
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table
CLCA3P for ontologies About GeneDecksing
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Drugs & Compounds
for CLCA3P gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Compounds for CLCA3P available from Tocris Bioscience About this table
| Compound | Action |
CAS
# |
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| DCEBIO | Activates Cl- conductance and hIK1 K+ channels | [60563-36-2] | | 9-AC | Chloride transport inhibitor | [723-62-6] | | NPPB | Chloride channel blocker | [107254-86-4] | | Talniflumate | Chloride channel blocker (hCLCA1/mCLCA3 and Cl-/HCO3- exchange) | [66898-62-2] |
Search CenterWatch for drugs/clinical trials and news about CLCA3P 
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Transcripts
for CLCA3P gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
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REFSEQ mRNAs for CLCA3P gene: NM_004921.2 Unigene Cluster for CLCA3P: Chloride channel accessory 3, pseudogene Hs.673847 [show with all ESTs]Unigene Representative Sequence: NR_0246043 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000284054 ENST00000490028 ENST00000466454(uc010osh.2)
Additional cDNA sequence: NR_024604.1 2 DOTS entries: DT.92035017 DT.91907582 6 AceView cDNA sequences: BE217974 NM_004921 BE738113 AF043976 BE738683 BU685983
GeneLoc Exon Structure
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Expression
for CLCA3P gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| CLCA3P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See CLCA3P Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CLCA3P
SOURCE GeneReport for Unigene cluster: Hs.673847
UniProtKB/Swiss-Prot: CLCA3_HUMAN, Q9Y6N3Tissue specificity: Expressed in the lung, trachea, spleen, thymus and mammary gland
SABiosciences Custom PCR Arrays for CLCA3P
Primer
Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CLCA3P
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat CLCA3P | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLCA3P | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLCA3P | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCA3P |
Orthologs
for CLCA3P gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
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--
ENSEMBL Gene Tree for CLCA3P (if available)
TreeFam Gene Tree for CLCA3P (if available) |
Paralogs
for CLCA3P gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for CLCA3P gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
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| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 1 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
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HapMap Linkage Disequilibrium report for CLCA3P (87099956 - 87121059 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for CLCA3P: -- | SABiosciences Cancer Mutation PCR Assays |
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Disorders
/ Diseases
for CLCA3P gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
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CLCA3P for disorders About GeneDecksing
OMIM gene information: 604337
OMIM disorders: --
3  diseases for CLCA3P: About MalaCardsintestinal obstruction cystic fibrosis fibrosis
Export disorders for CLCA3P gene to outside databases
|
Publications
for CLCA3P gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
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PubMed articles for CLCA3P gene integrated from 9 sources:
(articles sorted by number of sources associating them with CLCA3P) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Molecular cloning and biochemical characterization of a truncated, secreted member of the human family of Ca2+-activated Cl- channels. (PubMed id 10095065)1, 2, 3 Gruber A.D. and Pauli B.U. (1999)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
- Molecular characteristics and functional diversity of CLCA family members. (PubMed id 11071307)1 Pauli B.U....Elble R.C. (2000)
- Clustering of the human CLCA gene family on the short arm of chromosome 1 (1p22-31). (PubMed id 10584316)1 Gruber A.D. and Pauli B.U. (1999)
- Talniflumate increases survival in a cystic fibrosis mouse model of distal intestinal obstructive syndrome. (PubMed id 16354791)9 Walker N.M....Clarke L.L. (2006)
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External Searches for CLCA3P gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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Genome Databases showing CLCA3P gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
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Other Databases showing CLCA3P gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing CLCA3P gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for CLCA3P | Pharmacogenomics, SNPs, Pathways |
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About This Section
| Patent Information for CLCA3P gene:
Search GeneIP for patents involving CLCA3P
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for CLCA3P gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
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|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat CLCA3P | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CLCA3P | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLCA3P | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CLCA3P | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLCA3P | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLCA3P |
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 | | | CLCA3P Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCA3P |
|  |  |  |  | | | | Search ThermoFisher Antibodies for CLCA3P |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat CLCA3P |
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