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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CLCA3P Gene

pseudogene   GIFtS: 41
GCID: GC01P087099

Chloride Channel Accessory 3, Pseudogene

(Previous names: chloride channel, calcium activated, family member 3, chloride...)
(Previous symbol: CLCA3)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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
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
hCLCA33

External Ids:    HGNC: 20171   Entrez Gene: 96292   Ensembl: ENSG000001539237   OMIM: 6043375   UniProtKB: Q9Y6N33   
ORGUL members:         
NONCODE14:n386575      

Export aliases for CLCA3P gene to outside databases

Previous GC identifers: GC01P086873 GC01P085210


(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 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, and is affiliated with the lncRNA class. Diseases associated with CLCA3P include intestinal obstruction, and cystic fibrosis. GO annotations related to this gene include calcium channel activity and transporter activity.

summary for CLCA3P Gene:
Chloride channels are a family of anion-selective channels involved in a diverse range of biological
processes including the regulation of the excitability of neurons, skeletal, cardiac and smooth muscle, cell
volume regulation, transepithelial salt transport, the acidification of intra- and extracellular
compartments. Ca2+-activated chloride channels (CaCCs) are widely expressed in both excitable and
non-excitable cells, are activated by intracellular Ca2+, and modulated by CaMKII and calcineurin.

Gene Wiki entry for CLCA3P (CLCA3) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  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

SwitchGear Promoter luciferase reporter plasmidCLCA3P promoter sequence
   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-p22

CLCA3P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLCA3P gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P087099:  view genomic region     (about GC identifiers)

Start:
87,099,956 bp from pter      End:
87,121,059 bp from pter
Size:
21,104 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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 as a pseudogene by HGNC. PubMed:10095065 reports that it is expressed and glycosylated in mammalian cells

Explore the universe of human proteins at neXtProt for CLCA3P: NX_Q9Y6N3

Explore proteomics data for CLCA3P at MOPED 

Post-translational modifications:

  • UniProtKB: N-glycosylated
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y6N3

  • CLCA3P Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CLCA3P Protein Expression

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space TAS10095065
    GO:0034707chloride channel complex IEA--

    CLCA3P for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR013642 Cl_channel_Ca

    Graphical View of Domain Structure for InterPro Entry Q9Y6N3

    ProtoNet protein and cluster: Q9Y6N3

    UniProtKB/Swiss-Prot: CLCA3_HUMAN, Q9Y6N3
    Similarity: Belongs to the CLCR family


    CLCA3P for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, 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, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005215transporter activity TAS10095065
    GO:0005244voltage-gated ion channel activity IEA--
    GO:0005254chloride channel activity IEA--
    GO:0005262calcium channel activity IEA--
         
    CLCA3P for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for CLCA3P:
     Lamellipodia cells 

    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section



    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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport TAS10095065

    CLCA3P for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Compounds for CLCA3P available from Tocris Bioscience    About this table
    CompoundAction CAS #
    DCPIB Selective blocker of VSAC/ICl, swell. Inhibits glucose-stimulated insulin release [82749-70-0]
    Chromanol 293BIKs blocker. Also blocks ICFTR[163163-23-3]
    NPPBInhibits calcium-sensitive chloride currents[107254-86-4]
    LonidamineMitochondrial hexokinase inhibitor[50264-69-2]
    CFTRinh 172 Voltage-independent, selective CFTR chloride channel blocker [307510-92-5]

    Search CenterWatch for drugs/clinical trials and news about CLCA3P

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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_024604
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000284054 ENST00000490028 ENST00000466454(uc010osh.2)
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    Inhib. RNA
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    Additional mRNA sequence: NR_024604.1 

    2 DOTS entries:

    DT.92035017  DT.91907582 

    6 AceView cDNA sequences:

    BE217974 BE738113 AF043976 NM_004921 BE738683 BU685983 

    GeneLoc Exon Structure


    (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 <intensity>2/3
    CGAP TAG: --
    CLCA3P Expression
    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, Q9Y6N3
    Tissue specificity: Expressed in the lung, trachea, spleen, thymus and mammary gland

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCA3P

    (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
      --

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CLCA3P gene
    2 SIMAP similar genes for CLCA3P using alignment to 1 protein entry:     CLCA3_HUMAN:
    CLCA2    CLCA4

    CLCA3P for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    10/452 SNPs in CLCA3P are shown (see all 452)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs608348991,2
    C--87098052(+) TAACCC/TGACCT 1 -- us2k10--------
    rs1864749161,2
    --87098073(+) CATTAA/TCATTG 1 -- us2k10--------
    rs1913604021,2
    C--87098093(+) TTTCAA/GCTTTG 1 -- us2k10--------
    rs66765191,2
    C,F,A,H--87098109(+) tatgaC/Aaatta 1 -- us2k19Minor allele frequency- A:0.15NS NA CSA 1067
    rs618004451,2
    C--87098187(+) GTTGGC/TCTGCC 1 -- us2k10--------
    rs5310591,2
    C,F--87098262(+) ctcccC/Tgtcac 1 -- us2k12Minor allele frequency- T:0.15NA MN 186
    rs1811507001,2
    --87098345(+) TTCTTC/TTTATT 1 -- us2k10--------
    rs1465531141,2
    --87098376(+) TTCTCA/GCCTCA 1 -- us2k10--------
    rs1400381861,2
    C--87098436(+) AAATCA/GGCTAC 1 -- us2k10--------
    rs288487811,2
    C--87098463(+) ATCACA/GTAGTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CLCA3P (87099956 - 87121059 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CLCA3P:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2714407CNV Deletion23290073

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 604337    OMIM disorders: --

    2 diseases for CLCA3P:    About MalaCards
    intestinal obstruction    cystic fibrosis


    CLCA3P for disorders           About GeneDecksing


    Export disorders for CLCA3P gene to outside databases

    (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

    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

    1. 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)
    2. 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)
    3. Molecular characteristics and functional diversity of CLCA family members. (PubMed id 11071307)1 Pauli B.U....Elble R.C. (2000)
    4. 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)
    5. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 9629 HGNC: 2017 AceView: CLCA3 Ensembl:ENSG00000153923 euGenes: HUgn9629
    ECgene: CLCA3P H-InvDB: CLCA3P

    (According to HUGE)
    About This Section
      --

    (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
    NameDescription
    PharmGKB entry for CLCA3P Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    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



    (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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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