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    CLCA3P chloride channel accessory 3, pseudogene [ Homo sapiens (human) ]

    Gene ID: 9629, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CLCA3Pprovided by HGNC
    Official Full Name
    chloride channel accessory 3, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:2017
    See related
    Ensembl:ENSG00000291014 MIM:604337; AllianceGenome:HGNC:2017
    Gene type
    pseudo
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CLCA3
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See CLCA3P in Genome Data Viewer
    Location:
    1p22.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (86634276..86655376)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (86474301..86495405)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (87099959..87121059)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904210 Neighboring gene uncharacterized LOC105378826 Neighboring gene cell division cycle associated 4 pseudogene 2 Neighboring gene chloride channel accessory 4 Neighboring gene CLCA4 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:87075539-87075711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1278 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:87113290-87114489 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:87149909-87150556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1279 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:87170097-87170598 Neighboring gene SH3 domain containing GRB2 like, endophilin B1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:87221223-87221723 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:87239295-87240494 Neighboring gene ribosomal protein L17 pseudogene 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning and biochemical characterization of a truncated, secreted member of the human family of Ca2+-activated Cl- channels. Gruber AD, et al. Biochim Biophys Acta, 1999 Mar 19. PMID 10095065
    2. Clustering of the human CLCA gene family on the short arm of chromosome 1 (1p22-31). Gruber AD, et al. Genome, 1999 Oct. PMID 10584316
    3. Molecular characteristics and functional diversity of CLCA family members. Pauli BU, et al. Clin Exp Pharmacol Physiol, 2000 Nov. PMID 11071307
    4. A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells. Xie L, et al. PLoS Genet, 2012. PMID 23284306, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • chloride channel regulator 3 pseudogene
    • chloride channel, calcium activated, family member 3

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chloride channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metalloendopeptidase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    part_of chloride channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular space TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    RNA

    1. NR_024604.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AF043976, AL356270
      Related
      ENST00000466454.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      86634276..86655376
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      86474301..86495405
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_004921.2: Suppressed sequence

      Description
      NM_004921.2: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6N3.1 GenPept UniProtKB/Swiss-Prot:Q9Y6N3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials