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    CLNS1A chloride nucleotide-sensitive channel 1A [ Homo sapiens (human) ]

    Gene ID: 1207, updated on 3-Nov-2024

    Summary

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    Official Symbol
    CLNS1Aprovided by HGNC
    Official Full Name
    chloride nucleotide-sensitive channel 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:2080
    See related
    Ensembl:ENSG00000074201 MIM:602158; AllianceGenome:HGNC:2080
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CLCI; ICln; CLNS1B
    Summary
    This gene encodes a protein that functions in multiple regulatory pathways. The encoded protein complexes with numerous cytosolic proteins and performs diverse functions including regulation of small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization. The protein is also found associated with the plasma membrane where it functions as a chloride current regulator. Pseudogenes of this gene are found on chromosomes 1, 4 and 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]
    Expression
    Ubiquitous expression in adrenal (RPKM 36.6), brain (RPKM 32.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLNS1A in Genome Data Viewer
    Location:
    11q14.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (77614530..77637794, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (77547583..77570850, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (77325575..77348839, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak1361 silencer Neighboring gene long intergenic non-protein coding RNA 3030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3800 Neighboring gene MPRA-validated peak1362 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr11:77316282-77316821 Neighboring gene aquaporin 11 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:77348567-77349086 Neighboring gene uncharacterized LOC107984369 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4537 Neighboring gene MPRA-validated peak1363 silencer Neighboring gene remodeling and spacing factor 1 Neighboring gene ferritin heavy chain 1 pseudogene 16

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. O-GlcNAcylated LARP1 positively regulated by circCLNS1A facilitates hepatoblastoma progression through DKK4/beta-catenin signalling.
      Title: O-GlcNAcylated LARP1 positively regulated by circCLNS1A facilitates hepatoblastoma progression through DKK4/β-catenin signalling.
    2. Protein Arginine Methyltransferase 5 Promotes pICln-Dependent Androgen Receptor Transcription in Castration-Resistant Prostate Cancer.
      Title: Protein Arginine Methyltransferase 5 Promotes pICln-Dependent Androgen Receptor Transcription in Castration-Resistant Prostate Cancer.
    3. the S. pombe ICln protein is required for optimal production of the spliceosomal snRNPs and for efficient splicing in vivo
      Title: Characterization and in vivo functional analysis of the Schizosaccharomyces pombe ICLN gene.
    4. functional interaction between ICln and HSPC038
      Title: The molecular and functional interaction between ICln and HSPC038 proteins modulates the regulation of cell volume.
    5. RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity.
      Title: RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. ICln interacts with integrin alphaIIbbeta3 and regulates platelet activation.
      Title: ICln, a novel integrin alphaIIbbeta3-associated protein, functionally regulates platelet activation.
    8. revealed an increase of ICln in the mesothelioma cell membrane under hypotonic conditions, an event possibly related to the activation of Cl(-) channels
      Title: Volume-regulated Cl- channels in human pleural mesothelioma cells.
    9. Data show that ICln159, a truncated ICln mutant, belongs to the pleckstrin homology (PH) domain family of proteins and interacts with LSm4, a protein involved in splicing and mRNA degradation.
      Title: ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4.
    10. Lsm10 and Lsm11, which replace the Sm proteins D1 and D2 in the histone RNA processing U7 snRNPs, associate with pICln in vitro and in vivo without receiving sDMA modifications and with PRMT5 and SMN complexes
      Title: Toward an assembly line for U7 snRNPs: interactions of U7-specific Lsm proteins with PRMT5 and SMN complexes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of chloride channel, nucleotide-sensitive, 1A (CLNS1A) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell volume homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chloride transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA cis splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spliceosomal snRNP assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spliceosomal snRNP assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in spliceosomal snRNP assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of methylosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of pICln-Sm protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of pICln-Sm protein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    methylosome subunit pICln
    Names
    chloride channel regulatory protein
    chloride channel, nucleotide sensitive 1A
    chloride conductance regulatory protein ICln
    chloride ion current inducer protein
    i(Cln)
    reticulocyte pICln
    reticulocyte protein ICln

    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.

    mRNA and Protein(s)

    1. NM_001293.3 → NP_001284.1  methylosome subunit pICln isoform a

      See identical proteins and their annotated locations for NP_001284.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AA757599, AF005422, AP000609, DA004269
      Consensus CDS
      CCDS8252.1
      UniProtKB/Swiss-Prot
      B2RCS9, P54105, Q0VDK6, Q9NRD2, Q9NRD3
      Related
      ENSP00000433919.1, ENST00000525428.6
      Conserved Domains (1) summary
      pfam03517
      Location:35 → 137
      Voldacs; Regulator of volume decrease after cellular swelling

    2. NM_001311199.2 → NP_001298128.1  methylosome subunit pICln isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AP000609, BQ643786, DA004269
      Consensus CDS
      CCDS8252.1
      UniProtKB/Swiss-Prot
      B2RCS9, P54105, Q0VDK6, Q9NRD2, Q9NRD3
      Related
      ENSP00000434311.1, ENST00000528364.1
      Conserved Domains (1) summary
      pfam03517
      Location:35 → 137
      Voldacs; Regulator of volume decrease after cellular swelling

    3. NM_001311200.2 → NP_001298129.1  methylosome subunit pICln isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AA757599, AL530926, AP000609, DA004269, U53454
      Consensus CDS
      CCDS81601.1
      UniProtKB/TrEMBL
      J3KN38
      Related
      ENSP00000263309.3, ENST00000263309.7
      Conserved Domains (1) summary
      pfam03517
      Location:35 → 103
      Voldacs; Regulator of volume decrease after cellular swelling

    4. NM_001311201.2 → NP_001298130.1  methylosome subunit pICln isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AA757599, AP000609, BU538016, DA004269, U53454
      Consensus CDS
      CCDS81602.1
      UniProtKB/TrEMBL
      E9PJF4
      Related
      ENSP00000433741.1, ENST00000525064.5
      Conserved Domains (1) summary
      pfam03517
      Location:35 → 137
      Voldacs; Regulator of volume decrease after cellular swelling

    5. NM_001311202.2 → NP_001298131.1  methylosome subunit pICln isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AA757599, AP000609, BU169662, U53454
      Consensus CDS
      CCDS81600.1
      UniProtKB/TrEMBL
      E9PMI6
      Related
      ENSP00000434963.1, ENST00000532069.5
      Conserved Domains (1) summary
      cl17171
      Location:35 → 84
      PH-like; Pleckstrin homology-like domain

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      77614530..77637794 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      77547583..77570850 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P54105.1 GenPept UniProtKB/Swiss-Prot:P54105

    Gene LinkOut

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

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