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

Gene ID: 1207, updated on 9-Dec-2018

Summary

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
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

Genomic context

See CLNS1A in Genome Data Viewer
Location:
11q14.1
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (77616151..77637806, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (77327196..77348851, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC646029 Neighboring gene aquaporin 11 Neighboring gene uncharacterized LOC107984369 Neighboring gene remodeling and spacing factor 1 Neighboring gene ferritin heavy chain 1 pseudogene 16

Genomic regions, transcripts, and products

Expression

  • 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

Related articles in PubMed

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Metabolism of non-coding RNA, organism-specific biosystem (from REACTOME)
    Metabolism of non-coding RNA, organism-specific biosystemThe term non-coding is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. There is considerable evidence tha...
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • snRNP Assembly, organism-specific biosystem (from REACTOME)
    snRNP Assembly, organism-specific biosystemSmall nuclear ribonucleoproteins (snRNPs) are crucial for pre-mRNA processing to mRNAs. Each snRNP contains a small nuclear RNA (snRNA) and an extremely stable core of seven Sm proteins. The U6 snRNA...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cell volume homeostasis IEA
Inferred from Electronic Annotation
more info
 
chloride transport IEA
Inferred from Electronic Annotation
more info
 
spliceosomal snRNP assembly IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
methylosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
pICln-Sm protein complex IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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_001293.2NP_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, DA004269
    Consensus CDS
    CCDS8252.1
    UniProtKB/Swiss-Prot
    P54105
    Related
    ENSP00000433919.1, ENST00000525428.5
    Conserved Domains (1) summary
    pfam03517
    Location:35137
    Voldacs; Regulator of volume decrease after cellular swelling
  2. NM_001311199.1NP_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
    P54105
    Related
    ENSP00000434311.1, ENST00000528364.1
    Conserved Domains (1) summary
    pfam03517
    Location:35137
    Voldacs; Regulator of volume decrease after cellular swelling
  3. NM_001311200.1NP_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, DA004269, U53454
    Consensus CDS
    CCDS81601.1
    UniProtKB/Swiss-Prot
    P54105
    UniProtKB/TrEMBL
    J3KN38
    Related
    ENSP00000263309.3, ENST00000263309.7
    Conserved Domains (1) summary
    pfam03517
    Location:35103
    Voldacs; Regulator of volume decrease after cellular swelling
  4. NM_001311201.1NP_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, BU538016, DA004269, U53454
    Consensus CDS
    CCDS81602.1
    UniProtKB/Swiss-Prot
    P54105
    UniProtKB/TrEMBL
    E9PJF4
    Related
    ENSP00000433741.1, ENST00000525064.5
    Conserved Domains (1) summary
    pfam03517
    Location:35137
    Voldacs; Regulator of volume decrease after cellular swelling
  5. NM_001311202.1NP_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, BU169662, DA004269, U53454
    Consensus CDS
    CCDS81600.1
    UniProtKB/Swiss-Prot
    P54105
    UniProtKB/TrEMBL
    E9PMI6
    Related
    ENSP00000434963.1, ENST00000532069.5
    Conserved Domains (1) summary
    cl17171
    Location:3585
    PH-like; Pleckstrin homology-like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    77616151..77637806 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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