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Aliases for CLNS1A Gene

Aliases for CLNS1A Gene

  • Chloride Nucleotide-Sensitive Channel 1A 2 3 5
  • Chloride Conductance Regulatory Protein ICln 3 4
  • Chloride Channel, Nucleotide Sensitive 1A 3 4
  • Chloride Ion Current Inducer Protein 3 4
  • Methylosome Subunit PICln 2 3
  • Reticulocyte PICln 3 4
  • I(Cln) 3 4
  • ICln 3 4
  • CLCI 3 4
  • Chloride Channel, Nucleotide-Sensitive, 1A 2
  • Chloride Channel Regulatory Protein 3
  • Reticulocyte Protein ICln 3
  • CLNS1B 3

External Ids for CLNS1A Gene

Previous HGNC Symbols for CLNS1A Gene

  • CLCI

Previous GeneCards Identifiers for CLNS1A Gene

  • GC11M079654
  • GC11M078866
  • GC11M077053
  • GC11M077004
  • GC11M077327
  • GC11M073625
  • GC11M077225

Summaries for CLNS1A Gene

Entrez Gene Summary for CLNS1A Gene

  • 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]

GeneCards Summary for CLNS1A Gene

CLNS1A (Chloride Nucleotide-Sensitive Channel 1A) is a Protein Coding gene. Among its related pathways are Transport of the SLBP independent Mature mRNA and Hepatic ABC Transporters. GO annotations related to this gene include poly(A) RNA binding and protein heterodimerization activity.

UniProtKB/Swiss-Prot for CLNS1A Gene

  • Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway.

Gene Wiki entry for CLNS1A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLNS1A Gene

Genomics for CLNS1A Gene

Regulatory Elements for CLNS1A Gene

Enhancers for CLNS1A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F077588 1.4 Ensembl ENCODE 11.9 +47.4 47415 4.0 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF766 ZNF207 AAMDC CLNS1A INTS4 GDPD4 AQP11 GC11M077568
GH11F077630 1.2 Ensembl ENCODE 12.8 +6.8 6841 1.6 ELF3 PKNOX1 MLX ARID4B DMAP1 THRB RARA YY1 CREM MIXL1 CLNS1A INTS4 AQP11 GC11P077629
GH11F077601 1 Ensembl ENCODE 12.5 +35.0 35030 2.7 GTF2F1 TBP JUN MAX BACH1 SIN3A RFX5 ZNF316 POLR2A FOS AAMDC CLNS1A MYO7A AQP11 GC11M077568 GC11P077625
GH11F077557 1.1 Ensembl ENCODE 4.7 +77.9 77938 4.7 RAD21 GATA2 ZNF366 RCOR1 FOS SMARCC1 CEBPB USF2 MAFF SMARCA4 AQP11 MYO7A AAMDC INTS4 CLNS1A GC11M077551 GC11M077567
GH11F076652 1.1 Ensembl ENCODE 4.7 +982.4 982399 5.0 BCOR ATF1 TAL1 ZMYM3 ZNF316 ZFHX2 NCOR1 FOS NFE2 TRIM24 LOC107984360 ENSG00000255363 ENSG00000254810 CLNS1A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLNS1A on UCSC Golden Path with GeneCards custom track

Promoters for CLNS1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000320558 206 2001 PKNOX1 ARNT CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2

Genomic Location for CLNS1A Gene

Chromosome:
11
Start:
77,514,936 bp from pter
End:
77,637,806 bp from pter
Size:
122,871 bases
Orientation:
Minus strand

Genomic View for CLNS1A Gene

Genes around CLNS1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLNS1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLNS1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLNS1A Gene

Proteins for CLNS1A Gene

  • Protein details for CLNS1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P54105-ICLN_HUMAN
    Recommended name:
    Methylosome subunit pICln
    Protein Accession:
    P54105
    Secondary Accessions:
    • B2RCS9
    • Q0VDK6
    • Q9NRD2
    • Q9NRD3

    Protein attributes for CLNS1A Gene

    Size:
    237 amino acids
    Molecular mass:
    26215 Da
    Quaternary structure:
    • Component of the methylosome, a 20S complex containing at least CLNS1A/pICln, PRMT5/SKB1 and WDR77/MEP50; may mediate SNRPD1 and SNRPD3 methylation. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP. Interacts with LSM10 and LSM11.

neXtProt entry for CLNS1A Gene

Post-translational modifications for CLNS1A Gene

  • Ubiquitination at Lys 5 and Lys 30
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for CLNS1A

No data available for DME Specific Peptides for CLNS1A Gene

Domains & Families for CLNS1A Gene

Protein Domains for CLNS1A Gene

Suggested Antigen Peptide Sequences for CLNS1A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P54105

UniProtKB/Swiss-Prot:

ICLN_HUMAN :
  • Belongs to the pICln (TC 1.A.47) family.
Family:
  • Belongs to the pICln (TC 1.A.47) family.
genes like me logo Genes that share domains with CLNS1A: view

No data available for Gene Families for CLNS1A Gene

Function for CLNS1A Gene

Molecular function for CLNS1A Gene

GENATLAS Biochemistry:
chloride channel nucleotide sensitive,swelling-dependent outwardly rectifying,ICLN type 1A,26kDa,nucleotide sensitive expressed in ocular ciliary epithelium,mouse Icln ortholog
UniProtKB/Swiss-Prot Function:
Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway.

Gene Ontology (GO) - Molecular Function for CLNS1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16087681
GO:0044822 poly(A) RNA binding IDA 22658674
GO:0046982 protein heterodimerization activity IDA 18495660
genes like me logo Genes that share ontologies with CLNS1A: view
genes like me logo Genes that share phenotypes with CLNS1A: view

Animal Models for CLNS1A Gene

MGI Knock Outs for CLNS1A:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLNS1A Gene

Localization for CLNS1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLNS1A Gene

Cytoplasm, cytosol. Nucleus. Cytoplasm, cytoskeleton. Note=A small fraction is also associated with the cytoskeleton.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLNS1A gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
cytoskeleton 4
extracellular 2

Gene Ontology (GO) - Cellular Components for CLNS1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with CLNS1A: view

Pathways & Interactions for CLNS1A Gene

genes like me logo Genes that share pathways with CLNS1A: view

Pathways by source for CLNS1A Gene

Gene Ontology (GO) - Biological Process for CLNS1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000387 spliceosomal snRNP assembly TAS --
GO:0006821 chloride transport IEA --
GO:0006884 cell volume homeostasis IEA --
genes like me logo Genes that share ontologies with CLNS1A: view

No data available for SIGNOR curated interactions for CLNS1A Gene

Drugs & Compounds for CLNS1A Gene

(1) Drugs for CLNS1A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for CLNS1A Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
16887-00-6
genes like me logo Genes that share compounds with CLNS1A: view

Transcripts for CLNS1A Gene

Unigene Clusters for CLNS1A Gene

Chloride channel, nucleotide-sensitive, 1A:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLNS1A Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c · 8d · 8e
SP1: -
SP2: - -
SP3: - -
SP4: - - - -
SP5: - -
SP6: - - - -
SP7:
SP8:
SP9: - - - -

Relevant External Links for CLNS1A Gene

GeneLoc Exon Structure for
CLNS1A
ECgene alternative splicing isoforms for
CLNS1A

Expression for CLNS1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLNS1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLNS1A Gene

This gene is overexpressed in Lymph node (6.7) and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLNS1A Gene



Protein tissue co-expression partners for CLNS1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLNS1A Gene:

CLNS1A

SOURCE GeneReport for Unigene cluster for CLNS1A Gene:

Hs.430733
genes like me logo Genes that share expression patterns with CLNS1A: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CLNS1A Gene

Orthologs for CLNS1A Gene

This gene was present in the common ancestor of animals.

Orthologs for CLNS1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLNS1A 34 35
  • 99.86 (n)
cow
(Bos Taurus)
Mammalia CLNS1A 34 35
  • 93.11 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 93 (a)
OneToMany
-- 35
  • 81 (a)
OneToMany
dog
(Canis familiaris)
Mammalia CLNS1A 34 35
  • 91.21 (n)
-- 35
  • 91 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Clns1a 34 16 35
  • 88.28 (n)
rat
(Rattus norvegicus)
Mammalia Clns1a 34
  • 88.28 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLNS1A 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLNS1A 34 35
  • 75.32 (n)
lizard
(Anolis carolinensis)
Reptilia CLNS1A 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clns1a 34
  • 71.49 (n)
Str.2882 34
African clawed frog
(Xenopus laevis)
Amphibia ICLN 34
zebrafish
(Danio rerio)
Actinopterygii icln 34 35
  • 67.09 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1213 34
fruit fly
(Drosophila melanogaster)
Insecta icln 35
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea icln-1 35
  • 29 (a)
OneToOne
Species where no ortholog for CLNS1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLNS1A Gene

ENSEMBL:
Gene Tree for CLNS1A (if available)
TreeFam:
Gene Tree for CLNS1A (if available)

Paralogs for CLNS1A Gene

Pseudogenes.org Pseudogenes for CLNS1A Gene

genes like me logo Genes that share paralogs with CLNS1A: view

No data available for Paralogs for CLNS1A Gene

Variants for CLNS1A Gene

Sequence variations from dbSNP and Humsavar for CLNS1A Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs10466710 -- 77,639,292(+) tttcc(A/G)tcttg upstream-variant-2KB
rs10538015 -- 77,637,339(+) aaaag(A/G)aaaaa intron-variant
rs1053907 -- 77,637,039(+) CCTCT(C/T)CTTAC intron-variant
rs111248527 -- 77,635,439(+) CTCCG(A/C)CTCTC intron-variant
rs111256822 -- 77,637,002(+) TGCAT(A/G)TGACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLNS1A Gene

Variant ID Type Subtype PubMed ID
dgv1234n100 CNV gain 25217958
esv3626888 CNV loss 21293372
nsv468641 CNV gain 19166990
nsv555452 CNV gain 21841781

Variation tolerance for CLNS1A Gene

Residual Variation Intolerance Score: 51.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.79% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLNS1A Gene

Human Gene Mutation Database (HGMD)
CLNS1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLNS1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLNS1A Gene

Disorders for CLNS1A Gene

Relevant External Links for CLNS1A

Genetic Association Database (GAD)
CLNS1A
Human Genome Epidemiology (HuGE) Navigator
CLNS1A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLNS1A

No disorders were found for CLNS1A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLNS1A Gene

Publications for CLNS1A Gene

  1. Modulation of volume regulated anion current by I(Cln). (PMID: 10825435) Hubert M.D. … Garber S.S. (Biochim. Biophys. Acta 2000) 3 4 22 64
  2. The ubiquitously expressed pICln protein forms homomeric complexes in vitro. (PMID: 8579598) Buyse G. … Eggermont J. (Biochem. Biophys. Res. Commun. 1996) 3 4 22 64
  3. Chromosomal localization of the genes (CLNS1A and CLNS1B) coding for the swelling-dependent chloride channel ICln. (PMID: 8975725) Nagl U.O. … Paulmichl M. (Genomics 1996) 2 3 22 64
  4. Molecular cloning of the human volume-sensitive chloride conductance regulatory protein, pICln, from ocular ciliary epithelium. (PMID: 7887970) Anquita J. … Coca-Prados M. (Biochem. Biophys. Res. Commun. 1995) 2 3 4 64
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64

Products for CLNS1A Gene

Sources for CLNS1A Gene

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