Human Gene CLNS1A (ENST00000525428.6_10) from GENCODE V47lift37
  Description: chloride nucleotide-sensitive channel 1A, transcript variant 1 (from RefSeq NM_001293.3)
Gencode Transcript: ENST00000525428.6_10
Gencode Gene: ENSG00000074201.9_19
Transcript (Including UTRs)
   Position: hg19 chr11:77,325,575-77,348,839 Size: 23,265 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr11:77,330,673-77,348,759 Size: 18,087 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:77,325,575-77,348,839)mRNA (may differ from genome)Protein (237 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ICLN_HUMAN
DESCRIPTION: RecName: Full=Methylosome subunit pICln; AltName: Full=Chloride channel, nucleotide sensitive 1A; AltName: Full=Chloride conductance regulatory protein ICln; Short=I(Cln); AltName: Full=Chloride ion current inducer protein; Short=ClCI; AltName: Full=Reticulocyte pICln;
FUNCTION: The interaction with Sm proteins inhibits their assembly on U RNA and interferes with snRNP biogenesis. Inhibits the binding of survival motor neuron protein (SMN) to Sm proteins. May participate in cellular volume control by activation of a swelling-induced chloride conductance pathway.
SUBUNIT: Homooligomer. Component of the methylosome, a 20S complex containing SKB1. Interacts with Sm proteins. Interacts with LSM10, LSM11 and SNRPB.
INTERACTION: P62314:SNRPD1; NbExp=5; IntAct=EBI-724693, EBI-372177; P62318:SNRPD3; NbExp=5; IntAct=EBI-724693, EBI-372789;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, cytoskeleton. Note=A small fraction is also associated with the cytoskeleton.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the pICln (TC 1.A.47) family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.09 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 676.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.5080-0.344 Picture PostScript Text
3' UTR -549.602188-0.251 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003521 - ICln_channel

Pfam Domains:
PF03517 - Regulator of volume decrease after cellular swelling

ModBase Predicted Comparative 3D Structure on P54105
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000387 spliceosomal snRNP assembly
GO:0006821 chloride transport
GO:0006884 cell volume homeostasis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0034709 methylosome
GO:0034715 pICln-Sm protein complex


-  Descriptions from all associated GenBank mRNAs
  U17899 - Human chloride channel regulatory protein mRNA, complete cds.
U53454 - Human chloride ion current inducer protein (CLCI) mRNA, complete cds.
AF116664 - Homo sapiens PRO1478 mRNA, complete cds.
X91788 - H.sapiens mRNA for Icln protein.
AF005422 - Homo sapiens reticulocyte pICln mRNA, complete cds.
BC119634 - Homo sapiens chloride channel, nucleotide-sensitive, 1A, mRNA (cDNA clone MGC:149487 IMAGE:40115653), complete cds.
BC119635 - Homo sapiens chloride channel, nucleotide-sensitive, 1A, mRNA (cDNA clone MGC:149488 IMAGE:40115655), complete cds.
AF026003 - Homo sapiens chloride ion current inducer protein (ICln) mRNA, complete cds.
AK315259 - Homo sapiens cDNA, FLJ96264, Homo sapiens chloride channel, nucleotide-sensitive, 1A (CLNS1A),mRNA.
BT019907 - Homo sapiens chloride channel, nucleotide-sensitive, 1A mRNA, complete cds.
AB590787 - Synthetic construct DNA, clone: pFN21AE1729, Homo sapiens CLNS1A gene for chloride channel, nucleotide-sensitive, 1A, without stop codon, in Flexi system.
JD085848 - Sequence 66872 from Patent EP1572962.
JD223896 - Sequence 204920 from Patent EP1572962.
JD408942 - Sequence 389966 from Patent EP1572962.
JD534310 - Sequence 515334 from Patent EP1572962.
JD133635 - Sequence 114659 from Patent EP1572962.
JD193467 - Sequence 174491 from Patent EP1572962.
JD230634 - Sequence 211658 from Patent EP1572962.
JD222120 - Sequence 203144 from Patent EP1572962.
JD021869 - Sequence 2893 from Patent EP1572962.
JD031378 - Sequence 12402 from Patent EP1572962.
JD271246 - Sequence 252270 from Patent EP1572962.
JD463990 - Sequence 445014 from Patent EP1572962.
JD231064 - Sequence 212088 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P54105 (Reactome details) participates in the following event(s):

R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes
R-HSA-191859 snRNP Assembly
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2RCS9, CLCI, ENST00000525428.1, ENST00000525428.2, ENST00000525428.3, ENST00000525428.4, ENST00000525428.5, ICLN, ICLN_HUMAN, NM_001293, P54105, Q0VDK6, Q9NRD2, Q9NRD3, uc324aow.1, uc324aow.2
UCSC ID: ENST00000525428.6_10
RefSeq Accession: NM_001293.3
Protein: P54105 (aka ICLN_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.