Human Gene CLIC1 (ENST00000375784.8_8) from GENCODE V47lift37
  Description: chloride intracellular channel 1, transcript variant 2 (from RefSeq NM_001288.6)
Gencode Transcript: ENST00000375784.8_8
Gencode Gene: ENSG00000213719.8_12
Transcript (Including UTRs)
   Position: hg19 chr6:31,698,376-31,704,307 Size: 5,932 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr6:31,698,619-31,704,077 Size: 5,459 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:31,698,376-31,704,307)mRNA (may differ from genome)Protein (241 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q5SRT3_HUMAN
DESCRIPTION: SubName: Full=Chloride intracellular channel 1; SubName: Full=Chloride intracellular channel 1, isoform CRA_a; SubName: Full=cDNA, FLJ94671, Homo sapiens chloride intracellular channel 1 (CLIC1), mRNA;
SIMILARITY: Contains 1 GST C-terminal domain.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CLIC1
Diseases sorted by gene-association score: blackwater fever (2), hyperornithinemia-hyperammonemia-homocitrullinemia syndrome (1), penicilliosis (1), fructose-1,6-bisphosphatase deficiency (1)

-  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: 273.87 RPKM in Whole Blood
Total median expression: 3749.37 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 -104.30230-0.453 Picture PostScript Text
3' UTR -89.20243-0.367 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
IPR010987 - Glutathione-S-Trfase_C-like
IPR017933 - Glutathione_S_Trfase/Cl_chnl_C
IPR002946 - Int_Cl_channel
IPR012336 - Thioredoxin-like_fold

Pfam Domains:
PF00043 - Glutathione S-transferase, C-terminal domain
PF13409 - Glutathione S-transferase, N-terminal domain
PF13410 - Glutathione S-transferase, C-terminal domain
PF13417 - Glutathione S-transferase, N-terminal domain

SCOP Domains:
47616 - GST C-terminal domain-like
52833 - Thioredoxin-like

ModBase Predicted Comparative 3D Structure on Q5SRT3
FrontTopSide
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    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005244 voltage-gated ion channel activity
GO:0005254 chloride channel activity

Biological Process:
GO:0006811 ion transport
GO:0006821 chloride transport
GO:0034220 ion transmembrane transport
GO:0034765 regulation of ion transmembrane transport
GO:0045669 positive regulation of osteoblast differentiation
GO:0051726 regulation of cell cycle
GO:0051881 regulation of mitochondrial membrane potential
GO:1902476 chloride transmembrane transport

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0016020 membrane
GO:0034707 chloride channel complex


-  Descriptions from all associated GenBank mRNAs
  BC064527 - Homo sapiens chloride intracellular channel 1, mRNA (cDNA clone MGC:74817 IMAGE:5585323), complete cds.
X87689 - H.sapiens mRNA for putative p64 CLCP protein.
AF034607 - Homo sapiens chloride channel ABP mRNA, complete cds.
BC095469 - Homo sapiens chloride intracellular channel 1, mRNA (cDNA clone MGC:111374 IMAGE:30557606), complete cds.
U93205 - Homo sapiens nuclear chloride ion channel protein (NCC27) mRNA, complete cds.
AK129773 - Homo sapiens cDNA FLJ26262 fis, clone DMC05261, highly similar to Chloride intracellular channel protein 1.
AF109197 - Homo sapiens nuclear chloride channel (NCC27) mRNA, complete cds.
AK223379 - Homo sapiens mRNA for chloride intracellular channel 1 variant, clone: FCC106B04.
JD223787 - Sequence 204811 from Patent EP1572962.
JD279390 - Sequence 260414 from Patent EP1572962.
JD376176 - Sequence 357200 from Patent EP1572962.
JD039017 - Sequence 20041 from Patent EP1572962.
JD246216 - Sequence 227240 from Patent EP1572962.
JD075774 - Sequence 56798 from Patent EP1572962.
AK314014 - Homo sapiens cDNA, FLJ94671, Homo sapiens chloride intracellular channel 1 (CLIC1), mRNA.
KJ890930 - Synthetic construct Homo sapiens clone ccsbBroadEn_00324 CLIC1 gene, encodes complete protein.
CU687892 - Synthetic construct Homo sapiens gateway clone IMAGE:100021589 5' read CLIC1 mRNA.
AB528714 - Synthetic construct DNA, clone: pF1KB6966, Homo sapiens CLIC1 gene for chloride intracellular channel 1, without stop codon, in Flexi system.
CR542071 - Homo sapiens full open reading frame cDNA clone RZPDo834G0736D for gene CLIC1, chloride intracellular channel 1; complete cds, without stopcodon.
JD228086 - Sequence 209110 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CLIC1 , ENST00000375784.1, ENST00000375784.2, ENST00000375784.3, ENST00000375784.4, ENST00000375784.5, ENST00000375784.6, ENST00000375784.7, hCG_2005611 , NM_001288, Q5SRT3, Q5SRT3_HUMAN, uc318mmz.1, uc318mmz.2
UCSC ID: ENST00000375784.8_8
RefSeq Accession: NM_001288.6
Protein: Q5SRT3

-  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.