Human Gene CLIC2 (ENST00000369449.7_7) from GENCODE V47lift37
  Description: chloride intracellular channel 2 (from RefSeq NM_001289.6)
Gencode Transcript: ENST00000369449.7_7
Gencode Gene: ENSG00000155962.13_10
Transcript (Including UTRs)
   Position: hg19 chrX:154,505,500-154,563,923 Size: 58,424 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chrX:154,507,192-154,563,736 Size: 56,545 Coding Exon Count: 6 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:154,505,500-154,563,923)mRNA (may differ from genome)Protein (247 aa)
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-  Comments and Description Text from UniProtKB
  ID: CLIC2_HUMAN
DESCRIPTION: RecName: Full=Chloride intracellular channel protein 2; AltName: Full=XAP121;
FUNCTION: Can insert into membranes and form chloride ion channels. Channel activity depends on the pH. Membrane insertion seems to be redox-regulated and may occur only under oxydizing conditions. Modulates the activity of RYR2 and inhibits calcium influx.
SUBUNIT: Monomer. Interacts with TRAPPC2 and RYR2.
SUBCELLULAR LOCATION: Cytoplasm. Membrane; Single-pass membrane protein (Probable). Note=Exists both as soluble cytoplasmic protein and as membrane protein with probably a single transmembrane domain.
TISSUE SPECIFICITY: Expressed in adult and fetal brain, heart, skeletal muscle, liver, lung, and spleen. Detected in adult stomach and testis. Expressed in fetal thymus and kidney.
DOMAIN: Members of this family may change from a globular, soluble state to a state where the N-terminal domain is inserted into the membrane and functions as chloride channel. A conformation change of the N-terminal domain is thought to expose hydrophobic surfaces that trigger membrane insertion.
DISEASE: Note=Defects in CLIC2 are a cause of a mental retardation with cardiopathy and seizures. Cardiac features include atrial fibrillation, cardiomegaly, and congestive heart failure.
SIMILARITY: Belongs to the chloride channel CLIC family.
SIMILARITY: Contains 1 GST C-terminal domain.
SEQUENCE CAUTION: Sequence=CAA73228.1; Type=Frameshift; Positions=244;

-  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: CLIC2
Diseases sorted by gene-association score: mental retardation, x-linked, syndromic 32* (1730), patau syndrome (5)
* = Manually curated disease association

-  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: 20.87 RPKM in Spleen
Total median expression: 257.82 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 -50.20187-0.268 Picture PostScript Text
3' UTR -349.001692-0.206 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:
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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2PER - X-ray MuPIT 2R4V - X-ray MuPIT 2R5G - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O15247
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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:0004602 glutathione peroxidase activity
GO:0005244 voltage-gated ion channel activity
GO:0005254 chloride channel activity
GO:0005515 protein binding
GO:0004364 glutathione transferase activity

Biological Process:
GO:0006811 ion transport
GO:0006821 chloride transport
GO:0007165 signal transduction
GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
GO:0034765 regulation of ion transmembrane transport
GO:0051099 positive regulation of binding
GO:0060315 negative regulation of ryanodine-sensitive calcium-release channel activity
GO:0098869 cellular oxidant detoxification
GO:1902476 chloride transmembrane transport
GO:0006749 glutathione metabolic process

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0034707 chloride channel complex


-  Descriptions from all associated GenBank mRNAs
  LP895648 - Sequence 512 from Patent EP3253886.
AK292785 - Homo sapiens cDNA FLJ78074 complete cds, highly similar to Homo sapiens chloride intracellular channel 2, mRNA.
BC005367 - Homo sapiens chloride intracellular channel 2, mRNA (cDNA clone IMAGE:3930673).
BC022305 - Homo sapiens chloride intracellular channel 2, mRNA (cDNA clone MGC:22558 IMAGE:4663624), complete cds.
Y12696 - Homo sapiens mRNA homologous to the p64 bovine chloride channel peptide.
DQ892014 - Synthetic construct clone IMAGE:100004644; FLH182319.01X; RZPDo839E12138D chloride intracellular channel 2 (CLIC2) gene, encodes complete protein.
DQ895204 - Synthetic construct Homo sapiens clone IMAGE:100009664; FLH182315.01L; RZPDo839E12137D chloride intracellular channel 2 (CLIC2) gene, encodes complete protein.
KJ890931 - Synthetic construct Homo sapiens clone ccsbBroadEn_00325 CLIC2 gene, encodes complete protein.
AB463493 - Synthetic construct DNA, clone: pF1KB8318, Homo sapiens CLIC2 gene for chloride intracellular channel 2, without stop codon, in Flexi system.
AM393055 - Synthetic construct Homo sapiens clone IMAGE:100002064 for hypothetical protein (CLIC2 gene).
AY191592 - Homo sapiens chloride intracellular channel 2 isoform b (CLIC2) mRNA, partial cds.
JD145502 - Sequence 126526 from Patent EP1572962.
JD161187 - Sequence 142211 from Patent EP1572962.
JD046179 - Sequence 27203 from Patent EP1572962.
JD322345 - Sequence 303369 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9S0, CLIC2_HUMAN, ENST00000369449.1, ENST00000369449.2, ENST00000369449.3, ENST00000369449.4, ENST00000369449.5, ENST00000369449.6, NM_001289, O15174, O15247, Q5JT80, Q8TCE3, uc318hoq.1, uc318hoq.2
UCSC ID: ENST00000369449.7_7
RefSeq Accession: NM_001289.6
Protein: O15247 (aka CLIC2_HUMAN or CLI2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLIC2:
xq28-dup (Xq28 Duplication Syndrome, Int22h1/Int22h2 Mediated)

-  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.