Human Gene CCS (uc001oir.3)
  Description: Homo sapiens copper chaperone for superoxide dismutase (CCS), mRNA.
RefSeq Summary (NM_005125): Copper chaperone for superoxide dismutase specifically delivers Cu to copper/zinc superoxide dismutase and may activate copper/zinc superoxide dismutase through direct insertion of the Cu cofactor. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr11:66,360,690-66,373,490 Size: 12,801 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr11:66,360,733-66,373,326 Size: 12,594 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:66,360,690-66,373,490)mRNA (may differ from genome)Protein (274 aa)
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neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCS_HUMAN
DESCRIPTION: RecName: Full=Copper chaperone for superoxide dismutase; AltName: Full=Superoxide dismutase copper chaperone;
FUNCTION: Delivers copper to copper zinc superoxide dismutase (SOD1).
COFACTOR: Binds 2 copper ions per subunit.
COFACTOR: Binds 1 zinc ion per subunit.
SUBUNIT: Homodimer, and heterodimer with SOD1. Interacts with COMMD1. Interacts with XIAP/BIRC4.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Ubiquitous.
PTM: Ubiquitinion by XIAP/BIRC4 leads to enhancement of its chaperone activity toward its physiologic target, SOD1, rather than proteasomal degradation. XIAP/BIRC4 preferentially ubiquitinates at Lys-241.
SIMILARITY: In the C-terminal section; belongs to the Cu-Zn superoxide dismutase family.
SIMILARITY: Contains 1 HMA 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CCS
CDC HuGE Published Literature: CCS

-  MalaCards Disease Associations
  MalaCards Gene Search: CCS
Diseases sorted by gene-association score: entropion (7), amyotrophic lateral sclerosis 1 (4), lateral sclerosis (3)

-  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: 36.46 RPKM in Liver
Total median expression: 1054.96 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 -11.8043-0.274 Picture PostScript Text
3' UTR -59.71164-0.364 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
IPR006121 - HeavyMe-assoc_HMA
IPR024134 - SOD_Cu/Zn_/chaperones
IPR018152 - SOD_Cu/Zn_BS
IPR024142 - SOD_Cu_chaperone
IPR001424 - SOD_Cu_Zn_dom

Pfam Domains:
PF00080 - Copper/zinc superoxide dismutase (SODC)
PF00403 - Heavy-metal-associated domain

SCOP Domains:
49329 - Cu,Zn superoxide dismutase-like
55008 - HMA, heavy metal-associated domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1DO5 - X-ray MuPIT 2CRL - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O14618
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004784 superoxide dismutase activity
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0015035 protein disulfide oxidoreductase activity
GO:0016532 superoxide dismutase copper chaperone activity
GO:0045296 cadherin binding
GO:0046872 metal ion binding

Biological Process:
GO:0006801 superoxide metabolic process
GO:0015680 intracellular copper ion transport
GO:0019430 removal of superoxide radicals
GO:0030001 metal ion transport
GO:0034599 cellular response to oxidative stress
GO:0051353 positive regulation of oxidoreductase activity
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  AY113179 - Homo sapiens superoxide dismutase copper chaperone (CCS) mRNA, complete cds.
AF002210 - Homo sapiens copper chaperone for superoxide dismutase (CCS) mRNA, complete cds.
BC105016 - Homo sapiens copper chaperone for superoxide dismutase, mRNA (cDNA clone MGC:132676 IMAGE:8144019), complete cds.
BC112055 - Homo sapiens copper chaperone for superoxide dismutase, mRNA (cDNA clone MGC:138260 IMAGE:8327523), complete cds.
CR541928 - Homo sapiens full open reading frame cDNA clone RZPDo834C0134D for gene CCS, copper chaperone for superoxide dismutase; complete cds, without stopcodon.
JD165330 - Sequence 146354 from Patent EP1572962.
JD343042 - Sequence 324066 from Patent EP1572962.
JD262943 - Sequence 243967 from Patent EP1572962.
JD463610 - Sequence 444634 from Patent EP1572962.
JD394262 - Sequence 375286 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05014 - Amyotrophic lateral sclerosis (ALS)

Reactome (by CSHL, EBI, and GO)

Protein O14618 (Reactome details) participates in the following event(s):

R-HSA-3299753 CCS transfers Cu to SOD1 and oxidizes cysteine residues in SOD1
R-HSA-8951723 2xSOD1:CCS:Zn2+:2xCu1+ dimer dissociates
R-HSA-3697860 SOD1:Zn2+ apoenzyme binds CCS:Zn2+:2xCu1+
R-HSA-3780979 CCS transfers Cu to SOD1 (mitochondrial)
R-HSA-3780958 SOD1:Zn2+ apoenzyme binds CCS:Cu1+ (mitochondrial)
R-HSA-3299685 Detoxification of Reactive Oxygen Species
R-HSA-2262752 Cellular responses to stress
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: CCS_HUMAN, NM_005125, NP_005116, O14618, Q2M366
UCSC ID: uc001oir.3
RefSeq Accession: NM_005125
Protein: O14618 (aka CCS_HUMAN)
CCDS: CCDS8146.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005125.1
exon count: 8CDS single in 3' UTR: no RNA size: 1068
ORF size: 825CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1850.00frame shift in genome: no % Coverage: 96.63
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.