Human Gene SCO2 (ENST00000395693.8_8) from GENCODE V47lift37
  Description: synthesis of cytochrome C oxidase 2, transcript variant 1 (from RefSeq NM_005138.3)
Gencode Transcript: ENST00000395693.8_8
Gencode Gene: ENSG00000284194.3_12
Transcript (Including UTRs)
   Position: hg19 chr22:50,961,997-50,964,027 Size: 2,031 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr22:50,962,040-50,962,840 Size: 801 Coding Exon Count: 1 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:50,961,997-50,964,027)mRNA (may differ from genome)Protein (266 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SCO2_HUMAN
DESCRIPTION: RecName: Full=Protein SCO2 homolog, mitochondrial; Flags: Precursor;
FUNCTION: Acts as a copper chaperone, transporting copper to the Cu(A) site on the cytochrome c oxidase subunit II (COX2).
SUBCELLULAR LOCATION: Mitochondrion.
TISSUE SPECIFICITY: Ubiquitous.
DISEASE: Defects in SCO2 are the cause of fatal infantile cardioencephalomyopathy with cytochrome c oxidase deficiency (FIC) [MIM:604377]. This disease is characterized by hypertrophic cardiomyopathy, lactic acidosis, and gliosis. Heart and skeletal muscle show reductions in cytochrome c oxidase (COX) activity, whereas liver and fibroblasts show mild COX deficiencies.
SIMILARITY: Belongs to the SCO1/2 family.
SIMILARITY: Contains 1 thioredoxin domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SCO2";

-  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: SCO2
Diseases sorted by gene-association score: cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1* (1332), myopia 6* (1250), fatal infantile cytochrome c oxidase deficiency* (750), fatal infantile encephalocardiomyopathy* (419), rare isolated myopia* (350), leigh syndrome* (89), mitochondrial complex iv deficiency* (47), cardioencephalomyopathy (38), myopia (32), spinal muscular atrophy-1 (11), refractive error (11), anemia of prematurity (7), mitochondrial disorders (4), mitochondrial metabolism disease (4), spinal muscular atrophy (4), cardiomyopathy (3), cardiomyopathy, familial hypertrophic (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D001564 Benzo(a)pyrene
  • D003300 Copper
  • D019327 Copper Sulfate
  • D006861 Hydrogen Peroxide
  • D017382 Reactive Oxygen Species
  • D012643 Selenium
  • D013749 Tetrachlorodibenzodioxin
  • D013806 Theophylline

+  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: 34.57 RPKM in Lung
Total median expression: 939.62 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 -62.10140-0.444 Picture PostScript Text
3' UTR -12.4043-0.288 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
IPR003782 - SCO1/SenC
IPR017276 - Synth_of_cyt-c-oxidase_Sco1/2
IPR012336 - Thioredoxin-like_fold

Pfam Domains:
PF02630 - SCO1/SenC

SCOP Domains:
52833 - Thioredoxin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2RLI - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O43819
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0015035 protein disulfide oxidoreductase activity
GO:0046872 metal ion binding

Biological Process:
GO:0001654 eye development
GO:0006825 copper ion transport
GO:0006878 cellular copper ion homeostasis
GO:0008535 respiratory chain complex IV assembly
GO:0033617 mitochondrial respiratory chain complex IV assembly
GO:0045454 cell redox homeostasis
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030016 myofibril
GO:0031305 integral component of mitochondrial inner membrane


-  Descriptions from all associated GenBank mRNAs
  AL021683 - Homo sapiens cDNA homologous to Yeast SCO1 & SCO2 genes and C.elegans C01F1.2 gene.
BC102024 - Homo sapiens SCO cytochrome oxidase deficient homolog 2 (yeast), mRNA (cDNA clone MGC:125823 IMAGE:40030584), complete cds.
BC102025 - Homo sapiens SCO cytochrome oxidase deficient homolog 2 (yeast), mRNA (cDNA clone MGC:125825 IMAGE:40030589), complete cds.
CR456569 - Homo sapiens SCO2 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.SCO2).
CU013168 - Homo sapiens SCO2, mRNA (cDNA clone IMAGE:100000522), complete cds, with stop codon, in Gateway system.
KJ892890 - Synthetic construct Homo sapiens clone ccsbBroadEn_02284 SCO2 gene, encodes complete protein.
KR711510 - Synthetic construct Homo sapiens clone CCSBHm_00025113 SCO2 (SCO2) mRNA, encodes complete protein.
KR711511 - Synthetic construct Homo sapiens clone CCSBHm_00025114 SCO2 (SCO2) mRNA, encodes complete protein.
KR711512 - Synthetic construct Homo sapiens clone CCSBHm_00025115 SCO2 (SCO2) mRNA, encodes complete protein.
KR711513 - Synthetic construct Homo sapiens clone CCSBHm_00025119 SCO2 (SCO2) mRNA, encodes complete protein.
AB528229 - Synthetic construct DNA, clone: pF1KE0540, Homo sapiens SCO2 gene for SCO cytochrome oxidase deficient homolog 2, without stop codon, in Flexi system.
CU013456 - Homo sapiens SCO2, mRNA (cDNA clone IMAGE:100000426), complete cds, without stop codon, in Gateway system.
JD251618 - Sequence 232642 from Patent EP1572962.
JD447830 - Sequence 428854 from Patent EP1572962.
JD332094 - Sequence 313118 from Patent EP1572962.
JD186305 - Sequence 167329 from Patent EP1572962.

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

Protein O43819 (Reactome details) participates in the following event(s):

R-HSA-5628897 TP53 Regulates Metabolic Genes
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000395693.1, ENST00000395693.2, ENST00000395693.3, ENST00000395693.4, ENST00000395693.5, ENST00000395693.6, ENST00000395693.7, NM_005138, O43819, Q3T1B5, Q9UK87, SCO2_HUMAN, uc318xpu.1, uc318xpu.2
UCSC ID: ENST00000395693.8_8
RefSeq Accession: NM_005138.3
Protein: O43819 (aka SCO2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SCO2:
leigh-nucl-ov (Nuclear Gene-Encoded Leigh Syndrome Spectrum Overview)

-  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.