Human Gene SCO1 (ENST00000255390.10) from GENCODE V44
  Description: Homo sapiens synthesis of cytochrome C oxidase 1 (SCO1), mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_004589)
RefSeq Summary (NM_004589): Mammalian cytochrome c oxidase (COX) catalyzes the transfer of reducing equivalents from cytochrome c to molecular oxygen and pumps protons across the inner mitochondrial membrane. In yeast, 2 related COX assembly genes, SCO1 and SCO2 (synthesis of cytochrome c oxidase), enable subunits 1 and 2 to be incorporated into the holoprotein. This gene is the human homolog to the yeast SCO1 gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000255390.10
Gencode Gene: ENSG00000133028.12
Transcript (Including UTRs)
   Position: hg38 chr17:10,672,474-10,697,533 Size: 25,060 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr17:10,681,119-10,697,507 Size: 16,389 Coding Exon Count: 6 

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RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:10,672,474-10,697,533)mRNA (may differ from genome)Protein (301 aa)
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-  Comments and Description Text from UniProtKB
  ID: SCO1_HUMAN
DESCRIPTION: RecName: Full=Protein SCO1 homolog, mitochondrial; Flags: Precursor;
FUNCTION: Thought to play a role in cellular copper homeostasis, mitochondrial redox signaling or insertion of copper into the active site of COX.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Mitochondrion.
TISSUE SPECIFICITY: Predominantly expressed in tissues characterized by high rates of oxidative phosphorylation (OxPhos), including muscle, heart, and brain.
DISEASE: Defects in SCO1 are a cause of mitochondrial complex IV deficiency (MT-C4D) [MIM:220110]; also known as cytochrome c oxidase deficiency. A disorder of the mitochondrial respiratory chain with heterogeneous clinical manifestations, ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs. Features include hypertrophic cardiomyopathy, hepatomegaly and liver dysfunction, hypotonia, muscle weakness, excercise intolerance, developmental delay, delayed motor development and mental retardation. A subset of patients manifest Leigh syndrome.
SIMILARITY: Belongs to the SCO1/2 family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SCO1";

-  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.
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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: SCO1
Diseases sorted by gene-association score: mitochondrial complex iv deficiency* (644), fatal infantile cytochrome c oxidase deficiency* (247), hepatic failure, early-onset, and neurologic disorder due to cytochrome c oxidase deficiency* (100), leigh syndrome* (18), cardioencephalomyopathy (8), alzheimer disease mitochondrial (5), mitochondrial disorders (4), mitochondrial metabolism disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.59 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 430.44 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 -8.4026-0.323 Picture PostScript Text
3' UTR -3259.278645-0.377 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WP0 - X-ray MuPIT 2GGT - X-ray MuPIT 2GQK - NMR MuPIT 2GQL - NMR MuPIT 2GQM - NMR MuPIT 2GT5 - NMR MuPIT 2GT6 - NMR MuPIT 2GVP - NMR MuPIT 2HRF - NMR MuPIT 2HRN - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75880
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-  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
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006091 generation of precursor metabolites and energy
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:1901799 negative regulation of proteasomal protein catabolic process

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030016 myofibril
GO:0031305 integral component of mitochondrial inner membrane
GO:0072492 host cell mitochondrial intermembrane space


-  Descriptions from all associated GenBank mRNAs
  AK127533 - Homo sapiens cDNA FLJ45626 fis, clone BRTHA3028782.
AK127981 - Homo sapiens cDNA FLJ46096 fis, clone TESTI2019282.
JD081654 - Sequence 62678 from Patent EP1572962.
JD476742 - Sequence 457766 from Patent EP1572962.
JD053811 - Sequence 34835 from Patent EP1572962.
JD158988 - Sequence 140012 from Patent EP1572962.
JD483162 - Sequence 464186 from Patent EP1572962.
AF131816 - Homo sapiens clone 25222 h-sco1 mRNA sequence, partial cds.
AF026852 - Homo sapiens h-sco1 (SCO1) mRNA, nuclear gene encoding mitochondrial protein, complete cds.
AK098826 - Homo sapiens cDNA FLJ25960 fis, clone TST08985, highly similar to SCO1 PROTEIN PRECURSOR.
AK074588 - Homo sapiens cDNA FLJ90107 fis, clone HEMBA1006482, highly similar to SCO1 protein homolog, mitochondrial precursor.
JD323953 - Sequence 304977 from Patent EP1572962.
JD501060 - Sequence 482084 from Patent EP1572962.
JD267004 - Sequence 248028 from Patent EP1572962.
JD431698 - Sequence 412722 from Patent EP1572962.
BC015504 - Homo sapiens SCO cytochrome oxidase deficient homolog 1 (yeast), mRNA (cDNA clone MGC:9115 IMAGE:3914068), complete cds.
AF183424 - Homo sapiens SCO1/2 protein mRNA, complete cds.
JD129266 - Sequence 110290 from Patent EP1572962.
JD187776 - Sequence 168800 from Patent EP1572962.
JD138793 - Sequence 119817 from Patent EP1572962.
JD065009 - Sequence 46033 from Patent EP1572962.
JD080696 - Sequence 61720 from Patent EP1572962.
JD361589 - Sequence 342613 from Patent EP1572962.
JD350794 - Sequence 331818 from Patent EP1572962.
JD468936 - Sequence 449960 from Patent EP1572962.
JD560349 - Sequence 541373 from Patent EP1572962.
KJ892099 - Synthetic construct Homo sapiens clone ccsbBroadEn_01493 SCO1 gene, encodes complete protein.
KR709399 - Synthetic construct Homo sapiens clone CCSBHm_00001902 SCO1 (SCO1) mRNA, encodes complete protein.
DQ891605 - Synthetic construct clone IMAGE:100004235; FLH178569.01X; RZPDo839E08128D SCO cytochrome oxidase deficient homolog 1 (yeast) (SCO1) gene, encodes complete protein.
AK315595 - Homo sapiens cDNA, FLJ96673, Homo sapiens SCO cytochrome oxidase deficient homolog 1 (yeast)(SCO1), nuclear gene encoding mitochondrial protein, mRNA.
DQ894798 - Synthetic construct Homo sapiens clone IMAGE:100009258; FLH178565.01L; RZPDo839E08127D SCO cytochrome oxidase deficient homolog 1 (yeast) (SCO1) gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDM0, ENST00000255390.1, ENST00000255390.2, ENST00000255390.3, ENST00000255390.4, ENST00000255390.5, ENST00000255390.6, ENST00000255390.7, ENST00000255390.8, ENST00000255390.9, NM_004589, O75880, SCO1_HUMAN, SCOD1, uc002gmr.1, uc002gmr.2, uc002gmr.3, uc002gmr.4, uc002gmr.5, uc002gmr.6
UCSC ID: ENST00000255390.10
RefSeq Accession: NM_004589
Protein: O75880 (aka SCO1_HUMAN)
CCDS: CCDS11158.1

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