Human Gene COX4I1 (uc002fje.3) Description and Page Index
  Description: Homo sapiens cytochrome c oxidase subunit IV isoform 1 (COX4I1), nuclear gene encoding mitochondrial protein, mRNA.
RefSeq Summary (NM_001861): Cytochrome c oxidase (COX) is the terminal enzyme of the mitochondrial respiratory chain. It is a multi-subunit enzyme complex that couples the transfer of electrons from cytochrome c to molecular oxygen and contributes to a proton electrochemical gradient across the inner mitochondrial membrane. The complex consists of 13 mitochondrial- and nuclear-encoded subunits. The mitochondrially-encoded subunits perform the electron transfer and proton pumping activities. The functions of the nuclear-encoded subunits are unknown but they may play a role in the regulation and assembly of the complex. This gene encodes the nuclear-encoded subunit IV isoform 1 of the human mitochondrial respiratory chain enzyme. It is located at the 3' of the NOC4 (neighbor of COX4) gene in a head-to-head orientation, and shares a promoter with it. Pseudogenes related to this gene are located on chromosomes 13 and 14. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016].
Transcript (Including UTRs)
   Position: hg19 chr16:85,833,173-85,840,607 Size: 7,435 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr16:85,834,812-85,840,480 Size: 5,669 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:85,833,173-85,840,607)mRNA (may differ from genome)Protein (169 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cytochrome c oxidase subunit 4 isoform 1, mitochondrial; AltName: Full=Cytochrome c oxidase polypeptide IV; AltName: Full=Cytochrome c oxidase subunit IV isoform 1; Short=COX IV-1; Flags: Precursor;
FUNCTION: This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
INTERACTION: Q9HC24:TMBIM4; NbExp=1; IntAct=EBI-1056574, EBI-1045545;
SUBCELLULAR LOCATION: Mitochondrion inner membrane.
SIMILARITY: Belongs to the cytochrome c oxidase IV family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): COX4I1
CDC HuGE Published Literature: COX4I1

-  MalaCards Disease Associations
  MalaCards Gene Search: COX4I1
Diseases sorted by gene-association score: calvarial hyperostosis (13), neuronal ceroid lipofuscinosis (2)

-  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: 261.98 RPKM in Heart - Left Ventricle
Total median expression: 6012.91 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 -90.60187-0.484 Picture PostScript Text
3' UTR -28.62127-0.225 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
IPR013288 - Cyt_c_oxidase_su4
IPR004203 - Cyt_c_oxidase_su4_fam

Pfam Domains:
PF02936 - Cytochrome c oxidase subunit IV

SCOP Domains:
81406 - Mitochondrial cytochrome c oxidase subunit IV

ModBase Predicted Comparative 3D Structure on P13073
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 BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004129 cytochrome-c oxidase activity
GO:0005515 protein binding

Biological Process:
GO:0006091 generation of precursor metabolites and energy
GO:0006123 mitochondrial electron transport, cytochrome c to oxygen
GO:0007584 response to nutrient
GO:1902600 hydrogen ion transmembrane transport

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005751 mitochondrial respiratory chain complex IV
GO:0016020 membrane
GO:0031966 mitochondrial membrane

-  Descriptions from all associated GenBank mRNAs
  LF384479 - JP 2014500723-A/191982: Polycomb-Associated Non-Coding RNAs.
JD404679 - Sequence 385703 from Patent EP1572962.
JD461943 - Sequence 442967 from Patent EP1572962.
BC047869 - Homo sapiens cytochrome c oxidase subunit IV isoform 1, mRNA (cDNA clone IMAGE:5240622), complete cds.
U90915 - Human clone 23600 cytochrome c oxidase subunit IV mRNA, complete cds.
BC062437 - Homo sapiens cytochrome c oxidase subunit IV isoform 1, mRNA (cDNA clone MGC:72016 IMAGE:6451700), complete cds.
X54802 - Human mRNA for cytochrome c oxidase subunit IV (EC
AK311847 - Homo sapiens cDNA, FLJ92112, Homo sapiens cytochrome c oxidase subunit IV isoform 1 (COX4I1),mRNA.
JD227732 - Sequence 208756 from Patent EP1572962.
BC039013 - Homo sapiens cytochrome c oxidase subunit IV isoform 1, mRNA (cDNA clone IMAGE:5745435), with apparent retained intron.
BC008704 - Homo sapiens cytochrome c oxidase subunit IV isoform 1, mRNA (cDNA clone MGC:15503 IMAGE:2990066), complete cds.
BC021236 - Homo sapiens cytochrome c oxidase subunit IV isoform 1, mRNA (cDNA clone MGC:15331 IMAGE:4309698), complete cds.
LF375009 - JP 2014500723-A/182512: Polycomb-Associated Non-Coding RNAs.
M21575 - Human cytochrome c oxidase COX subunit IV (COX IV) mRNA, complete cds.
BT019825 - Homo sapiens cytochrome c oxidase subunit IV isoform 1 mRNA, complete cds.
DQ893162 - Synthetic construct clone IMAGE:100005792; FLH194512.01X; RZPDo839C0280D cytochrome c oxidase subunit IV isoform 1 (COX4I1) gene, encodes complete protein.
DQ896459 - Synthetic construct Homo sapiens clone IMAGE:100010919; FLH194508.01L; RZPDo839C0270D cytochrome c oxidase subunit IV isoform 1 (COX4I1) gene, encodes complete protein.
M34600 - Human cytochrome c oxidase subunit IV (COX4) mRNA, complete cds.
KJ901351 - Synthetic construct Homo sapiens clone ccsbBroadEn_10745 COX4I1 gene, encodes complete protein.
KJ890955 - Synthetic construct Homo sapiens clone ccsbBroadEn_00349 COX4I1 gene, encodes complete protein.
DQ592498 - Homo sapiens piRNA piR-59610, complete sequence.
AK027136 - Homo sapiens cDNA: FLJ23483 fis, clone KAIA04052.
LF375011 - JP 2014500723-A/182514: Polycomb-Associated Non-Coding RNAs.
LF375014 - JP 2014500723-A/182517: Polycomb-Associated Non-Coding RNAs.
LF375019 - JP 2014500723-A/182522: Polycomb-Associated Non-Coding RNAs.
JD205280 - Sequence 186304 from Patent EP1572962.
LF375020 - JP 2014500723-A/182523: Polycomb-Associated Non-Coding RNAs.
MA620056 - JP 2018138019-A/191982: Polycomb-Associated Non-Coding RNAs.
MA610586 - JP 2018138019-A/182512: Polycomb-Associated Non-Coding RNAs.
MA610588 - JP 2018138019-A/182514: Polycomb-Associated Non-Coding RNAs.
MA610591 - JP 2018138019-A/182517: Polycomb-Associated Non-Coding RNAs.
MA610596 - JP 2018138019-A/182522: Polycomb-Associated Non-Coding RNAs.
MA610597 - JP 2018138019-A/182523: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00190 - Oxidative phosphorylation
hsa01100 - Metabolic pathways
hsa04260 - Cardiac muscle contraction
hsa05010 - Alzheimer's disease
hsa05012 - Parkinson's disease
hsa05016 - Huntington's disease

Reactome (by CSHL, EBI, and GO)

Protein P13073 (Reactome details) participates in the following event(s):

R-HSA-163214 Electron transfer from reduced cytochrome c to molecular oxygen
R-HSA-611105 Respiratory electron transport
R-HSA-5628897 TP53 Regulates Metabolic Genes
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-212436 Generic Transcription Pathway
R-HSA-1430728 Metabolism
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2R4J2, COX4, COX41_HUMAN, D3DUM7, NM_001861, NP_001852, P13073, Q6P666
UCSC ID: uc002fje.3
RefSeq Accession: NM_001861
Protein: P13073 (aka COX41_HUMAN or CX41_HUMAN)
CCDS: CCDS10955.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001861.3
exon count: 5CDS single in 3' UTR: no RNA size: 839
ORF size: 510CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1220.00frame shift in genome: no % Coverage: 98.21
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.