Human Gene COX6A1 (ENST00000229379.3) from GENCODE V44
  Description: Homo sapiens cytochrome c oxidase subunit 6A1 (COX6A1), mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_004373)
RefSeq Summary (NM_004373): Cytochrome c oxidase (COX), the terminal enzyme of the mitochondrial respiratory chain, catalyzes the electron transfer from reduced cytochrome c to oxygen. It is a heteromeric complex consisting of 3 catalytic subunits encoded by mitochondrial genes and multiple structural subunits encoded by nuclear genes. The mitochondrially-encoded subunits function in the electron transfer and the nuclear-encoded subunits may function in the regulation and assembly of the complex. This nuclear gene encodes polypeptide 1 (liver isoform) of subunit VIa, and polypeptide 1 is found in all non-muscle tissues. Polypeptide 2 (heart/muscle isoform) of subunit VIa is encoded by a different gene, and is present only in striated muscles. These two polypeptides share 66% amino acid sequence identity. It has been reported that there may be several pseudogenes on chromosomes 1, 6, 7q21, 7q31-32 and 12. However, only one pseudogene (COX6A1P) on chromosome 1p31.1 has been documented. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000229379.3
Gencode Gene: ENSG00000111775.3
Transcript (Including UTRs)
   Position: hg38 chr12:120,438,113-120,440,730 Size: 2,618 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr12:120,438,127-120,440,537 Size: 2,411 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:120,438,113-120,440,730)mRNA (may differ from genome)Protein (109 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cytochrome c oxidase subunit 6A1, mitochondrial; AltName: Full=Cytochrome c oxidase polypeptide VIa-liver; AltName: Full=Cytochrome c oxidase subunit VIA-liver; Short=COX VIa-L; Flags: Precursor;
FUNCTION: This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
SUBCELLULAR LOCATION: Mitochondrion inner membrane.
SIMILARITY: Belongs to the cytochrome c oxidase subunit 6A family.
SEQUENCE CAUTION: Sequence=CAA33392.1; Type=Frameshift; Positions=17;

-  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: COX6A1
Diseases sorted by gene-association score: charcot-marie-tooth disease, recessive intermediate d* (1267), charcot-marie-tooth neuropathy recessive intermediate d* (500), charcot-marie-tooth disease, type 2r (12), spastic paraplegia 55, autosomal recessive (12), charcot-marie-tooth disease type 2a2 (12), charcot-marie-tooth disease, axonal, type 2p (12), charcot-marie-tooth disease, axonal, type 2t (10), charcot-marie-tooth disease, axonal, type 2h (10), charcot-marie-tooth disease, type 2b2 (10), charcot-marie-tooth disease, type 2b1 (10), amyotrophic lateral sclerosis type 5 (9), spastic paraplegia 46, autosomal recessive (8), charcot-marie-tooth disease intermediate type (8), spastic paraplegia 56, autosomal recessive (7), charcot-marie-tooth disease, axonal, type 2s (5), charcot-marie-tooth disease (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 451.89 RPKM in Brain - Amygdala
Total median expression: 9243.08 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
3' UTR -43.60193-0.226 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
IPR001349 - Cyt_c_oxidase_su6a
IPR018507 - Cyt_c_oxidase_su6a_CS

Pfam Domains:
PF02046 - Cytochrome c oxidase subunit VIa

ModBase Predicted Comparative 3D Structure on P12074
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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsemblEnsembl SGD
Protein SequenceProtein SequenceProtein SequenceProtein Sequence Protein Sequence
AlignmentAlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004129 cytochrome-c oxidase activity
GO:0030234 enzyme regulator activity

Biological Process:
GO:0006091 generation of precursor metabolites and energy
GO:0006123 mitochondrial electron transport, cytochrome c to oxygen
GO:0009060 aerobic respiration
GO:0050790 regulation of catalytic activity
GO:1902600 hydrogen ion transmembrane transport

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

-  Descriptions from all associated GenBank mRNAs
  AK312009 - Homo sapiens cDNA, FLJ92283, Homo sapiens cytochrome c oxidase subunit VIa polypeptide 1(COX6A1), nuclear gene encoding mitochondrial protein, mRNA.
LF384007 - JP 2014500723-A/191510: Polycomb-Associated Non-Coding RNAs.
MA619584 - JP 2018138019-A/191510: Polycomb-Associated Non-Coding RNAs.
JD453850 - Sequence 434874 from Patent EP1572962.
BC107861 - Homo sapiens cytochrome c oxidase subunit VIa polypeptide 1, mRNA (cDNA clone MGC:104500 IMAGE:4664958), complete cds.
BC070186 - Homo sapiens cytochrome c oxidase subunit VIa polypeptide 1, mRNA (cDNA clone MGC:88167 IMAGE:6654310), complete cds.
BC007723 - Homo sapiens cytochrome c oxidase subunit VIa polypeptide 1, mRNA (cDNA clone MGC:12782 IMAGE:4300921), complete cds.
DQ896371 - Synthetic construct Homo sapiens clone IMAGE:100010831; FLH193730.01L; RZPDo839B0669D cytochrome c oxidase subunit VIa polypeptide 1 (COX6A1) gene, encodes complete protein.
DQ893099 - Synthetic construct clone IMAGE:100005729; FLH193734.01X; RZPDo839B0679D cytochrome c oxidase subunit VIa polypeptide 1 (COX6A1) gene, encodes complete protein.
KJ890957 - Synthetic construct Homo sapiens clone ccsbBroadEn_00351 COX6A1 gene, encodes complete protein.
HE647860 - Homo sapiens mRNA for cytochrome c oxidase subunit VIa polypeptide 1 (COX6A1 gene).
X15341 - Human COX VIa-L mRNA for cytochrome c oxidase liver-specific subunit VIa (EC
LF359471 - JP 2014500723-A/166974: Polycomb-Associated Non-Coding RNAs.
MA595048 - JP 2018138019-A/166974: Polycomb-Associated Non-Coding RNAs.
LF359470 - JP 2014500723-A/166973: Polycomb-Associated Non-Coding RNAs.
MA595047 - JP 2018138019-A/166973: Polycomb-Associated Non-Coding RNAs.
LF359469 - JP 2014500723-A/166972: Polycomb-Associated Non-Coding RNAs.
MA595046 - JP 2018138019-A/166972: Polycomb-Associated Non-Coding RNAs.
JD111600 - Sequence 92624 from Patent EP1572962.

-  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

BioCyc Knowledge Library
PWY-3781 - aerobic respiration I (cytochrome c)

Reactome (by CSHL, EBI, and GO)

Protein P12074 (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: B2R500, COX6AL, CX6A1_HUMAN, ENST00000229379.1, ENST00000229379.2, NM_004373, O43714, P12074, Q32Q37, uc001tyf.1, uc001tyf.2, uc001tyf.3
UCSC ID: ENST00000229379.3
RefSeq Accession: NM_004373
Protein: P12074 (aka CX6A1_HUMAN or COXE_HUMAN)
CCDS: CCDS9197.1

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