COX3Cytochrome c oxidase subunit III

COX3 is a core membrane subunit of cytochrome c oxidase (Complex IV) that carries no metal centres of its own. Together with COX1 and COX2 it forms the catalytic core of the enzyme encoded by mtDNA.

Median length

784 bp

Range 735–936 bp

Median GC content

45.6%

Middle half 43.1%–47.8%

Species with data

2,335

Of 2,335 genomes

Strand

+ strand

In 2,326 of 2,335 genomes

COX3 in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · COX3 at 9,207–9,990, 784 bp, + strand · Species page

COX3Protein-coding gene

Cytochrome c oxidase subunit III

Position: 9,207–9,990
Length: 784 bp
Strand: +
GC content: 46.6%

COX3 across all species

Protein-coding13
rRNA2
tRNA22
D-loop1

Outer ring: + strand, arrows run clockwise. Inner ring: − strand.
Middle ring: GC% of each gene against the whole genome (44.4%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

GC content of COX3 across classes

2,335 species, reference strand as deposited in RefSeq

Mammalsn 627 · median 43.2% · middle half 41.6%–44.8%

Birdsn 423 · median 47.8% · middle half 46.6%–49.2%

Ray-finned fishesn 895 · median 47.0% · middle half 45.6%–48.6%

Reptilesn 136 · median 43.2% · middle half 41.8%–45.3%

Sharks and raysn 87 · median 41.9% · middle half 40.9%–44.8%

Amphibiansn 47 · median 41.2% · middle half 38.6%–44.8%

Other classesn 120 · median 38.6% · middle half 35.1%–41.7%

Each dot is one species. Boxes span the middle half of the species (25th to 75th percentile) and the thick line marks the median; thin lines run from the lowest to the highest value.

Compare COX3 across taxa

GC content of COX3 against lifespan

One point per species, coloured by class

Hover or tap a point to see the species; select it again to open its page. Legend buttons spotlight a class.

Open in the plot

Correlation with maximum lifespan

All species, each class and each order with enough species

MeasureGC%LengthGC skewAT skew

GC content of COX3 against log₁₀ maximum lifespan in 32 groups; 4 pass q < 0.05. Plot it in the explorer

Correlation of GC content of COX3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.09	−0.04	< 0.001 (significant)	+0.06	+0.19
Ray-finned fishesclass Actinopterygii	827	+0.02	−0.03	0.60	+0.02	−0.11
Mammalsclass Mammalia	615	+0.40	+0.36	< 0.001 (significant)	+0.11	+0.24
Birdsclass Aves	405	−0.08	−0.11	0.17	+0.01	−0.04
Reptilesclass Reptilia	126	+0.13	+0.15	0.33	+0.10	+0.05
Sharks and raysclass Chondrichthyes	82	+0.01	−0.02	1.00	+0.41	−0.06
Amphibiansclass Amphibia	44	+0.02	+0.01	1.00	+0.05	–
Bivalvesclass Bivalvia	35	−0.25	−0.22	0.69	+0.05	–
Perciformesorder	208	−0.20	−0.32	0.013 (significant)	−0.01	−0.33
Passeriformesorder	140	−0.15	−0.15	0.19	−0.02	−0.06
Artiodactylaorder	134	+0.18	+0.16	0.080	+0.02	+0.03
Cypriniformesorder	127	+0.02	−0.02	0.87	+0.05	+0.30
Carnivoraorder	123	+0.13	+0.14	0.25	+0.24	+0.15
Primatesorder	112	+0.41	+0.38	< 0.001 (significant)	+0.07	+0.31
Rodentiaorder	87	+0.16	+0.12	0.27	+0.13	+0.17
Squamataorder	60	+0.28	+0.30	0.30	+0.17	+0.30
Charadriiformesorder	51	+0.33	+0.30	0.12	+0.13	+0.21
Testudinesorder	49	+0.19	+0.18	0.61	+0.10	+0.00
Psittaciformesorder	44	−0.05	−0.04	0.88	+0.01	+0.03
Chiropteraorder	43	+0.03	−0.00	0.94	+0.21	−0.04
Clupeiformesorder	38	+0.09	+0.16	0.94	+0.26	–
Pleuronectiformesorder	35	+0.13	−0.12	0.72	−0.29	−0.47
Salmoniformesorder	35	+0.06	−0.00	0.95	−0.10	+0.08
Carcharhiniformesorder	31	+0.10	−0.02	0.78	+0.09	+0.28
Cetaceaorder	28	−0.26	+0.23	0.43	−0.16	−0.46
Anseriformesorder	25	−0.23	−0.28	0.60	+0.07	−0.08
Caudataorder	25	+0.11	−0.04	0.87	+0.01	–
Siluriformesorder	24	+0.22	+0.21	0.51	+0.22	–
Centrarchiformesorder	22	+0.44	+0.23	0.23	+0.35	–
Acipenseriformesorder	21	+0.08	−0.11	0.85	+0.13	−0.07
Rajiformesorder	21	−0.15	−0.07	0.90	+0.50	–
Scombriformesorder	21	+0.20	+0.13	0.85	+0.05	–

Length of COX3 against log₁₀ maximum lifespan in 26 groups; 3 pass q < 0.05. Plot it in the explorer

Correlation of Length of COX3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.03	−0.12	0.25	−0.01	−0.04
Ray-finned fishesclass Actinopterygii	827	+0.04	+0.16	0.36	−0.02	−0.03
Mammalsclass Mammalia	615	+0.07	+0.15	0.14	+0.03	+0.06
Birdsclass Aves	405	−0.20	−0.20	< 0.001 (significant)	−0.02	+0.03
Reptilesclass Reptilia	126	−0.15	−0.03	0.27	−0.05	−0.09
Amphibiansclass Amphibia	44	−0.24	−0.26	1.00	−0.04	–
Bivalvesclass Bivalvia	35	−0.04	−0.14	0.95	+0.00	–
Perciformesorder	208	−0.04	−0.04	0.69	+0.02	−0.14
Passeriformesorder	140	−0.15	−0.13	0.18	−0.00	−0.03
Artiodactylaorder	134	+0.09	+0.07	0.45	−0.02	+0.17
Cypriniformesorder	127	+0.30	+0.35	0.006 (significant)	−0.01	−0.49
Carnivoraorder	123	−0.00	+0.02	0.98	+0.11	+0.10
Rodentiaorder	87	−0.28	−0.27	0.040 (significant)	−0.32	−0.23
Squamataorder	60	+0.04	+0.04	0.92	+0.11	+0.02
Testudinesorder	49	−0.22	−0.03	0.60	−0.11	−0.13
Psittaciformesorder	44	−0.04	−0.04	0.89	−0.22	−0.16
Chiropteraorder	43	+0.04	+0.06	0.94	+0.10	+0.03
Clupeiformesorder	38	−0.05	−0.16	0.98	−0.94	–
Pleuronectiformesorder	35	−0.11	+0.12	0.76	+0.12	+0.27
Salmoniformesorder	35	−0.15	−0.17	0.72	+0.24	−0.32
Cetaceaorder	28	+0.22	+0.30	0.52	+0.11	−0.38
Caudataorder	25	−0.23	−0.23	0.79	+0.07	–
Siluriformesorder	24	−0.21	−0.17	0.51	−0.04	–
Centrarchiformesorder	22	+0.31	+0.39	0.37	+0.44	–
Acipenseriformesorder	21	+0.16	+0.16	0.71	+0.30	−0.41
Scombriformesorder	21	+0.02	−0.04	0.98	−0.19	–

GC skew of COX3 against log₁₀ maximum lifespan in 32 groups; 7 pass q < 0.05. Plot it in the explorer

Correlation of GC skew of COX3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.24	−0.31	< 0.001 (significant)	−0.06	−0.15
Ray-finned fishesclass Actinopterygii	827	−0.16	−0.20	< 0.001 (significant)	−0.10	+0.10
Mammalsclass Mammalia	615	−0.38	−0.40	< 0.001 (significant)	−0.02	−0.20
Birdsclass Aves	405	+0.00	−0.00	0.97	+0.03	+0.02
Reptilesclass Reptilia	126	−0.05	−0.07	0.80	+0.18	+0.15
Sharks and raysclass Chondrichthyes	82	−0.01	−0.06	1.00	+0.40	+0.20
Amphibiansclass Amphibia	44	−0.05	−0.02	1.00	+0.12	–
Bivalvesclass Bivalvia	35	+0.18	+0.28	0.81	+0.23	–
Perciformesorder	208	−0.01	+0.05	0.93	−0.05	+0.29
Passeriformesorder	140	+0.22	+0.21	0.050 (significant)	+0.10	+0.13
Artiodactylaorder	134	+0.03	+0.06	0.79	−0.13	+0.03
Cypriniformesorder	127	−0.28	−0.30	0.012 (significant)	+0.01	+0.46
Carnivoraorder	123	+0.12	+0.10	0.31	+0.10	−0.03
Primatesorder	112	−0.44	−0.45	< 0.001 (significant)	+0.06	−0.06
Rodentiaorder	87	+0.16	+0.13	0.28	+0.08	+0.08
Squamataorder	60	−0.08	−0.20	0.88	+0.02	+0.06
Charadriiformesorder	51	+0.16	+0.15	0.57	+0.27	+0.11
Testudinesorder	49	−0.03	−0.06	0.95	+0.31	+0.19
Psittaciformesorder	44	+0.26	+0.24	0.26	+0.07	−0.12
Chiropteraorder	43	+0.10	+0.08	0.90	−0.04	+0.17
Clupeiformesorder	38	−0.13	−0.23	0.87	+0.11	–
Pleuronectiformesorder	35	−0.23	−0.15	0.41	−0.15	+0.22
Salmoniformesorder	35	−0.20	−0.29	0.63	−0.28	−0.06
Carcharhiniformesorder	31	−0.34	−0.25	0.42	−0.17	−0.01
Cetaceaorder	28	−0.16	−0.02	0.65	−0.17	−0.42
Anseriformesorder	25	−0.21	−0.18	0.61	+0.17	−0.29
Caudataorder	25	−0.25	−0.17	0.79	−0.03	–
Siluriformesorder	24	−0.35	−0.47	0.27	−0.20	–
Centrarchiformesorder	22	−0.46	−0.16	0.23	−0.21	–
Acipenseriformesorder	21	−0.64	−0.26	0.013 (significant)	−0.71	−0.36
Rajiformesorder	21	+0.25	+0.27	0.89	+0.56	–
Scombriformesorder	21	−0.23	−0.16	0.85	+0.01	–

AT skew of COX3 against log₁₀ maximum lifespan in 32 groups; 5 pass q < 0.05. Plot it in the explorer

Correlation of AT skew of COX3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.25	+0.26	< 0.001 (significant)	+0.02	+0.26
Ray-finned fishesclass Actinopterygii	827	+0.26	+0.23	< 0.001 (significant)	+0.06	+0.07
Mammalsclass Mammalia	615	+0.05	+0.09	0.28	+0.05	+0.08
Birdsclass Aves	405	+0.10	+0.15	0.10	−0.04	+0.08
Reptilesclass Reptilia	126	−0.03	−0.07	0.86	−0.13	−0.14
Sharks and raysclass Chondrichthyes	82	−0.03	+0.00	1.00	−0.14	−0.28
Amphibiansclass Amphibia	44	−0.07	−0.07	1.00	−0.10	–
Bivalvesclass Bivalvia	35	−0.03	+0.05	0.97	−0.05	–
Perciformesorder	208	+0.18	+0.18	0.027 (significant)	+0.02	−0.18
Passeriformesorder	140	−0.13	−0.08	0.29	−0.10	−0.02
Artiodactylaorder	134	+0.14	+0.11	0.19	+0.17	+0.03
Cypriniformesorder	127	+0.28	+0.35	0.012 (significant)	−0.01	−0.52
Carnivoraorder	123	−0.01	+0.03	0.98	+0.00	+0.17
Primatesorder	112	+0.20	+0.22	0.065	−0.05	+0.20
Rodentiaorder	87	−0.34	−0.33	0.009 (significant)	+0.07	−0.14
Squamataorder	60	+0.01	−0.01	0.99	−0.12	−0.12
Charadriiformesorder	51	+0.09	+0.21	0.76	−0.18	+0.08
Testudinesorder	49	+0.07	+0.10	0.92	−0.04	−0.14
Psittaciformesorder	44	−0.18	−0.19	0.48	+0.08	−0.02
Chiropteraorder	43	−0.09	−0.09	0.90	+0.00	−0.20
Clupeiformesorder	38	+0.38	+0.46	0.45	−0.40	–
Pleuronectiformesorder	35	+0.00	−0.02	0.99	+0.08	+0.02
Salmoniformesorder	35	+0.20	+0.31	0.63	+0.09	+0.11
Carcharhiniformesorder	31	−0.01	+0.09	0.98	+0.09	+0.10
Cetaceaorder	28	+0.41	+0.38	0.14	+0.07	+0.17
Anseriformesorder	25	+0.28	+0.16	0.47	−0.19	+0.19
Caudataorder	25	−0.02	+0.06	0.96	−0.10	–
Siluriformesorder	24	+0.56	+0.51	0.051	+0.29	–
Centrarchiformesorder	22	+0.37	+0.16	0.28	+0.30	–
Acipenseriformesorder	21	+0.39	+0.27	0.23	+0.77	−0.42
Rajiformesorder	21	−0.40	−0.39	0.89	−0.20	–
Scombriformesorder	21	+0.32	+0.29	0.72	+0.10	–

n: species with both values in the group.
Pearson r, Spearman ρ: strength of the link with log₁₀ lifespan, from −1 to +1; Spearman uses ranks, so a few extreme species weigh less.
q: p-value adjusted for testing every mtDNA feature in the same group (Benjamini–Hochberg); rows with q < 0.05 are highlighted.
PIC r: the same test on phylogenetically independent contrasts, which removes similarity that comes from shared ancestry.
Partial r: the link with lifespan after accounting for body mass (log₁₀ adult weight), since bigger animals tend to live longer.

COX3 aligned across species

2,316 species, 468 columns; 261 columns have a residue in at least half of the species, and in 167 of those one residue is in 90% or more. MAFFT v7.526, FFT-NS-2 (progressive)

Loading the alignment of COX3: 2,316 species, 468 columns.

All alignment files

Codon usage of COX3

Vertebrates, vertebrate mitochondrial code

Most used codons

Share of all 582,203 sense codons of COX3 in 2,231 vertebrates

UUCPhe5.7%
CUALeu4.7%
CACHis4.4%
UGATrp4.2%
ACAThr4.1%
GCCAla3.4%
UUUPhe3.3%
GGAGly3.2%

Preferred codon for each amino acid

Most used synonymous codon and its RSCU, pooled by class; darker cells show a stronger preference

Preferred codon and RSCU for each amino acid in COX3, by class
Amino acid	All vertebratesn 2,231	Mammalsn 627	Birdsn 423	Ray-finned fishesn 895	Reptilesn 136	Sharks and raysn 87	Amphibiansn 47
PheF · 2 codons	UUC1.26	UUC1.19	UUC1.65	UUC1.20	UUC1.25	UUC1.00	UUU1.28
LeuL · 6 codons	CUA2.27	CUA2.42	CUA3.05	CUA1.82	CUA2.81	CUU1.57	UUA1.82
IleI · 2 codons	AUC1.02	AUU1.06	AUC1.45	AUU1.11	AUC1.09	AUU1.23	AUU1.41
MetM · 2 codons	AUA1.50	AUA1.57	AUA1.54	AUA1.34	AUA1.70	AUA1.66	AUA1.64
ValV · 4 codons	GUA1.62	GUA1.87	GUA1.71	GUA1.37	GUA2.08	GUA1.63	GUA1.55
SerS · 6 codons	UCA2.08	UCA2.26	UCA1.90	UCA1.81	UCA2.76	UCA2.83	UCA2.38
ProP · 4 codons	CCA1.52	CCA1.72	CCA1.69	CCC1.79	CCA2.55	CCA2.18	CCA2.05
ThrT · 4 codons	ACA1.91	ACA1.89	ACA1.88	ACA1.92	ACA1.90	ACA2.16	ACA2.06
AlaA · 4 codons	GCC1.78	GCC1.89	GCC1.81	GCC1.74	GCC1.84	GCC1.73	GCA1.64
TyrY · 2 codons	UAC1.24	UAC1.01	UAC1.60	UAC1.30	UAC1.24	UAU1.14	UAU1.08
HisH · 2 codons	CAC1.43	CAC1.33	CAC1.64	CAC1.45	CAC1.44	CAC1.14	CAC1.33
GlnQ · 2 codons	CAA1.79	CAA1.84	CAA1.84	CAA1.72	CAA1.85	CAA1.92	CAA1.86
AsnN · 2 codons	AAC1.32	AAC1.21	AAC1.69	AAC1.13	AAC1.48	AAC1.14	AAC1.17
LysK · 2 codons	AAA1.79	AAA1.77	AAA1.82	AAA1.75	AAA1.86	AAA1.94	AAA1.87
AspD · 2 codons	GAC1.37	GAC1.10	GAC1.54	GAC1.47	GAC1.22	GAC1.04	GAC1.30
GluE · 2 codons	GAA1.68	GAA1.75	GAA1.68	GAA1.61	GAA1.73	GAA1.88	GAA1.60
CysC · 2 codons	UGC1.56	UGC1.55	UGC1.78	UGC1.61	UGC1.30	UGU1.00	UGC1.43
TrpW · 2 codons	UGA1.83	UGA1.84	UGA1.90	UGA1.79	UGA1.85	UGA1.91	UGA1.84
ArgR · 4 codons	CGA2.60	CGA2.37	CGA2.99	CGA2.51	CGA3.04	CGA2.58	CGA2.74
GlyG · 4 codons	GGA1.62	GGA1.74	GGA1.99	GGC1.57	GGA1.81	GGA1.70	GGA1.68

RSCU (relative synonymous codon usage) compares a codon with even use of all codons for its amino acid: 1 means no preference, and the maximum equals the number of synonymous codons. Counts are summed over vertebrate species and read with the vertebrate mitochondrial code (NCBI table 2); other animals use different codes and are left out.