COX2Cytochrome c oxidase subunit II

COX2 is a catalytic subunit of cytochrome c oxidase (Complex IV). It binds cytochrome c and carries the CuA centre, which takes electrons from cytochrome c and passes them on to COX1.

Median length

688 bp

Range 666–1,569 bp

Median GC content

42.7%

Middle half 39.4%–45.2%

Species with data

2,335

Of 2,335 genomes

Strand

+ strand

In 2,330 of 2,335 genomes

COX2 in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · COX2 at 7,586–8,269, 684 bp, + strand · Species page

COX2Protein-coding gene

Cytochrome c oxidase subunit II

Position: 7,586–8,269
Length: 684 bp
Strand: +
GC content: 46.2%

COX2 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 COX2 across classes

2,335 species, reference strand as deposited in RefSeq

Mammalsn 627 · median 39.3% · middle half 37.7%–40.9%

Birdsn 423 · median 46.2% · middle half 45.2%–47.5%

Ray-finned fishesn 895 · median 43.9% · middle half 42.6%–45.2%

Reptilesn 136 · median 41.0% · middle half 38.4%–43.5%

Sharks and raysn 87 · median 38.4% · middle half 37.3%–39.3%

Amphibiansn 47 · median 39.1% · middle half 36.0%–41.4%

Other classesn 120 · median 36.6% · middle half 33.5%–38.2%

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 COX2 across taxa

GC content of COX2 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 COX2 against log₁₀ maximum lifespan in 32 groups; 5 pass q < 0.05. Plot it in the explorer

Correlation of GC content of COX2 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.07	−0.02	< 0.001 (significant)	+0.04	+0.26
Ray-finned fishesclass Actinopterygii	827	+0.05	+0.01	0.23	−0.00	−0.17
Mammalsclass Mammalia	615	+0.32	+0.29	< 0.001 (significant)	+0.08	+0.36
Birdsclass Aves	405	−0.08	−0.07	0.18	+0.04	−0.00
Reptilesclass Reptilia	126	−0.12	−0.10	0.41	+0.00	−0.09
Sharks and raysclass Chondrichthyes	82	+0.13	+0.16	1.00	+0.28	+0.08
Amphibiansclass Amphibia	44	+0.07	+0.05	1.00	+0.01	–
Bivalvesclass Bivalvia	35	−0.30	−0.22	0.58	−0.02	–
Perciformesorder	208	−0.16	−0.27	0.056	+0.09	−0.47
Passeriformesorder	140	−0.13	−0.14	0.27	−0.03	−0.06
Artiodactylaorder	134	+0.25	+0.15	0.013 (significant)	−0.07	+0.08
Cypriniformesorder	127	+0.30	+0.28	0.007 (significant)	+0.08	+0.33
Carnivoraorder	123	+0.20	+0.24	0.076	+0.20	+0.19
Primatesorder	112	+0.45	+0.32	< 0.001 (significant)	+0.05	+0.22
Rodentiaorder	87	+0.04	+0.02	0.79	+0.07	+0.03
Squamataorder	60	+0.30	+0.37	0.30	+0.03	+0.27
Charadriiformesorder	51	−0.02	+0.01	0.94	−0.07	+0.07
Testudinesorder	49	+0.11	+0.08	0.85	+0.02	−0.03
Psittaciformesorder	44	−0.38	−0.40	0.057	−0.03	−0.32
Chiropteraorder	43	+0.16	+0.11	0.90	+0.24	+0.14
Clupeiformesorder	38	+0.07	+0.09	0.98	+0.02	–
Pleuronectiformesorder	35	+0.15	−0.04	0.65	−0.06	+0.19
Salmoniformesorder	35	+0.44	+0.38	0.18	−0.15	+0.65
Carcharhiniformesorder	31	+0.14	+0.21	0.72	+0.32	+0.53
Cetaceaorder	28	−0.26	+0.01	0.44	−0.06	−0.38
Anseriformesorder	25	+0.13	−0.06	0.76	+0.31	+0.19
Caudataorder	25	+0.22	+0.16	0.79	+0.10	–
Siluriformesorder	24	+0.49	+0.45	0.090	+0.50	–
Centrarchiformesorder	22	+0.33	+0.24	0.34	+0.14	–
Acipenseriformesorder	21	+0.15	+0.08	0.74	+0.26	−0.09
Rajiformesorder	21	−0.16	−0.07	0.90	+0.30	–
Scombriformesorder	21	+0.34	+0.42	0.66	+0.38	–

Length of COX2 against log₁₀ maximum lifespan in 20 groups; 1 passes q < 0.05. Plot it in the explorer

Correlation of Length of COX2 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.02	−0.23	0.31	−0.01	−0.01
Ray-finned fishesclass Actinopterygii	827	+0.02	+0.02	0.68	+0.03	+0.10
Mammalsclass Mammalia	615	+0.10	+0.13	0.019 (significant)	+0.00	+0.14
Birdsclass Aves	405	+0.11	+0.03	0.058	−0.02	−0.06
Reptilesclass Reptilia	126	+0.08	+0.02	0.62	+0.11	+0.13
Sharks and raysclass Chondrichthyes	82	−0.01	−0.03	1.00	+0.03	–
Amphibiansclass Amphibia	44	−0.06	−0.02	1.00	+0.08	–
Bivalvesclass Bivalvia	35	+0.07	+0.05	0.94	−0.27	–
Perciformesorder	208	+0.03	+0.08	0.81	−0.00	+0.11
Passeriformesorder	140	−0.11	−0.13	0.36	−0.07	−0.07
Artiodactylaorder	134	+0.06	+0.05	0.64	+0.10	+0.19
Carnivoraorder	123	−0.00	+0.09	1.00	−0.10	−0.11
Primatesorder	112	−0.16	−0.22	0.14	−0.03	−0.05
Rodentiaorder	87	−0.00	−0.02	1.00	+0.18	+0.16
Squamataorder	60	+0.31	+0.26	0.27	+0.19	+0.33
Testudinesorder	49	+0.01	−0.13	0.98	+0.05	+0.05
Chiropteraorder	43	−0.15	−0.18	0.90	−0.06	−0.14
Carcharhiniformesorder	31	+0.01	−0.06	0.98	+0.14	–
Caudataorder	25	+0.06	+0.03	0.89	+0.04	–
Acipenseriformesorder	21	+0.19	+0.20	0.65	+0.11	−0.00

GC skew of COX2 against log₁₀ maximum lifespan in 32 groups; 7 pass q < 0.05. Plot it in the explorer

Correlation of GC skew of COX2 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.21	−0.24	< 0.001 (significant)	−0.08	−0.23
Ray-finned fishesclass Actinopterygii	827	−0.04	−0.06	0.29	−0.14	+0.15
Mammalsclass Mammalia	615	−0.21	−0.23	< 0.001 (significant)	+0.03	−0.28
Birdsclass Aves	405	−0.01	−0.03	0.92	+0.04	−0.02
Reptilesclass Reptilia	126	−0.18	−0.22	0.16	−0.05	−0.06
Sharks and raysclass Chondrichthyes	82	+0.05	−0.01	1.00	+0.53	−0.06
Amphibiansclass Amphibia	44	−0.02	−0.04	1.00	−0.19	–
Bivalvesclass Bivalvia	35	+0.22	+0.31	0.74	+0.16	–
Perciformesorder	208	−0.02	+0.04	0.85	−0.07	+0.22
Passeriformesorder	140	+0.28	+0.24	0.014 (significant)	+0.00	−0.03
Artiodactylaorder	134	−0.09	+0.12	0.40	−0.00	−0.06
Cypriniformesorder	127	−0.06	−0.13	0.66	+0.02	+0.37
Carnivoraorder	123	+0.28	+0.14	0.009 (significant)	+0.10	+0.06
Primatesorder	112	−0.39	−0.43	< 0.001 (significant)	−0.03	−0.25
Rodentiaorder	87	+0.09	+0.05	0.55	+0.17	+0.02
Squamataorder	60	+0.10	+0.03	0.85	−0.08	+0.08
Charadriiformesorder	51	+0.17	+0.16	0.57	+0.11	+0.21
Testudinesorder	49	−0.11	−0.13	0.85	+0.03	+0.18
Psittaciformesorder	44	+0.48	+0.47	0.016 (significant)	+0.30	+0.34
Chiropteraorder	43	+0.13	+0.09	0.90	+0.13	+0.22
Clupeiformesorder	38	−0.23	−0.24	0.58	−0.08	–
Pleuronectiformesorder	35	+0.39	+0.32	0.14	−0.04	+0.53
Salmoniformesorder	35	+0.06	+0.15	0.95	+0.27	+0.17
Carcharhiniformesorder	31	+0.20	+0.09	0.61	+0.23	+0.03
Cetaceaorder	28	−0.43	−0.32	0.14	−0.10	−0.02
Anseriformesorder	25	+0.22	+0.06	0.60	+0.33	+0.22
Caudataorder	25	−0.15	−0.16	0.84	−0.21	–
Siluriformesorder	24	−0.14	−0.16	0.69	+0.02	–
Centrarchiformesorder	22	−0.03	+0.27	0.93	+0.18	–
Acipenseriformesorder	21	−0.66	−0.24	0.013 (significant)	−0.72	−0.43
Rajiformesorder	21	+0.22	+0.23	0.90	+0.61	–
Scombriformesorder	21	−0.11	−0.21	0.92	+0.06	–

AT skew of COX2 against log₁₀ maximum lifespan in 32 groups; 6 pass q < 0.05. Plot it in the explorer

Correlation of AT skew of COX2 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.31	+0.31	< 0.001 (significant)	+0.14	+0.14
Ray-finned fishesclass Actinopterygii	827	+0.16	+0.10	< 0.001 (significant)	+0.24	+0.14
Mammalsclass Mammalia	615	+0.20	+0.17	< 0.001 (significant)	+0.00	−0.13
Birdsclass Aves	405	−0.10	−0.12	0.076	−0.01	−0.01
Reptilesclass Reptilia	126	+0.08	+0.05	0.63	+0.12	−0.09
Sharks and raysclass Chondrichthyes	82	−0.17	−0.13	1.00	−0.36	+0.09
Amphibiansclass Amphibia	44	+0.00	+0.04	1.00	+0.14	–
Bivalvesclass Bivalvia	35	+0.12	+0.24	0.88	+0.01	–
Perciformesorder	208	+0.12	+0.09	0.15	+0.08	−0.06
Passeriformesorder	140	−0.19	−0.18	0.084	−0.03	+0.05
Artiodactylaorder	134	−0.10	−0.16	0.38	+0.03	−0.13
Cypriniformesorder	127	+0.04	+0.04	0.75	+0.01	−0.42
Carnivoraorder	123	+0.21	+0.16	0.062	+0.02	+0.33
Primatesorder	112	+0.13	+0.18	0.25	−0.06	+0.06
Rodentiaorder	87	−0.28	−0.31	0.040 (significant)	−0.00	−0.13
Squamataorder	60	+0.08	+0.10	0.88	+0.07	−0.10
Charadriiformesorder	51	−0.26	−0.20	0.27	−0.16	−0.24
Testudinesorder	49	+0.21	+0.17	0.60	+0.25	−0.11
Psittaciformesorder	44	−0.50	−0.49	0.010 (significant)	−0.24	−0.32
Chiropteraorder	43	−0.06	−0.06	0.92	−0.09	−0.17
Clupeiformesorder	38	+0.32	+0.34	0.47	+0.81	–
Pleuronectiformesorder	35	+0.09	+0.20	0.80	+0.09	+0.05
Salmoniformesorder	35	+0.10	+0.03	0.89	−0.30	−0.00
Carcharhiniformesorder	31	+0.01	+0.05	0.98	−0.03	+0.24
Cetaceaorder	28	+0.45	+0.49	0.10	+0.00	−0.25
Anseriformesorder	25	+0.06	+0.02	0.88	+0.17	+0.09
Caudataorder	25	−0.19	−0.03	0.79	−0.09	–
Siluriformesorder	24	+0.17	+0.21	0.60	−0.02	–
Centrarchiformesorder	22	−0.43	−0.40	0.23	−0.41	–
Acipenseriformesorder	21	+0.69	+0.35	0.013 (significant)	+0.73	+0.40
Rajiformesorder	21	−0.28	−0.37	0.89	−0.42	–
Scombriformesorder	21	+0.36	+0.43	0.66	+0.06	–

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.

COX2 aligned across species

2,316 species, 988 columns; 229 columns have a residue in at least half of the species, and in 119 of those one residue is in 90% or more. MAFFT v7.526, FFT-NS-2 (progressive)

Loading the alignment of COX2: 2,316 species, 988 columns.

All alignment files

Codon usage of COX2

Vertebrates, vertebrate mitochondrial code

Most used codons

Share of all 509,769 sense codons of COX2 in 2,231 vertebrates

GAAGlu5.3%
CUALeu4.8%
AUUIle4.5%
AUAMet4.0%
AUCIle3.8%
GACAsp3.6%
CAAGln3.0%
ACAThr2.8%

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 COX2, 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	UUC1.07	UUU1.03	UUC1.58	UUU1.03	UUC1.01	UUU1.32	UUU1.39
LeuL · 6 codons	CUA2.19	CUA2.48	CUA2.76	CUU1.80	CUA2.55	UUA2.20	UUA2.06
IleI · 2 codons	AUU1.08	AUU1.08	AUC1.47	AUU1.26	AUC1.03	AUU1.31	AUU1.45
MetM · 2 codons	AUA1.47	AUA1.54	AUA1.55	AUA1.32	AUA1.68	AUA1.56	AUA1.56
ValV · 4 codons	GUA1.54	GUA1.75	GUA1.51	GUA1.36	GUA2.16	GUA1.60	GUA1.58
SerS · 6 codons	UCA1.97	UCA2.14	UCA2.26	UCC1.97	UCA2.68	UCA2.50	UCA2.08
ProP · 4 codons	CCA1.76	CCA1.91	CCA2.09	CCC1.57	CCA2.57	CCA1.89	CCA2.38
ThrT · 4 codons	ACA1.79	ACA1.92	ACA1.64	ACA1.72	ACA1.80	ACA1.92	ACA1.77
AlaA · 4 codons	GCC1.57	GCC1.41	GCC2.03	GCC1.51	GCA1.93	GCA1.71	GCA1.74
TyrY · 2 codons	UAC1.13	UAU1.03	UAC1.61	UAC1.13	UAC1.24	UAU1.33	UAU1.27
HisH · 2 codons	CAC1.31	CAC1.16	CAC1.56	CAC1.30	CAC1.27	CAC1.31	CAC1.20
GlnQ · 2 codons	CAA1.78	CAA1.78	CAA1.84	CAA1.73	CAA1.78	CAA1.89	CAA1.84
AsnN · 2 codons	AAC1.29	AAC1.18	AAC1.69	AAC1.26	AAC1.38	AAU1.25	AAC1.04
LysK · 2 codons	AAA1.77	AAA1.76	AAA1.85	AAA1.73	AAA1.86	AAA1.81	AAA1.83
AspD · 2 codons	GAC1.37	GAC1.19	GAC1.54	GAC1.44	GAC1.34	GAC1.08	GAC1.03
GluE · 2 codons	GAA1.70	GAA1.67	GAA1.75	GAA1.68	GAA1.82	GAA1.83	GAA1.62
CysC · 2 codons	UGC1.39	UGC1.31	UGC1.66	UGC1.41	UGC1.32	UGU1.75	UGC1.22
TrpW · 2 codons	UGA1.82	UGA1.85	UGA1.85	UGA1.78	UGA1.80	UGA1.84	UGA1.83
ArgR · 4 codons	CGA2.26	CGA2.56	CGA2.08	CGA2.15	CGA2.33	CGA1.92	CGA2.39
GlyG · 4 codons	GGA1.81	GGA1.60	GGA2.25	GGA1.73	GGA2.13	GGA1.77	GGA1.84

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.