COX1Cytochrome c oxidase subunit I

COX1 is the largest catalytic subunit of cytochrome c oxidase (Complex IV), the enzyme that reduces oxygen to water at the end of the respiratory chain. It holds haem a and the haem a3–CuB centre where oxygen is reduced. A fragment of COX1 is the standard DNA barcode for animals.

Median length

1,551 bp

Range 1,513–1,755 bp

Median GC content

44.2%

Middle half 41.4%–46.5%

Species with data

2,335

Of 2,335 genomes

Strand

+ strand

In 2,329 of 2,335 genomes

COX1 in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · COX1 at 5,904–7,445, 1,542 bp, + strand · Species page

COX1Protein-coding gene

Cytochrome c oxidase subunit I

Position: 5,904–7,445
Length: 1,542 bp
Strand: +
GC content: 46.2%

COX1 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 COX1 across classes

2,335 species, reference strand as deposited in RefSeq

Mammalsn 627 · median 41.3% · middle half 39.9%–42.9%

Birdsn 423 · median 47.4% · middle half 46.1%–48.3%

Ray-finned fishesn 895 · median 45.6% · middle half 44.0%–46.9%

Reptilesn 136 · median 42.2% · middle half 41.2%–44.0%

Sharks and raysn 87 · median 39.9% · middle half 37.7%–42.0%

Amphibiansn 47 · median 41.0% · middle half 37.9%–44.3%

Other classesn 120 · median 37.3% · middle half 35.3%–39.2%

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 COX1 across taxa

GC content of COX1 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 COX1 against log₁₀ maximum lifespan in 32 groups; 6 pass q < 0.05. Plot it in the explorer

Correlation of GC content of COX1 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.09	−0.01	< 0.001 (significant)	+0.10	+0.27
Ray-finned fishesclass Actinopterygii	827	+0.09	+0.04	0.014 (significant)	+0.12	−0.02
Mammalsclass Mammalia	615	+0.35	+0.33	< 0.001 (significant)	+0.11	+0.31
Birdsclass Aves	405	+0.06	+0.03	0.37	+0.00	+0.06
Reptilesclass Reptilia	126	−0.05	−0.02	0.80	+0.06	+0.03
Sharks and raysclass Chondrichthyes	82	+0.01	−0.01	1.00	+0.32	+0.01
Amphibiansclass Amphibia	44	+0.06	−0.02	1.00	+0.07	–
Bivalvesclass Bivalvia	35	−0.18	−0.12	0.79	+0.18	–
Perciformesorder	208	−0.12	−0.27	0.16	+0.05	−0.23
Passeriformesorder	140	−0.09	−0.15	0.45	+0.01	+0.00
Artiodactylaorder	134	+0.34	+0.27	< 0.001 (significant)	+0.10	+0.10
Cypriniformesorder	127	+0.19	+0.11	0.097	+0.08	+0.50
Carnivoraorder	123	+0.27	+0.28	0.010 (significant)	+0.19	+0.21
Primatesorder	112	+0.43	+0.34	< 0.001 (significant)	+0.12	+0.24
Rodentiaorder	87	−0.01	−0.04	0.96	+0.05	−0.04
Squamataorder	60	+0.24	+0.26	0.43	+0.19	+0.33
Charadriiformesorder	51	+0.11	+0.08	0.71	−0.10	+0.07
Testudinesorder	49	−0.04	−0.09	0.95	−0.22	−0.12
Psittaciformesorder	44	−0.28	−0.21	0.22	−0.00	+0.02
Chiropteraorder	43	+0.18	+0.14	0.90	+0.28	+0.17
Clupeiformesorder	38	+0.02	+0.11	0.98	+0.47	–
Pleuronectiformesorder	35	+0.16	−0.08	0.62	−0.10	+0.44
Salmoniformesorder	35	+0.31	+0.19	0.41	+0.35	+0.31
Carcharhiniformesorder	31	−0.20	−0.24	0.61	−0.26	+0.13
Cetaceaorder	28	−0.03	+0.08	0.95	−0.22	−0.53
Anseriformesorder	25	−0.10	−0.25	0.84	+0.14	+0.13
Caudataorder	25	+0.19	−0.03	0.79	+0.08	–
Siluriformesorder	24	+0.23	+0.20	0.47	+0.26	–
Centrarchiformesorder	22	+0.37	+0.17	0.28	+0.31	–
Acipenseriformesorder	21	+0.25	+0.25	0.54	+0.49	−0.25
Rajiformesorder	21	−0.12	+0.08	0.90	+0.51	–
Scombriformesorder	21	+0.10	+0.01	0.93	+0.24	–

Length of COX1 against log₁₀ maximum lifespan in 26 groups; 6 pass q < 0.05. Plot it in the explorer

Correlation of Length of COX1 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.03	−0.02	0.25	−0.01	+0.08
Ray-finned fishesclass Actinopterygii	827	+0.12	+0.14	0.001 (significant)	+0.04	+0.07
Mammalsclass Mammalia	615	+0.27	+0.28	< 0.001 (significant)	−0.04	+0.24
Birdsclass Aves	405	−0.27	−0.33	< 0.001 (significant)	−0.03	−0.20
Reptilesclass Reptilia	126	−0.16	−0.09	0.21	+0.01	−0.25
Sharks and raysclass Chondrichthyes	82	−0.07	−0.07	1.00	+0.07	+0.15
Amphibiansclass Amphibia	44	+0.02	+0.06	1.00	−0.02	–
Bivalvesclass Bivalvia	35	−0.04	−0.16	0.95	−0.32	–
Perciformesorder	208	−0.09	−0.09	0.30	+0.01	−0.31
Passeriformesorder	140	−0.11	−0.13	0.37	−0.04	−0.07
Artiodactylaorder	134	+0.45	+0.32	< 0.001 (significant)	−0.07	+0.32
Carnivoraorder	123	+0.13	+0.10	0.24	+0.09	+0.09
Primatesorder	112	−0.01	+0.01	0.96	−0.12	−0.12
Rodentiaorder	87	−0.45	−0.61	< 0.001 (significant)	−0.13	−0.27
Squamataorder	60	+0.19	+0.15	0.63	+0.09	−0.04
Testudinesorder	49	+0.06	−0.08	0.94	−0.03	+0.23
Psittaciformesorder	44	+0.20	+0.21	0.40	+0.17	+0.21
Chiropteraorder	43	+0.12	+0.16	0.90	+0.05	+0.11
Clupeiformesorder	38	−0.09	+0.13	0.94	−0.01	–
Pleuronectiformesorder	35	+0.73	+0.70	< 0.001 (significant)	+0.26	+0.65
Carcharhiniformesorder	31	+0.09	+0.14	0.82	+0.00	−0.18
Cetaceaorder	28	−0.41	−0.38	0.14	−0.27	−0.12
Caudataorder	25	−0.01	−0.13	0.96	+0.03	–
Siluriformesorder	24	+0.04	+0.09	0.90	+0.11	–
Centrarchiformesorder	22	+0.25	+0.32	0.49	−0.13	–
Scombriformesorder	21	+0.40	+0.40	0.53	+0.30	–

GC skew of COX1 against log₁₀ maximum lifespan in 32 groups; 7 pass q < 0.05. Plot it in the explorer

Correlation of GC skew of COX1 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.21	−0.22	< 0.001 (significant)	−0.08	−0.25
Ray-finned fishesclass Actinopterygii	827	−0.13	−0.18	< 0.001 (significant)	−0.11	+0.06
Mammalsclass Mammalia	615	−0.24	−0.27	< 0.001 (significant)	−0.05	−0.17
Birdsclass Aves	405	−0.03	−0.03	0.69	+0.02	+0.07
Reptilesclass Reptilia	126	−0.01	−0.01	0.98	+0.04	+0.19
Sharks and raysclass Chondrichthyes	82	+0.03	+0.14	1.00	+0.24	+0.11
Amphibiansclass Amphibia	44	−0.06	+0.01	1.00	−0.00	–
Bivalvesclass Bivalvia	35	+0.15	+0.17	0.83	+0.04	–
Perciformesorder	208	−0.05	+0.04	0.61	+0.01	+0.18
Passeriformesorder	140	+0.25	+0.27	0.027 (significant)	+0.12	+0.14
Artiodactylaorder	134	−0.08	+0.06	0.46	−0.10	+0.08
Cypriniformesorder	127	−0.12	−0.09	0.34	−0.02	+0.37
Carnivoraorder	123	+0.13	+0.15	0.27	+0.05	−0.06
Primatesorder	112	−0.55	−0.51	< 0.001 (significant)	−0.21	−0.21
Rodentiaorder	87	+0.26	+0.30	0.054	−0.03	+0.18
Squamataorder	60	−0.15	−0.22	0.76	−0.04	+0.10
Charadriiformesorder	51	+0.19	+0.17	0.48	+0.06	+0.19
Testudinesorder	49	−0.15	−0.18	0.74	+0.08	+0.06
Psittaciformesorder	44	+0.34	+0.34	0.10	+0.27	−0.09
Chiropteraorder	43	+0.03	+0.04	0.94	+0.00	+0.10
Clupeiformesorder	38	−0.00	+0.02	1.00	−0.06	–
Pleuronectiformesorder	35	+0.04	−0.11	0.90	−0.05	+0.32
Salmoniformesorder	35	+0.01	+0.17	0.99	−0.24	+0.53
Carcharhiniformesorder	31	−0.12	+0.03	0.74	+0.20	+0.19
Cetaceaorder	28	−0.60	−0.59	0.022 (significant)	−0.36	+0.05
Anseriformesorder	25	−0.02	+0.06	0.95	−0.08	−0.02
Caudataorder	25	−0.20	−0.20	0.79	−0.26	–
Siluriformesorder	24	−0.31	−0.36	0.35	−0.26	–
Centrarchiformesorder	22	−0.23	−0.02	0.52	−0.06	–
Acipenseriformesorder	21	−0.63	−0.11	0.014 (significant)	−0.71	−0.31
Rajiformesorder	21	+0.27	+0.50	0.89	+0.31	–
Scombriformesorder	21	−0.15	−0.14	0.89	+0.04	–

AT skew of COX1 against log₁₀ maximum lifespan in 32 groups; 9 pass q < 0.05. Plot it in the explorer

Correlation of AT skew of COX1 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.25	+0.27	< 0.001 (significant)	−0.03	+0.21
Ray-finned fishesclass Actinopterygii	827	+0.19	+0.17	< 0.001 (significant)	−0.05	+0.03
Mammalsclass Mammalia	615	+0.13	+0.12	0.002 (significant)	+0.06	−0.08
Birdsclass Aves	405	−0.08	−0.08	0.22	−0.05	+0.11
Reptilesclass Reptilia	126	+0.15	+0.16	0.28	−0.02	−0.13
Sharks and raysclass Chondrichthyes	82	+0.10	+0.03	1.00	−0.06	−0.14
Amphibiansclass Amphibia	44	−0.14	−0.07	1.00	−0.10	–
Bivalvesclass Bivalvia	35	−0.01	+0.05	1.00	−0.10	–
Perciformesorder	208	+0.29	+0.39	< 0.001 (significant)	−0.04	−0.02
Passeriformesorder	140	−0.07	+0.01	0.59	−0.11	+0.07
Artiodactylaorder	134	+0.08	+0.03	0.46	+0.08	−0.12
Cypriniformesorder	127	+0.29	+0.25	0.008 (significant)	+0.07	−0.38
Carnivoraorder	123	−0.14	−0.16	0.22	+0.05	+0.04
Primatesorder	112	+0.31	+0.28	0.002 (significant)	+0.10	+0.38
Rodentiaorder	87	−0.21	−0.26	0.14	+0.08	−0.01
Squamataorder	60	−0.02	−0.00	0.97	+0.06	−0.28
Charadriiformesorder	51	+0.02	+0.00	0.94	−0.04	−0.07
Testudinesorder	49	+0.19	+0.24	0.61	−0.15	−0.02
Psittaciformesorder	44	−0.46	−0.45	0.019 (significant)	−0.31	−0.14
Chiropteraorder	43	−0.04	−0.04	0.94	−0.06	−0.16
Clupeiformesorder	38	+0.21	+0.28	0.66	+0.56	–
Pleuronectiformesorder	35	+0.19	+0.15	0.51	−0.27	−0.09
Salmoniformesorder	35	−0.34	−0.34	0.41	+0.03	−0.66
Carcharhiniformesorder	31	+0.02	−0.04	0.98	−0.17	+0.15
Cetaceaorder	28	+0.58	+0.52	0.025 (significant)	+0.34	−0.01
Anseriformesorder	25	+0.48	+0.39	0.22	+0.14	+0.40
Caudataorder	25	−0.04	+0.07	0.93	+0.09	–
Siluriformesorder	24	+0.37	+0.36	0.23	+0.22	–
Centrarchiformesorder	22	−0.21	−0.24	0.57	−0.15	–
Acipenseriformesorder	21	−0.59	−0.07	0.024 (significant)	−0.69	−0.51
Rajiformesorder	21	−0.35	−0.54	0.89	−0.06	–
Scombriformesorder	21	+0.36	+0.47	0.66	+0.12	–

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.

COX1 aligned across species

2,316 species, 679 columns; 516 columns have a residue in at least half of the species, and in 415 of those one residue is in 90% or more. MAFFT v7.526, FFT-NS-2 (progressive)

Loading the alignment of COX1: 2,316 species, 679 columns.

All alignment files

Codon usage of COX1

Vertebrates, vertebrate mitochondrial code

Most used codons

Share of all 1,151,641 sense codons of COX1 in 2,231 vertebrates

UUCPhe4.7%
CUALeu4.3%
AUUIle4.3%
AUAMet3.7%
GGAGly3.7%
GCCAla3.5%
UUUPhe3.4%
AUCIle3.4%

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 COX1, 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	UUC1.16	UUC1.08	UUC1.56	UUC1.09	UUC1.06	UUU1.15	UUU1.29
LeuL · 6 codons	CUA2.16	CUA2.34	CUA3.11	CUA1.67	CUA2.46	UUA1.75	UUA1.70
IleI · 2 codons	AUU1.11	AUU1.23	AUC1.40	AUU1.26	AUU1.00	AUU1.36	AUU1.40
MetM · 2 codons	AUA1.40	AUA1.57	AUA1.62	AUA1.05	AUA1.70	AUA1.65	AUA1.53
ValV · 4 codons	GUA1.82	GUA2.01	GUA1.95	GUA1.67	GUA2.03	GUA1.58	GUA1.76
SerS · 6 codons	UCA2.15	UCA2.43	UCA2.25	UCA1.81	UCA2.40	UCA2.19	UCA2.50
ProP · 4 codons	CCA1.59	CCA1.43	CCA2.09	CCC1.31	CCA2.18	CCA1.97	CCA1.75
ThrT · 4 codons	ACA1.79	ACA1.85	ACC1.64	ACA1.84	ACA1.72	ACA1.97	ACA1.93
AlaA · 4 codons	GCC1.63	GCA1.49	GCC1.96	GCC1.75	GCA1.62	GCA1.64	GCC1.51
TyrY · 2 codons	UAC1.16	UAU1.02	UAC1.56	UAC1.17	UAC1.20	UAU1.24	UAU1.13
HisH · 2 codons	CAC1.36	CAC1.22	CAC1.57	CAC1.43	CAC1.36	CAU1.08	CAC1.13
GlnQ · 2 codons	CAA1.65	CAA1.68	CAA1.79	CAA1.52	CAA1.74	CAA1.67	CAA1.63
AsnN · 2 codons	AAC1.19	AAC1.06	AAC1.67	AAC1.12	AAC1.29	AAU1.27	AAU1.15
LysK · 2 codons	AAA1.86	AAA1.84	AAA1.89	AAA1.85	AAA1.86	AAA1.94	AAA1.87
AspD · 2 codons	GAC1.31	GAC1.10	GAC1.63	GAC1.38	GAC1.29	GAU1.17	GAC1.04
GluE · 2 codons	GAA1.60	GAA1.62	GAA1.78	GAA1.49	GAA1.62	GAA1.80	GAA1.56
CysC · 2 codons	UGC1.50	UGC1.02	UGC1.95	UGC1.72	UGC1.31	UGC1.17	UGC1.31
TrpW · 2 codons	UGA1.80	UGA1.80	UGA1.89	UGA1.74	UGA1.80	UGA1.89	UGA1.77
ArgR · 4 codons	CGA2.39	CGA2.42	CGA2.71	CGA2.22	CGA2.35	CGA2.47	CGA2.55
GlyG · 4 codons	GGA1.62	GGA1.76	GGA1.89	GGA1.38	GGA1.79	GGA1.35	GGA1.64

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.