CYTBCytochrome b

Cytochrome b is the only mtDNA-encoded subunit of Complex III (cytochrome bc1 complex), which passes electrons from ubiquinol to cytochrome c. It carries two haem groups and forms both quinone-binding sites of the complex. Its sequence is widely used in phylogenetics and species identification.

Median length

1,141 bp

Range 1,079–1,920 bp

Median GC content

44.6%

Middle half 41.9%–46.8%

Species with data

2,334

Of 2,335 genomes

Strand

+ strand

In 2,315 of 2,334 genomes

CYTB in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · CYTB at 14,747–15,887, 1,141 bp, + strand · Species page

CYTBProtein-coding gene

Cytochrome b

Position: 14,747–15,887
Length: 1,141 bp
Strand: +
GC content: 46.3%

CYTB 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 CYTB across classes

2,334 species, reference strand as deposited in RefSeq

Mammalsn 627 · median 42.4% · middle half 40.8%–44.0%

Birdsn 422 · median 47.1% · middle half 46.1%–48.4%

Ray-finned fishesn 895 · median 46.0% · middle half 44.4%–47.7%

Reptilesn 136 · median 42.3% · middle half 41.1%–44.0%

Sharks and raysn 87 · median 40.6% · middle half 39.3%–43.0%

Amphibiansn 47 · median 40.9% · middle half 36.5%–43.6%

Other classesn 120 · median 36.3% · middle half 33.3%–38.1%

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 CYTB across taxa

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

Correlation of GC content of CYTB with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,201	+0.13	+0.00	< 0.001 (significant)	+0.04	+0.22
Ray-finned fishesclass Actinopterygii	827	+0.04	−0.02	0.39	+0.02	−0.15
Mammalsclass Mammalia	615	+0.41	+0.36	< 0.001 (significant)	+0.09	+0.31
Birdsclass Aves	404	+0.11	+0.10	0.065	+0.06	−0.01
Reptilesclass Reptilia	126	+0.21	+0.22	0.090	+0.00	+0.11
Sharks and raysclass Chondrichthyes	82	+0.04	−0.02	1.00	−0.03	−0.11
Amphibiansclass Amphibia	44	+0.04	−0.00	1.00	+0.06	–
Bivalvesclass Bivalvia	35	−0.21	−0.18	0.75	+0.20	–
Perciformesorder	208	−0.16	−0.30	0.056	−0.02	−0.40
Passeriformesorder	140	−0.18	−0.17	0.10	+0.02	+0.07
Artiodactylaorder	134	+0.30	+0.21	0.002 (significant)	−0.00	+0.12
Cypriniformesorder	127	−0.03	−0.07	0.77	−0.03	+0.48
Carnivoraorder	123	+0.27	+0.34	0.009 (significant)	+0.13	+0.30
Primatesorder	112	+0.33	+0.31	0.001 (significant)	+0.08	+0.11
Rodentiaorder	87	+0.26	+0.23	0.061	+0.17	+0.17
Squamataorder	60	+0.12	+0.18	0.82	+0.01	+0.20
Charadriiformesorder	50	+0.16	+0.14	0.57	+0.06	+0.03
Testudinesorder	49	+0.00	−0.13	0.99	+0.03	−0.03
Psittaciformesorder	44	−0.18	−0.15	0.48	+0.02	+0.15
Chiropteraorder	43	+0.05	+0.02	0.94	+0.20	−0.01
Clupeiformesorder	38	−0.03	+0.06	0.98	+0.16	–
Pleuronectiformesorder	35	+0.20	+0.07	0.48	+0.13	−0.24
Salmoniformesorder	35	+0.22	+0.15	0.60	+0.18	+0.13
Carcharhiniformesorder	31	+0.05	+0.02	0.91	−0.08	−0.17
Cetaceaorder	28	+0.10	+0.29	0.80	−0.04	−0.38
Anseriformesorder	25	−0.48	−0.53	0.22	−0.09	−0.40
Caudataorder	25	+0.14	−0.03	0.84	+0.23	–
Siluriformesorder	24	+0.34	+0.40	0.28	+0.42	–
Centrarchiformesorder	22	+0.50	+0.39	0.23	+0.43	–
Acipenseriformesorder	21	−0.13	−0.17	0.76	+0.28	−0.10
Rajiformesorder	21	−0.19	−0.07	0.90	−0.05	–
Scombriformesorder	21	+0.10	−0.04	0.93	+0.06	–

Length of CYTB against log₁₀ maximum lifespan in 26 groups; 4 pass q < 0.05. Plot it in the explorer

Correlation of Length of CYTB with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,201	−0.04	−0.08	0.067	−0.01	−0.02
Ray-finned fishesclass Actinopterygii	827	+0.04	+0.07	0.32	+0.00	+0.06
Mammalsclass Mammalia	615	−0.41	−0.21	< 0.001 (significant)	−0.02	−0.35
Birdsclass Aves	404	−0.21	−0.23	< 0.001 (significant)	+0.02	−0.21
Reptilesclass Reptilia	126	+0.37	+0.38	< 0.001 (significant)	+0.05	+0.26
Sharks and raysclass Chondrichthyes	82	+0.31	+0.25	0.88	+0.09	+0.09
Amphibiansclass Amphibia	44	−0.07	−0.24	1.00	−0.10	–
Bivalvesclass Bivalvia	35	−0.38	−0.33	0.50	−0.37	–
Perciformesorder	208	−0.08	−0.01	0.41	−0.07	+0.05
Passeriformesorder	140	−0.05	−0.09	0.79	−0.21	−0.10
Artiodactylaorder	134	−0.02	−0.02	0.86	+0.01	+0.01
Cypriniformesorder	127	−0.05	−0.02	0.71	−0.03	+0.27
Carnivoraorder	123	+0.01	+0.03	0.95	−0.03	+0.12
Primatesorder	112	+0.15	+0.36	0.19	+0.04	+0.27
Rodentiaorder	87	−0.70	−0.66	< 0.001 (significant)	−0.10	−0.54
Squamataorder	60	−0.22	−0.26	0.53	−0.05	+0.07
Testudinesorder	49	+0.03	−0.13	0.95	−0.02	+0.11
Psittaciformesorder	44	−0.03	+0.03	0.92	+0.16	+0.13
Chiropteraorder	43	−0.14	−0.15	0.90	−0.04	−0.14
Clupeiformesorder	38	+0.08	+0.14	0.95	+0.03	–
Pleuronectiformesorder	35	+0.36	+0.50	0.17	+0.09	–
Carcharhiniformesorder	31	−0.06	−0.04	0.88	−0.16	−0.17
Anseriformesorder	25	+0.36	+0.31	0.40	+0.18	+0.33
Caudataorder	25	−0.24	−0.40	0.79	−0.25	–
Centrarchiformesorder	22	+0.15	+0.22	0.67	+0.07	–
Scombriformesorder	21	+0.07	+0.18	0.96	−0.06	–

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

Correlation of GC skew of CYTB with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,201	−0.29	−0.35	< 0.001 (significant)	−0.11	−0.22
Ray-finned fishesclass Actinopterygii	827	−0.15	−0.19	< 0.001 (significant)	−0.13	+0.11
Mammalsclass Mammalia	615	−0.36	−0.43	< 0.001 (significant)	−0.01	−0.30
Birdsclass Aves	404	−0.10	−0.14	0.077	−0.14	+0.08
Reptilesclass Reptilia	126	+0.06	+0.07	0.73	+0.09	+0.17
Sharks and raysclass Chondrichthyes	82	−0.01	−0.02	1.00	−0.04	+0.23
Amphibiansclass Amphibia	44	−0.10	−0.10	1.00	+0.02	–
Bivalvesclass Bivalvia	35	+0.08	+0.20	0.92	+0.23	–
Perciformesorder	208	−0.03	+0.01	0.81	−0.10	+0.33
Passeriformesorder	140	+0.15	+0.20	0.20	−0.14	−0.05
Artiodactylaorder	134	−0.23	−0.13	0.020 (significant)	+0.04	−0.00
Cypriniformesorder	127	−0.11	−0.08	0.38	−0.19	+0.42
Carnivoraorder	123	+0.10	+0.03	0.43	+0.15	−0.07
Primatesorder	112	−0.47	−0.46	< 0.001 (significant)	−0.03	+0.08
Rodentiaorder	87	−0.24	−0.22	0.080	−0.08	−0.15
Squamataorder	60	−0.13	−0.16	0.80	+0.08	+0.11
Charadriiformesorder	50	+0.29	+0.26	0.20	+0.03	+0.21
Testudinesorder	49	−0.16	−0.20	0.71	−0.07	−0.06
Psittaciformesorder	44	+0.51	+0.55	0.009 (significant)	+0.34	+0.39
Chiropteraorder	43	+0.06	+0.06	0.94	−0.11	+0.12
Clupeiformesorder	38	+0.00	−0.02	1.00	−0.18	–
Pleuronectiformesorder	35	−0.21	−0.27	0.47	−0.15	+0.02
Salmoniformesorder	35	−0.08	−0.07	0.93	−0.43	+0.17
Carcharhiniformesorder	31	−0.19	−0.10	0.61	+0.05	+0.49
Cetaceaorder	28	−0.07	+0.07	0.85	+0.04	+0.05
Anseriformesorder	25	−0.15	−0.21	0.72	−0.27	+0.00
Caudataorder	25	−0.13	−0.09	0.84	+0.06	–
Siluriformesorder	24	−0.51	−0.58	0.078	−0.41	–
Centrarchiformesorder	22	−0.26	−0.00	0.47	+0.02	–
Acipenseriformesorder	21	−0.64	−0.07	0.013 (significant)	−0.71	−0.38
Rajiformesorder	21	+0.28	+0.42	0.89	−0.06	–
Scombriformesorder	21	−0.12	−0.16	0.89	−0.23	–

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

Correlation of AT skew of CYTB with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,201	+0.29	+0.32	< 0.001 (significant)	+0.20	+0.14
Ray-finned fishesclass Actinopterygii	827	+0.20	+0.14	< 0.001 (significant)	+0.31	+0.11
Mammalsclass Mammalia	615	+0.31	+0.28	< 0.001 (significant)	+0.07	−0.04
Birdsclass Aves	404	−0.11	−0.11	0.068	+0.11	−0.01
Reptilesclass Reptilia	126	+0.28	+0.25	0.014 (significant)	+0.12	+0.10
Sharks and raysclass Chondrichthyes	82	+0.10	+0.10	1.00	−0.02	−0.26
Amphibiansclass Amphibia	44	−0.04	−0.02	1.00	−0.08	–
Bivalvesclass Bivalvia	35	−0.11	−0.12	0.89	−0.31	–
Perciformesorder	208	+0.23	+0.21	0.004 (significant)	+0.04	+0.01
Passeriformesorder	140	+0.01	+0.08	0.96	+0.13	+0.11
Artiodactylaorder	134	+0.02	+0.02	0.84	−0.03	−0.21
Cypriniformesorder	127	+0.20	+0.16	0.085	+0.10	−0.44
Carnivoraorder	123	+0.31	+0.25	0.004 (significant)	−0.02	+0.30
Primatesorder	112	+0.27	+0.29	0.008 (significant)	+0.04	+0.11
Rodentiaorder	87	−0.24	−0.24	0.077	+0.21	−0.08
Squamataorder	60	+0.05	+0.01	0.90	+0.11	−0.08
Charadriiformesorder	50	−0.07	−0.07	0.84	+0.14	−0.08
Testudinesorder	49	+0.25	+0.23	0.60	+0.19	+0.06
Psittaciformesorder	44	−0.25	−0.22	0.27	−0.19	−0.02
Chiropteraorder	43	−0.04	+0.00	0.94	+0.14	−0.13
Clupeiformesorder	38	+0.34	+0.35	0.45	+0.25	–
Pleuronectiformesorder	35	−0.44	−0.36	0.092	+0.02	−0.63
Salmoniformesorder	35	+0.18	+0.35	0.66	+0.48	+0.32
Carcharhiniformesorder	31	+0.14	+0.14	0.71	−0.12	−0.45
Cetaceaorder	28	+0.18	+0.35	0.61	−0.02	−0.28
Anseriformesorder	25	+0.21	+0.13	0.61	+0.19	+0.06
Caudataorder	25	−0.07	+0.03	0.89	−0.28	–
Siluriformesorder	24	+0.48	+0.50	0.091	+0.27	–
Centrarchiformesorder	22	−0.16	−0.27	0.67	−0.42	–
Acipenseriformesorder	21	+0.30	−0.03	0.44	+0.70	+0.03
Rajiformesorder	21	−0.40	−0.49	0.89	−0.02	–
Scombriformesorder	21	−0.29	−0.38	0.74	−0.23	–

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.

CYTB aligned across species

2,315 species, 548 columns; 379 columns have a residue in at least half of the species, and in 220 of those one residue is in 90% or more. MAFFT v7.526, FFT-NS-2 (progressive)

Loading the alignment of CYTB: 2,315 species, 548 columns.

All alignment files

Codon usage of CYTB

Vertebrates, vertebrate mitochondrial code

Most used codons

Share of all 846,792 sense codons of CYTB in 2,230 vertebrates

CUALeu6.4%
UUCPhe5.2%
AUCIle5.2%
CUCLeu3.7%
AUUIle3.7%
AACAsn3.5%
GCCAla3.2%
UGATrp2.9%

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 CYTB, by class
Amino acid	All vertebratesn 2,230	Mammalsn 627	Birdsn 422	Ray-finned fishesn 895	Reptilesn 136	Sharks and raysn 87	Amphibiansn 47
PheF · 2 codons	UUC1.36	UUC1.30	UUC1.66	UUC1.31	UUC1.41	UUC1.22	UUU1.10
LeuL · 6 codons	CUA2.40	CUA2.77	CUA3.15	CUA1.82	CUA2.69	CUA1.83	CUA1.67
IleI · 2 codons	AUC1.17	AUC1.19	AUC1.55	AUC1.01	AUC1.25	AUU1.06	AUU1.17
MetM · 2 codons	AUA1.50	AUA1.66	AUA1.58	AUA1.21	AUA1.73	AUA1.64	AUA1.64
ValV · 4 codons	GUA1.69	GUA1.95	GUA2.00	GUA1.45	GUA2.24	GUA1.37	GUA1.69
SerS · 6 codons	UCA2.38	UCA2.60	UCA2.54	UCA2.02	UCA2.90	UCA2.33	UCA2.84
ProP · 4 codons	CCA1.78	CCA2.10	CCA1.82	CCC1.63	CCA2.47	CCA1.96	CCA2.29
ThrT · 4 codons	ACA1.65	ACA2.01	ACC1.89	ACC1.75	ACC1.73	ACA1.74	ACA1.92
AlaA · 4 codons	GCC1.78	GCA1.81	GCC2.25	GCC1.71	GCC1.91	GCC2.19	GCC1.69
TyrY · 2 codons	UAC1.36	UAC1.23	UAC1.64	UAC1.35	UAC1.47	UAC1.16	UAC1.01
HisH · 2 codons	CAC1.47	CAC1.43	CAC1.58	CAC1.48	CAC1.47	CAC1.14	CAC1.32
GlnQ · 2 codons	CAA1.76	CAA1.81	CAA1.75	CAA1.69	CAA1.82	CAA1.91	CAA1.71
AsnN · 2 codons	AAC1.44	AAC1.40	AAC1.70	AAC1.38	AAC1.52	AAC1.18	AAC1.13
LysK · 2 codons	AAA1.76	AAA1.79	AAA1.84	AAA1.65	AAA1.88	AAA1.85	AAA1.82
AspD · 2 codons	GAC1.45	GAC1.47	GAC1.66	GAC1.39	GAC1.53	GAC1.21	GAC1.29
GluE · 2 codons	GAA1.65	GAA1.74	GAA1.73	GAA1.51	GAA1.79	GAA1.79	GAA1.71
CysC · 2 codons	UGC1.50	UGC1.66	UGC1.64	UGC1.35	UGC1.47	UGU1.00	UGC1.35
TrpW · 2 codons	UGA1.83	UGA1.87	UGA1.86	UGA1.78	UGA1.82	UGA1.85	UGA1.75
ArgR · 4 codons	CGA2.56	CGA2.88	CGA2.23	CGA2.50	CGA2.84	CGA2.24	CGA2.48
GlyG · 4 codons	GGA1.72	GGA1.96	GGA1.86	GGA1.48	GGA1.91	GGA1.70	GGA1.81

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.