ND4NADH dehydrogenase subunit 4

ND4 is a membrane subunit of Complex I (NADH:ubiquinone oxidoreductase). With ND2 and ND5 it forms the set of antiporter-like subunits of the membrane arm that take part in pumping protons.

Median length

1,378 bp

Range 948–1,458 bp

Median GC content

43.2%

Middle half 39.2%–46.4%

Species with data

2,335

Of 2,335 genomes

Strand

+ strand

In 2,283 of 2,335 genomes

ND4 in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · ND4 at 10,760–12,137, 1,378 bp, + strand · Species page

ND4Protein-coding gene

NADH dehydrogenase subunit 4

Position: 10,760–12,137
Length: 1,378 bp
Strand: +
GC content: 44.3%

ND4 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 ND4 across classes

2,335 species, reference strand as deposited in RefSeq

Mammalsn 627 · median 39.1% · middle half 37.4%–40.7%

Birdsn 423 · median 46.2% · middle half 44.7%–47.4%

Ray-finned fishesn 895 · median 46.0% · middle half 43.9%–47.5%

Reptilesn 136 · median 40.0% · middle half 38.4%–42.9%

Sharks and raysn 87 · median 39.1% · middle half 37.5%–42.0%

Amphibiansn 47 · median 37.7% · middle half 33.9%–42.3%

Other classesn 120 · median 33.6% · middle half 30.1%–36.6%

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 ND4 across taxa

GC content of ND4 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 ND4 against log₁₀ maximum lifespan in 32 groups; 5 pass q < 0.05. Plot it in the explorer

Correlation of GC content of ND4 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.07	−0.05	0.002 (significant)	+0.08	+0.23
Ray-finned fishesclass Actinopterygii	827	+0.07	+0.02	0.074	+0.10	−0.02
Mammalsclass Mammalia	615	+0.46	+0.40	< 0.001 (significant)	+0.18	+0.32
Birdsclass Aves	405	+0.02	−0.00	0.77	−0.03	+0.06
Reptilesclass Reptilia	126	+0.01	+0.05	0.96	−0.07	−0.05
Sharks and raysclass Chondrichthyes	82	+0.02	−0.00	1.00	−0.09	−0.08
Amphibiansclass Amphibia	44	+0.11	+0.05	1.00	+0.11	–
Bivalvesclass Bivalvia	35	−0.28	−0.22	0.61	−0.02	–
Perciformesorder	208	+0.10	−0.07	0.25	+0.06	−0.10
Passeriformesorder	140	−0.19	−0.21	0.088	−0.04	−0.09
Artiodactylaorder	134	+0.36	+0.25	< 0.001 (significant)	+0.18	+0.15
Cypriniformesorder	127	+0.04	−0.04	0.75	+0.15	+0.48
Carnivoraorder	123	+0.32	+0.34	0.002 (significant)	+0.31	+0.33
Primatesorder	112	+0.48	+0.41	< 0.001 (significant)	+0.22	+0.24
Rodentiaorder	87	+0.11	+0.06	0.47	+0.07	+0.06
Squamataorder	60	+0.17	+0.24	0.72	+0.08	+0.22
Charadriiformesorder	51	+0.33	+0.35	0.12	+0.08	+0.28
Testudinesorder	49	−0.14	−0.15	0.75	−0.17	−0.25
Psittaciformesorder	44	−0.34	−0.23	0.10	−0.25	−0.04
Chiropteraorder	43	+0.14	+0.08	0.90	+0.29	+0.11
Clupeiformesorder	38	+0.01	+0.03	0.99	−0.12	–
Pleuronectiformesorder	35	+0.30	+0.21	0.26	−0.04	+0.65
Salmoniformesorder	35	+0.09	+0.04	0.92	+0.10	+0.07
Carcharhiniformesorder	31	+0.13	+0.07	0.74	−0.09	+0.02
Cetaceaorder	28	+0.27	+0.36	0.40	+0.12	−0.24
Anseriformesorder	25	−0.31	−0.36	0.43	−0.05	−0.17
Caudataorder	25	+0.23	+0.04	0.79	+0.23	–
Siluriformesorder	24	+0.48	+0.43	0.091	+0.35	–
Centrarchiformesorder	22	+0.32	+0.13	0.36	+0.32	–
Acipenseriformesorder	21	−0.23	−0.07	0.59	+0.14	−0.10
Rajiformesorder	21	−0.18	−0.16	0.90	−0.23	–
Scombriformesorder	21	+0.07	+0.01	0.97	+0.17	–

Length of ND4 against log₁₀ maximum lifespan in 24 groups; 4 pass q < 0.05. Plot it in the explorer

Correlation of Length of ND4 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.11	−0.11	< 0.001 (significant)	+0.01	+0.07
Ray-finned fishesclass Actinopterygii	827	−0.08	−0.13	0.034 (significant)	−0.02	+0.02
Mammalsclass Mammalia	615	−0.06	−0.06	0.16	−0.08	−0.18
Birdsclass Aves	405	+0.26	+0.22	< 0.001 (significant)	+0.05	+0.34
Reptilesclass Reptilia	126	+0.39	+0.39	< 0.001 (significant)	+0.18	+0.36
Sharks and raysclass Chondrichthyes	82	−0.01	−0.07	1.00	−0.02	−0.19
Amphibiansclass Amphibia	44	−0.02	−0.06	1.00	−0.01	–
Bivalvesclass Bivalvia	35	+0.10	+0.21	0.90	+0.15	–
Perciformesorder	208	+0.04	+0.03	0.67	−0.03	+0.04
Passeriformesorder	140	−0.07	−0.09	0.59	−0.15	+0.15
Artiodactylaorder	134	−0.09	−0.12	0.41	−0.15	−0.16
Cypriniformesorder	127	−0.08	−0.09	0.55	−0.04	+0.43
Carnivoraorder	123	−0.00	+0.12	0.98	−0.01	+0.16
Primatesorder	112	+0.10	+0.15	0.39	+0.00	−0.09
Rodentiaorder	87	+0.00	−0.07	1.00	−0.23	−0.06
Squamataorder	60	−0.02	−0.01	0.95	+0.13	+0.17
Charadriiformesorder	51	+0.03	+0.00	0.92	+0.04	+0.03
Testudinesorder	49	+0.25	+0.46	0.60	+0.18	+0.12
Psittaciformesorder	44	+0.06	+0.08	0.82	+0.02	−0.00
Pleuronectiformesorder	35	+0.33	+0.34	0.21	+0.04	–
Salmoniformesorder	35	+0.32	+0.34	0.41	+0.29	+0.21
Caudataorder	25	−0.31	−0.34	0.79	−0.07	–
Centrarchiformesorder	22	+0.15	+0.22	0.67	+0.07	–
Scombriformesorder	21	−0.33	−0.41	0.68	−0.05	–

GC skew of ND4 against log₁₀ maximum lifespan in 32 groups; 8 pass q < 0.05. Plot it in the explorer

Correlation of GC skew of ND4 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.23	−0.30	< 0.001 (significant)	−0.07	−0.16
Ray-finned fishesclass Actinopterygii	827	−0.11	−0.17	0.005 (significant)	−0.09	+0.11
Mammalsclass Mammalia	615	−0.24	−0.27	< 0.001 (significant)	−0.00	−0.14
Birdsclass Aves	405	−0.04	−0.07	0.57	+0.01	+0.03
Reptilesclass Reptilia	126	+0.19	+0.22	0.12	−0.08	+0.17
Sharks and raysclass Chondrichthyes	82	+0.03	−0.02	1.00	−0.35	+0.32
Amphibiansclass Amphibia	44	−0.02	−0.00	1.00	+0.07	–
Bivalvesclass Bivalvia	35	+0.14	+0.23	0.84	+0.06	–
Perciformesorder	208	−0.12	−0.12	0.17	−0.07	+0.30
Passeriformesorder	140	+0.24	+0.25	0.033 (significant)	+0.04	+0.06
Artiodactylaorder	134	−0.21	−0.04	0.040 (significant)	−0.01	−0.02
Cypriniformesorder	127	+0.04	+0.02	0.75	+0.10	+0.46
Carnivoraorder	123	+0.24	+0.16	0.025 (significant)	+0.09	+0.06
Primatesorder	112	−0.50	−0.48	< 0.001 (significant)	−0.13	−0.11
Rodentiaorder	87	−0.06	−0.02	0.71	−0.01	−0.10
Squamataorder	60	−0.13	−0.08	0.80	−0.00	+0.05
Charadriiformesorder	51	+0.29	+0.31	0.20	+0.25	+0.32
Testudinesorder	49	−0.24	−0.30	0.60	−0.12	−0.04
Psittaciformesorder	44	+0.30	+0.27	0.17	+0.20	−0.01
Chiropteraorder	43	+0.17	+0.13	0.90	+0.09	+0.22
Clupeiformesorder	38	+0.12	+0.17	0.87	−0.06	–
Pleuronectiformesorder	35	+0.37	+0.42	0.16	+0.27	+0.36
Salmoniformesorder	35	+0.03	+0.12	0.96	+0.07	+0.64
Carcharhiniformesorder	31	−0.22	−0.14	0.60	−0.02	+0.45
Cetaceaorder	28	−0.41	−0.40	0.14	−0.01	+0.05
Anseriformesorder	25	−0.01	−0.03	0.97	−0.07	+0.05
Caudataorder	25	+0.04	−0.03	0.91	+0.24	–
Siluriformesorder	24	−0.05	−0.09	0.89	+0.20	–
Centrarchiformesorder	22	+0.01	+0.18	0.98	+0.07	–
Acipenseriformesorder	21	−0.64	+0.03	0.013 (significant)	−0.71	−0.39
Rajiformesorder	21	+0.31	+0.40	0.89	−0.43	–
Scombriformesorder	21	−0.11	−0.05	0.92	−0.27	–

AT skew of ND4 against log₁₀ maximum lifespan in 32 groups; 7 pass q < 0.05. Plot it in the explorer

Correlation of AT skew of ND4 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.21	+0.25	< 0.001 (significant)	+0.06	+0.19
Ray-finned fishesclass Actinopterygii	827	+0.24	+0.21	< 0.001 (significant)	+0.08	−0.01
Mammalsclass Mammalia	615	+0.15	+0.14	< 0.001 (significant)	+0.05	+0.08
Birdsclass Aves	405	−0.11	−0.09	0.067	−0.07	−0.05
Reptilesclass Reptilia	126	+0.06	+0.01	0.71	+0.05	−0.09
Sharks and raysclass Chondrichthyes	82	+0.04	+0.13	1.00	+0.41	−0.23
Amphibiansclass Amphibia	44	−0.09	−0.12	1.00	−0.15	–
Bivalvesclass Bivalvia	35	+0.04	+0.19	0.95	−0.03	–
Perciformesorder	208	+0.15	+0.21	0.071	+0.02	−0.26
Passeriformesorder	140	−0.15	−0.09	0.20	−0.04	+0.01
Artiodactylaorder	134	+0.18	+0.04	0.097	+0.07	+0.01
Cypriniformesorder	127	+0.34	+0.37	0.001 (significant)	−0.06	−0.56
Carnivoraorder	123	+0.01	+0.06	0.95	+0.05	+0.26
Primatesorder	112	+0.23	+0.27	0.024 (significant)	+0.08	+0.20
Rodentiaorder	87	−0.22	−0.22	0.12	+0.06	−0.07
Squamataorder	60	−0.05	−0.06	0.90	−0.02	−0.26
Charadriiformesorder	51	−0.11	−0.10	0.74	−0.20	−0.05
Testudinesorder	49	+0.21	+0.32	0.60	+0.03	+0.07
Psittaciformesorder	44	−0.43	−0.38	0.027 (significant)	−0.33	−0.09
Chiropteraorder	43	+0.00	−0.02	0.99	+0.07	−0.11
Clupeiformesorder	38	+0.26	+0.24	0.58	+0.10	–
Pleuronectiformesorder	35	−0.21	−0.24	0.46	−0.24	−0.26
Salmoniformesorder	35	+0.27	+0.19	0.46	−0.18	+0.27
Carcharhiniformesorder	31	+0.12	+0.13	0.75	−0.02	−0.28
Cetaceaorder	28	+0.22	+0.24	0.52	−0.05	−0.28
Anseriformesorder	25	+0.08	+0.05	0.87	+0.29	−0.01
Caudataorder	25	−0.37	−0.31	0.70	−0.42	–
Siluriformesorder	24	+0.30	+0.33	0.37	+0.01	–
Centrarchiformesorder	22	+0.25	+0.16	0.49	+0.24	–
Acipenseriformesorder	21	+0.59	−0.08	0.026 (significant)	+0.69	+0.32
Rajiformesorder	21	−0.35	−0.44	0.89	+0.53	–
Scombriformesorder	21	+0.61	+0.65	0.095	+0.50	–

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.

ND4 aligned across species

2,316 species, 671 columns; 460 columns have a residue in at least half of the species, and in 187 of those one residue is in 90% or more. MAFFT v7.526, FFT-NS-2 (progressive)

Loading the alignment of ND4: 2,316 species, 671 columns.

All alignment files

Codon usage of ND4

Vertebrates, vertebrate mitochondrial code

Most used codons

Share of all 1,024,154 sense codons of ND4 in 2,231 vertebrates

CUALeu7.7%
AUAMet4.9%
AUCIle4.3%
AUUIle4.3%
CUCLeu4.2%
ACAThr3.9%
ACCThr3.5%
CUULeu3.5%

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 ND4, 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	UUC1.12	UUC1.14	UUC1.56	UUU1.00	UUC1.17	UUU1.09	UUU1.32
LeuL · 6 codons	CUA2.28	CUA2.67	CUA2.97	CUA1.68	CUA2.81	CUA1.58	UUA1.87
IleI · 2 codons	AUC1.00	AUU1.04	AUC1.48	AUU1.17	AUC1.07	AUU1.21	AUU1.43
MetM · 2 codons	AUA1.56	AUA1.71	AUA1.69	AUA1.31	AUA1.74	AUA1.72	AUA1.68
ValV · 4 codons	GUA1.80	GUA2.16	GUA1.93	GUA1.55	GUA2.35	GUA1.62	GUA1.81
SerS · 6 codons	UCA1.72	UCA1.80	UCA1.91	UCC1.82	UCA2.44	UCC1.70	UCA2.19
ProP · 4 codons	CCC1.64	CCC1.61	CCC1.72	CCC1.77	CCA2.38	CCA1.88	CCA2.12
ThrT · 4 codons	ACA1.67	ACA1.92	ACC1.80	ACC1.63	ACA1.88	ACA1.74	ACA1.72
AlaA · 4 codons	GCC1.78	GCC1.58	GCC1.97	GCC1.81	GCC1.84	GCC1.68	GCC1.66
TyrY · 2 codons	UAC1.20	UAC1.12	UAC1.57	UAC1.15	UAC1.25	UAC1.05	UAU1.19
HisH · 2 codons	CAC1.40	CAC1.27	CAC1.63	CAC1.39	CAC1.44	CAC1.01	CAC1.16
GlnQ · 2 codons	CAA1.75	CAA1.81	CAA1.82	CAA1.63	CAA1.86	CAA1.88	CAA1.82
AsnN · 2 codons	AAC1.37	AAC1.27	AAC1.71	AAC1.35	AAC1.40	AAC1.17	AAC1.03
LysK · 2 codons	AAA1.74	AAA1.83	AAA1.84	AAA1.57	AAA1.86	AAA1.90	AAA1.83
AspD · 2 codons	GAC1.48	GAC1.41	GAC1.69	GAC1.51	GAC1.56	GAC1.09	GAC1.27
GluE · 2 codons	GAA1.62	GAA1.72	GAA1.69	GAA1.50	GAA1.79	GAA1.74	GAA1.66
CysC · 2 codons	UGC1.44	UGC1.40	UGC1.75	UGC1.40	UGC1.46	UGC1.22	UGC1.24
TrpW · 2 codons	UGA1.68	UGA1.80	UGA1.83	UGA1.56	UGA1.74	UGA1.85	UGA1.74
ArgR · 4 codons	CGA2.47	CGA2.71	CGA2.71	CGA2.14	CGA2.85	CGA2.84	CGA2.41
GlyG · 4 codons	GGA1.47	GGA1.71	GGC1.64	GGC1.43	GGA1.82	GGA1.51	GGA1.63

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.