ND3NADH dehydrogenase subunit 3

ND3 is a small membrane subunit of Complex I (NADH:ubiquinone oxidoreductase), close to the junction of the membrane and peripheral arms. A loop of ND3 near the ubiquinone-binding site changes conformation when the enzyme switches between its active and deactive states.

Median length

349 bp

Range 304–423 bp

Median GC content

43.8%

Middle half 40.2%–47.3%

Species with data

2,335

Of 2,335 genomes

Strand

+ strand

In 2,326 of 2,335 genomes

ND3 in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · ND3 at 10,059–10,404, 346 bp, + strand · Species page

ND3Protein-coding gene

NADH dehydrogenase subunit 3

Position: 10,059–10,404
Length: 346 bp
Strand: +
GC content: 40.2%

ND3 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 ND3 across classes

2,335 species, reference strand as deposited in RefSeq

Mammalsn 627 · median 39.9% · middle half 37.3%–41.9%

Birdsn 423 · median 45.6% · middle half 44.2%–47.5%

Ray-finned fishesn 895 · median 47.3% · middle half 44.4%–49.3%

Reptilesn 136 · median 40.1% · middle half 38.2%–43.4%

Sharks and raysn 87 · median 42.1% · middle half 40.3%–45.0%

Amphibiansn 47 · median 39.1% · middle half 35.5%–42.8%

Other classesn 120 · median 34.9% · middle half 30.6%–38.5%

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 ND3 across taxa

GC content of ND3 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 ND3 against log₁₀ maximum lifespan in 32 groups; 5 pass q < 0.05. Plot it in the explorer

Correlation of GC content of ND3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.07	−0.04	0.001 (significant)	+0.12	+0.15
Ray-finned fishesclass Actinopterygii	827	+0.17	+0.13	< 0.001 (significant)	+0.19	−0.00
Mammalsclass Mammalia	615	+0.34	+0.27	< 0.001 (significant)	+0.05	+0.10
Birdsclass Aves	405	−0.00	−0.03	0.97	+0.07	−0.09
Reptilesclass Reptilia	126	+0.10	+0.12	0.48	+0.08	+0.10
Sharks and raysclass Chondrichthyes	82	−0.02	−0.04	1.00	+0.24	−0.06
Amphibiansclass Amphibia	44	+0.09	+0.06	1.00	+0.09	–
Bivalvesclass Bivalvia	35	−0.16	−0.12	0.81	+0.12	–
Perciformesorder	208	+0.11	+0.01	0.20	−0.02	−0.15
Passeriformesorder	140	−0.02	+0.00	0.91	+0.03	+0.06
Artiodactylaorder	134	+0.15	+0.05	0.17	−0.05	−0.01
Cypriniformesorder	127	+0.07	−0.02	0.61	+0.10	+0.13
Carnivoraorder	123	+0.35	+0.33	< 0.001 (significant)	+0.17	+0.22
Primatesorder	112	+0.04	+0.04	0.78	−0.05	+0.02
Rodentiaorder	87	+0.32	+0.30	0.017 (significant)	+0.10	+0.24
Squamataorder	60	+0.19	+0.17	0.63	+0.12	+0.31
Charadriiformesorder	51	−0.07	−0.12	0.81	−0.06	−0.26
Testudinesorder	49	+0.32	+0.29	0.60	+0.09	+0.19
Psittaciformesorder	44	−0.10	−0.02	0.72	+0.12	+0.14
Chiropteraorder	43	−0.00	−0.04	0.99	+0.15	−0.08
Clupeiformesorder	38	+0.02	+0.05	0.99	+0.74	–
Pleuronectiformesorder	35	+0.30	+0.23	0.25	−0.07	+0.60
Salmoniformesorder	35	+0.43	+0.44	0.21	+0.10	+0.36
Carcharhiniformesorder	31	−0.05	−0.03	0.91	−0.23	+0.05
Cetaceaorder	28	+0.10	+0.30	0.80	+0.11	−0.33
Anseriformesorder	25	+0.15	+0.20	0.73	+0.22	+0.25
Caudataorder	25	+0.22	+0.14	0.79	+0.13	–
Siluriformesorder	24	+0.56	+0.55	0.051	+0.34	–
Centrarchiformesorder	22	+0.46	+0.29	0.23	+0.43	–
Acipenseriformesorder	21	+0.44	+0.42	0.15	+0.09	−0.26
Rajiformesorder	21	−0.14	+0.07	0.90	+0.36	–
Scombriformesorder	21	+0.21	+0.11	0.85	+0.15	–

Length of ND3 against log₁₀ maximum lifespan in 31 groups; 5 pass q < 0.05. Plot it in the explorer

Correlation of Length of ND3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.08	−0.18	< 0.001 (significant)	−0.06	+0.07
Ray-finned fishesclass Actinopterygii	827	−0.10	−0.11	0.008 (significant)	−0.19	−0.12
Mammalsclass Mammalia	615	−0.26	−0.34	< 0.001 (significant)	−0.03	−0.13
Birdsclass Aves	405	−0.11	−0.24	0.060	−0.01	−0.10
Reptilesclass Reptilia	126	+0.14	+0.31	0.29	−0.07	+0.21
Sharks and raysclass Chondrichthyes	82	−0.07	−0.11	1.00	−0.02	+0.19
Amphibiansclass Amphibia	44	+0.04	+0.04	1.00	+0.10	–
Bivalvesclass Bivalvia	35	+0.41	+0.37	0.50	+0.30	–
Perciformesorder	208	−0.11	−0.06	0.22	+0.05	−0.14
Passeriformesorder	140	−0.02	−0.03	0.92	−0.01	−0.07
Artiodactylaorder	134	+0.22	+0.26	0.028 (significant)	+0.01	+0.21
Cypriniformesorder	127	+0.05	+0.01	0.69	+0.06	−0.12
Carnivoraorder	123	−0.07	−0.03	0.58	−0.01	−0.08
Primatesorder	112	−0.01	−0.06	0.94	+0.03	+0.08
Rodentiaorder	87	−0.31	−0.58	0.018 (significant)	−0.10	−0.09
Squamataorder	60	−0.34	−0.28	0.19	−0.09	−0.22
Charadriiformesorder	51	−0.19	−0.21	0.48	−0.09	−0.18
Testudinesorder	49	−0.04	−0.04	0.95	−0.09	−0.10
Psittaciformesorder	44	−0.35	−0.31	0.100	−0.22	−0.19
Chiropteraorder	43	−0.36	−0.33	0.38	−0.24	−0.47
Clupeiformesorder	38	−0.19	−0.15	0.75	−0.96	–
Pleuronectiformesorder	35	+0.16	+0.18	0.62	+0.17	+0.54
Salmoniformesorder	35	−0.05	−0.12	0.95	+0.26	−0.16
Carcharhiniformesorder	31	−0.18	−0.21	0.62	−0.15	+0.05
Cetaceaorder	28	+0.07	+0.09	0.85	−0.22	−0.06
Caudataorder	25	−0.07	+0.02	0.89	+0.11	–
Siluriformesorder	24	+0.26	+0.26	0.42	+0.13	–
Centrarchiformesorder	22	+0.26	+0.29	0.48	+0.37	–
Acipenseriformesorder	21	+0.21	+0.27	0.63	+0.11	−0.14
Rajiformesorder	21	−0.00	0.00	1.00	+0.08	–
Scombriformesorder	21	−0.17	−0.14	0.85	−0.32	–

GC skew of ND3 against log₁₀ maximum lifespan in 32 groups; 7 pass q < 0.05. Plot it in the explorer

Correlation of GC skew of ND3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	−0.23	−0.27	< 0.001 (significant)	−0.09	−0.09
Ray-finned fishesclass Actinopterygii	827	−0.14	−0.18	< 0.001 (significant)	−0.11	+0.14
Mammalsclass Mammalia	615	−0.28	−0.34	< 0.001 (significant)	−0.05	−0.13
Birdsclass Aves	405	+0.01	−0.04	0.91	−0.08	+0.10
Reptilesclass Reptilia	126	+0.21	+0.19	0.096	−0.02	+0.22
Sharks and raysclass Chondrichthyes	82	+0.09	−0.00	1.00	−0.11	+0.11
Amphibiansclass Amphibia	44	−0.03	−0.06	1.00	−0.21	–
Bivalvesclass Bivalvia	35	+0.24	+0.37	0.71	+0.23	–
Perciformesorder	208	−0.00	+0.00	0.99	+0.03	+0.28
Passeriformesorder	140	+0.31	+0.29	0.012 (significant)	−0.05	+0.03
Artiodactylaorder	134	−0.07	+0.02	0.54	−0.09	+0.03
Cypriniformesorder	127	−0.18	−0.20	0.12	−0.06	+0.38
Carnivoraorder	123	−0.08	−0.12	0.54	+0.03	+0.04
Primatesorder	112	−0.38	−0.36	< 0.001 (significant)	−0.02	−0.02
Rodentiaorder	87	+0.07	+0.09	0.65	+0.01	+0.08
Squamataorder	60	+0.06	−0.00	0.90	−0.01	+0.32
Charadriiformesorder	51	+0.28	+0.26	0.21	+0.03	+0.33
Testudinesorder	49	+0.02	+0.00	0.97	+0.00	+0.15
Psittaciformesorder	44	+0.02	+0.04	0.94	−0.13	−0.08
Chiropteraorder	43	−0.09	−0.12	0.90	−0.11	−0.06
Clupeiformesorder	38	+0.09	+0.10	0.94	+0.51	–
Pleuronectiformesorder	35	+0.31	+0.24	0.24	−0.04	−0.10
Salmoniformesorder	35	+0.16	+0.19	0.72	+0.25	+0.50
Carcharhiniformesorder	31	−0.18	−0.24	0.62	+0.08	+0.15
Cetaceaorder	28	−0.46	−0.44	0.10	−0.47	−0.42
Anseriformesorder	25	+0.49	+0.49	0.22	+0.32	+0.45
Caudataorder	25	−0.15	−0.30	0.84	−0.43	–
Siluriformesorder	24	−0.57	−0.65	0.044 (significant)	−0.30	–
Centrarchiformesorder	22	−0.18	−0.08	0.60	+0.01	–
Acipenseriformesorder	21	−0.62	+0.00	0.015 (significant)	−0.71	−0.40
Rajiformesorder	21	+0.28	+0.36	0.89	−0.20	–
Scombriformesorder	21	+0.03	+0.03	0.98	−0.02	–

AT skew of ND3 against log₁₀ maximum lifespan in 32 groups; 7 pass q < 0.05. Plot it in the explorer

Correlation of AT skew of ND3 with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	2,202	+0.28	+0.29	< 0.001 (significant)	+0.01	+0.10
Ray-finned fishesclass Actinopterygii	827	+0.05	+0.01	0.21	−0.01	−0.08
Mammalsclass Mammalia	615	+0.32	+0.29	< 0.001 (significant)	+0.07	+0.11
Birdsclass Aves	405	−0.07	−0.04	0.25	+0.01	+0.05
Reptilesclass Reptilia	126	−0.01	−0.01	0.98	+0.05	−0.24
Sharks and raysclass Chondrichthyes	82	+0.07	+0.13	1.00	−0.05	−0.07
Amphibiansclass Amphibia	44	−0.10	−0.11	1.00	+0.10	–
Bivalvesclass Bivalvia	35	+0.12	+0.35	0.87	−0.05	–
Perciformesorder	208	+0.01	+0.03	0.93	−0.03	−0.27
Passeriformesorder	140	−0.22	−0.18	0.046 (significant)	−0.05	−0.05
Artiodactylaorder	134	+0.01	−0.02	0.94	+0.04	−0.07
Cypriniformesorder	127	+0.15	+0.09	0.22	+0.07	−0.46
Carnivoraorder	123	−0.09	−0.00	0.45	+0.07	+0.03
Primatesorder	112	+0.26	+0.36	0.011 (significant)	+0.00	+0.10
Rodentiaorder	87	−0.27	−0.27	0.046 (significant)	+0.03	−0.10
Squamataorder	60	−0.00	+0.03	1.00	+0.06	−0.34
Charadriiformesorder	51	−0.33	−0.33	0.12	−0.11	−0.26
Testudinesorder	49	+0.21	+0.25	0.60	+0.05	−0.01
Psittaciformesorder	44	−0.14	−0.11	0.60	+0.06	+0.09
Chiropteraorder	43	+0.15	+0.03	0.90	+0.28	+0.13
Clupeiformesorder	38	+0.19	+0.14	0.75	−0.69	–
Pleuronectiformesorder	35	+0.11	+0.23	0.76	+0.35	−0.13
Salmoniformesorder	35	−0.26	−0.31	0.46	−0.25	−0.38
Carcharhiniformesorder	31	+0.24	+0.25	0.56	−0.08	−0.18
Cetaceaorder	28	+0.57	+0.64	0.028 (significant)	+0.52	−0.09
Anseriformesorder	25	−0.34	−0.31	0.43	−0.25	−0.24
Caudataorder	25	−0.08	+0.07	0.89	+0.22	–
Siluriformesorder	24	+0.14	+0.10	0.68	−0.02	–
Centrarchiformesorder	22	−0.05	−0.20	0.92	−0.14	–
Acipenseriformesorder	21	−0.60	−0.28	0.022 (significant)	−0.66	−0.25
Rajiformesorder	21	−0.32	−0.40	0.89	−0.07	–
Scombriformesorder	21	+0.44	+0.37	0.44	+0.11	–

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.

ND3 aligned across species

2,316 species, 203 columns; 116 columns have a residue in at least half of the species, and in 54 of those one residue is in 90% or more. MAFFT v7.526, FFT-NS-2 (progressive)

Loading the alignment of ND3: 2,316 species, 203 columns.

All alignment files

Codon usage of ND3

Vertebrates, vertebrate mitochondrial code

Most used codons

Share of all 257,831 sense codons of ND3 in 2,231 vertebrates

CUALeu8.6%
CUCLeu5.2%
GAAGlu4.4%
UUCPhe3.9%
AUUIle3.9%
AUCIle3.8%
GCCAla3.7%
CUULeu3.7%

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 ND3, 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	UUC1.05	UUC1.57	UUC1.00	UUC1.11	UUU1.10	UUU1.45
LeuL · 6 codons	CUA2.22	CUA2.65	CUA2.93	CUA1.61	CUA2.72	UUA1.55	UUA1.68
IleI · 2 codons	AUU1.01	AUU1.08	AUC1.53	AUU1.21	AUC1.07	AUU1.06	AUU1.42
MetM · 2 codons	AUA1.51	AUA1.81	AUA1.72	AUG1.01	AUA1.70	AUG1.37	AUA1.37
ValV · 4 codons	GUA1.64	GUA2.27	GUA2.51	GUC1.37	GUA2.25	GUA1.44	GUA1.64
SerS · 6 codons	UCC2.20	UCA1.94	UCC2.42	UCC2.72	UCA2.32	UCC2.20	UCA2.79
ProP · 4 codons	CCC1.57	CCC1.52	CCA2.23	CCC1.94	CCA2.61	CCA1.88	CCA2.26
ThrT · 4 codons	ACC1.62	ACA1.84	ACC2.23	ACC1.72	ACA1.85	ACA1.77	ACA1.72
AlaA · 4 codons	GCC1.92	GCC1.75	GCC2.16	GCC2.08	GCC1.66	GCA1.78	GCC1.53
TyrY · 2 codons	UAC1.12	UAC1.08	UAC1.47	UAC1.03	UAC1.22	UAU1.29	UAU1.14
HisH · 2 codons	CAC1.45	CAC1.37	CAC1.53	CAC1.46	CAC1.43	CAU1.50	CAC1.71
GlnQ · 2 codons	CAA1.76	CAA1.82	CAA1.84	CAA1.65	CAA1.81	CAA1.91	CAA1.89
AsnN · 2 codons	AAC1.38	AAC1.26	AAC1.79	AAC1.35	AAC1.32	AAC1.14	AAC1.13
LysK · 2 codons	AAA1.68	AAA1.79	AAA1.90	AAA1.19	AAA1.90	AAA1.96	AAA1.96
AspD · 2 codons	GAC1.51	GAC1.47	GAC1.78	GAC1.51	GAC1.44	GAU1.05	GAC1.20
GluE · 2 codons	GAA1.67	GAA1.78	GAA1.77	GAA1.54	GAA1.67	GAA1.79	GAA1.64
CysC · 2 codons	UGC1.13	UGU1.01	UGC1.08	UGC1.28	UGC1.21	UGU1.40	UGC1.32
TrpW · 2 codons	UGA1.70	UGA1.82	UGA1.78	UGA1.58	UGA1.75	UGA1.78	UGA1.63
ArgR · 4 codons	CGA1.97	CGC2.71	CGA2.96	CGA2.05	CGA1.88	CGC2.53	CGA2.64
GlyG · 4 codons	GGA1.80	GGA2.27	GGA2.12	GGA1.52	GGA1.66	GGA1.87	GGA1.74

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.