D-loopControl region (D-loop)

The control region, or D-loop, is the main non-coding region of animal mtDNA. In vertebrates it holds the origin of heavy-strand replication and the promoters that start transcription of both strands, and it often carries a short third strand of DNA (7S DNA) that forms the displacement loop. It evolves faster and varies more in length than the genes.

Median length

1,051 bp

Range 1–4,608 bp

Median GC content

38.3%

Middle half 35.4%–41.5%

Species with data

1,976

Of 2,335 genomes

Annotated D-loop

1,983

Two copies in 126 genomes

D-loop in the mitochondrial genome of

Human Homo sapiens

RefSeq NC_012920.1 · 16,569 bp · GC 44.4% · D-loop at 16,024–576, 1,122 bp · Species page

D-loopControl region

Control region (D-loop)

Position: 16,024–576 (across the origin)
Length: 1,122 bp
Strand: Non-coding
GC content: 46.6%

D-loop 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 D-loop across classes

1,975 species, reference strand as deposited in RefSeq

Mammalsn 552 · median 40.6% · middle half 38.3%–42.8%

Birdsn 368 · median 42.3% · middle half 40.5%–44.0%

Ray-finned fishesn 772 · median 36.7% · middle half 34.7%–38.4%

Reptilesn 116 · median 33.1% · middle half 30.8%–38.9%

Sharks and raysn 73 · median 33.9% · middle half 33.0%–34.9%

Amphibiansn 44 · median 34.9% · middle half 34.1%–36.7%

Other classesn 50 · median 28.2% · middle half 21.4%–34.7%

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 D-loop across taxa

GC content of D-loop 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 D-loop against log₁₀ maximum lifespan in 31 groups; 5 pass q < 0.05. Plot it in the explorer

Correlation of GC content of D-loop with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	1,873	+0.13	+0.18	< 0.001 (significant)	+0.03	+0.17
Ray-finned fishesclass Actinopterygii	716	−0.09	−0.13	0.028 (significant)	−0.00	−0.11
Mammalsclass Mammalia	543	+0.37	+0.33	< 0.001 (significant)	+0.08	+0.38
Birdsclass Aves	354	+0.10	−0.06	0.10	+0.08	+0.18
Reptilesclass Reptilia	111	−0.23	−0.24	0.083	−0.02	−0.06
Sharks and raysclass Chondrichthyes	69	+0.17	+0.03	1.00	+0.04	+0.30
Amphibiansclass Amphibia	41	−0.12	−0.12	1.00	−0.01	–
Perciformesorder	155	−0.24	−0.30	0.008 (significant)	−0.06	−0.24
Artiodactylaorder	118	+0.17	+0.10	0.13	+0.08	+0.04
Cypriniformesorder	116	+0.03	−0.05	0.80	+0.09	+0.35
Carnivoraorder	113	−0.05	−0.11	0.73	+0.13	+0.10
Passeriformesorder	111	−0.12	−0.23	0.38	−0.04	+0.16
Primatesorder	95	+0.51	+0.45	< 0.001 (significant)	−0.01	+0.18
Rodentiaorder	73	+0.22	+0.32	0.15	+0.22	+0.08
Testudinesorder	48	+0.09	+0.08	0.87	−0.09	−0.16
Squamataorder	47	+0.21	+0.30	0.63	+0.13	+0.34
Charadriiformesorder	46	+0.10	+0.10	0.76	+0.08	+0.13
Psittaciformesorder	42	+0.04	+0.08	0.89	+0.30	+0.04
Clupeiformesorder	36	−0.06	−0.09	0.98	−0.13	–
Chiropteraorder	35	−0.19	−0.17	0.90	+0.10	−0.25
Salmoniformesorder	35	−0.09	−0.16	0.92	+0.08	−0.10
Carcharhiniformesorder	28	+0.35	+0.19	0.42	+0.26	+0.53
Cetaceaorder	28	−0.13	+0.01	0.73	−0.19	−0.52
Caudataorder	24	+0.23	+0.17	0.79	+0.31	–
Siluriformesorder	23	−0.30	+0.06	0.37	−0.23	–
Anseriformesorder	22	−0.55	−0.68	0.22	−0.34	−0.54
Centrarchiformesorder	22	+0.14	−0.08	0.69	−0.21	–
Acipenseriformesorder	21	−0.03	+0.01	0.95	−0.59	+0.28
Pleuronectiformesorder	21	+0.40	+0.47	0.24	+0.38	–
Scombriformesorder	19	−0.05	−0.22	0.98	+0.17	–
Rajiformesorder	14	−0.12	−0.16	0.91	−0.15	–

Length of D-loop against log₁₀ maximum lifespan in 31 groups; 3 pass q < 0.05. Plot it in the explorer

Correlation of Length of D-loop with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	1,873	+0.10	+0.17	< 0.001 (significant)	+0.01	+0.15
Ray-finned fishesclass Actinopterygii	716	+0.02	−0.03	0.75	+0.09	+0.10
Mammalsclass Mammalia	543	−0.03	+0.02	0.49	+0.16	+0.13
Birdsclass Aves	354	+0.02	+0.01	0.80	−0.14	−0.00
Reptilesclass Reptilia	111	−0.13	−0.21	0.38	−0.01	−0.07
Sharks and raysclass Chondrichthyes	69	−0.06	−0.02	1.00	−0.05	−0.08
Amphibiansclass Amphibia	41	−0.07	+0.01	1.00	+0.02	–
Perciformesorder	155	+0.08	−0.03	0.46	+0.11	−0.04
Artiodactylaorder	118	+0.13	+0.18	0.26	+0.31	+0.01
Cypriniformesorder	116	−0.06	−0.32	0.67	+0.13	+0.11
Carnivoraorder	113	+0.37	+0.38	< 0.001 (significant)	+0.20	+0.18
Passeriformesorder	111	+0.04	+0.07	0.85	−0.02	+0.05
Primatesorder	95	−0.12	−0.14	0.34	+0.23	+0.12
Rodentiaorder	73	+0.05	+0.30	0.76	−0.13	−0.01
Testudinesorder	48	+0.14	+0.14	0.75	+0.12	+0.11
Squamataorder	47	−0.01	−0.09	1.00	−0.25	−0.08
Charadriiformesorder	46	−0.16	−0.13	0.60	−0.14	−0.30
Psittaciformesorder	42	−0.09	−0.11	0.76	−0.32	+0.00
Clupeiformesorder	36	−0.05	−0.00	0.98	−0.08	–
Chiropteraorder	35	+0.43	+0.44	0.37	+0.18	+0.44
Salmoniformesorder	35	−0.01	+0.01	0.99	−0.21	−0.02
Carcharhiniformesorder	28	−0.36	−0.02	0.42	−0.26	−0.55
Cetaceaorder	28	−0.16	+0.16	0.65	−0.16	−0.04
Caudataorder	24	+0.03	+0.19	0.93	−0.04	–
Siluriformesorder	23	−0.12	−0.14	0.75	−0.10	–
Anseriformesorder	22	+0.41	+0.23	0.40	+0.18	+0.18
Centrarchiformesorder	22	+0.11	+0.35	0.77	+0.34	–
Acipenseriformesorder	21	+0.60	+0.31	0.022 (significant)	+0.68	+0.37
Pleuronectiformesorder	21	+0.55	+0.62	0.092	+0.16	–
Scombriformesorder	19	−0.01	+0.22	0.98	−0.16	–
Rajiformesorder	14	+0.01	−0.27	0.99	+0.06	–

GC skew of D-loop against log₁₀ maximum lifespan in 31 groups; 4 pass q < 0.05. Plot it in the explorer

Correlation of GC skew of D-loop with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	1,853	−0.16	−0.21	< 0.001 (significant)	−0.03	−0.13
Ray-finned fishesclass Actinopterygii	697	−0.06	−0.10	0.15	+0.01	+0.03
Mammalsclass Mammalia	542	−0.08	−0.07	0.11	−0.10	−0.25
Birdsclass Aves	354	+0.12	+0.29	0.048 (significant)	−0.06	+0.00
Reptilesclass Reptilia	111	+0.24	+0.20	0.057	−0.07	+0.23
Sharks and raysclass Chondrichthyes	69	−0.10	+0.07	1.00	−0.17	−0.26
Amphibiansclass Amphibia	41	+0.06	+0.06	1.00	−0.01	–
Perciformesorder	150	−0.04	−0.09	0.74	−0.05	+0.17
Artiodactylaorder	117	−0.27	−0.35	0.011 (significant)	−0.21	−0.09
Cypriniformesorder	115	+0.13	+0.12	0.34	−0.24	+0.00
Carnivoraorder	113	+0.13	+0.17	0.27	−0.02	−0.01
Passeriformesorder	111	+0.09	+0.07	0.56	+0.02	−0.06
Primatesorder	95	−0.38	−0.37	< 0.001 (significant)	−0.37	+0.05
Rodentiaorder	73	+0.25	+0.19	0.098	+0.12	+0.12
Testudinesorder	48	+0.01	−0.01	0.98	−0.08	+0.07
Squamataorder	47	+0.11	−0.20	0.85	−0.06	+0.25
Charadriiformesorder	46	−0.11	+0.03	0.75	−0.04	+0.05
Psittaciformesorder	42	+0.14	+0.20	0.62	−0.24	+0.10
Chiropteraorder	35	−0.30	−0.23	0.67	−0.06	−0.31
Clupeiformesorder	35	+0.26	+0.27	0.58	+0.49	–
Salmoniformesorder	35	−0.39	−0.34	0.27	−0.35	−0.42
Carcharhiniformesorder	28	−0.32	+0.12	0.45	−0.23	−0.48
Cetaceaorder	28	+0.47	+0.45	0.092	+0.06	−0.27
Caudataorder	24	−0.46	−0.44	0.63	−0.27	–
Anseriformesorder	22	−0.32	−0.20	0.43	−0.23	−0.09
Centrarchiformesorder	22	+0.38	+0.30	0.28	+0.64	–
Siluriformesorder	22	−0.12	−0.28	0.75	−0.10	–
Acipenseriformesorder	21	−0.50	−0.19	0.080	−0.65	−0.21
Pleuronectiformesorder	21	−0.56	−0.50	0.092	+0.14	–
Scombriformesorder	19	−0.20	−0.15	0.85	−0.02	–
Rajiformesorder	14	+0.16	+0.18	0.90	−0.42	–

AT skew of D-loop against log₁₀ maximum lifespan in 31 groups; 2 pass q < 0.05. Plot it in the explorer

Correlation of AT skew of D-loop with log10 maximum lifespan by group
Group	n	Pearson r	Spearman ρ	q	PIC r	Partial r
All speciesevery class	1,862	+0.05	+0.13	0.031 (significant)	−0.01	−0.02
Ray-finned fishesclass Actinopterygii	712	+0.06	+0.24	0.13	−0.02	+0.08
Mammalsclass Mammalia	543	+0.06	+0.09	0.19	+0.05	+0.12
Birdsclass Aves	348	−0.05	−0.05	0.51	+0.01	−0.02
Reptilesclass Reptilia	111	+0.08	+0.21	0.63	−0.05	+0.04
Sharks and raysclass Chondrichthyes	68	+0.12	+0.14	1.00	+0.21	+0.22
Amphibiansclass Amphibia	41	+0.25	+0.32	1.00	+0.08	–
Perciformesorder	155	+0.18	+0.34	0.063	+0.05	+0.18
Artiodactylaorder	118	−0.15	−0.07	0.19	+0.00	−0.04
Cypriniformesorder	116	+0.01	+0.29	0.95	−0.10	−0.22
Carnivoraorder	113	+0.37	+0.36	< 0.001 (significant)	+0.17	+0.34
Passeriformesorder	111	−0.12	−0.12	0.38	−0.04	−0.09
Primatesorder	95	+0.15	+0.11	0.21	+0.28	+0.30
Rodentiaorder	73	−0.12	−0.15	0.46	−0.27	−0.18
Testudinesorder	48	+0.07	+0.05	0.92	−0.17	−0.04
Squamataorder	47	−0.08	+0.07	0.90	+0.02	+0.11
Charadriiformesorder	46	−0.13	−0.21	0.70	−0.03	−0.02
Clupeiformesorder	36	+0.12	+0.28	0.87	+0.08	–
Psittaciformesorder	36	+0.04	−0.17	0.89	+0.10	−0.09
Chiropteraorder	35	+0.34	+0.32	0.48	+0.28	+0.39
Salmoniformesorder	35	+0.49	+0.46	0.11	+0.23	+0.69
Cetaceaorder	28	+0.07	+0.20	0.85	+0.05	−0.12
Carcharhiniformesorder	27	−0.27	−0.39	0.52	−0.31	−0.31
Caudataorder	24	+0.37	+0.49	0.79	+0.07	–
Siluriformesorder	23	+0.38	+0.71	0.23	+0.30	–
Anseriformesorder	22	+0.19	+0.09	0.69	+0.04	−0.18
Centrarchiformesorder	22	−0.15	−0.17	0.67	−0.17	–
Acipenseriformesorder	21	+0.09	+0.06	0.83	−0.53	+0.02
Pleuronectiformesorder	21	+0.12	+0.23	0.80	−0.27	–
Scombriformesorder	19	+0.16	+0.09	0.89	+0.18	–
Rajiformesorder	14	+0.08	+0.12	0.96	+0.44	–

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.