family · mtDNA statistics

Rajidae

19 species in 8 genera. Every region of their mitochondrial genomes, side by side.

Group

species

41.2%

mean GC, whole genome

SD 0.7, range 39.6–42.4%

16,911

median genome length, bp

Range 16,719–17,127 bp

genera

Regions

GC content of each region across Rajidae, % of A + C + G + T

Parameter

Chart

GC % of every region
Region
Whole genome	19	41.18%	0.67	0.016	39.60%Raja undulata	41.24%	42.39%Okamejei kenojei	0.14	0.56
Protein-coding	19	42.41%	0.82	0.019	40.72%Raja undulata	42.54%	43.92%Okamejei kenojei	0.10	0.67
All rRNA	19	40.09%	0.43	0.011	39.42%Leucoraja erinaceus	40.07%	40.86%Okamejei kenojei	0.34	0.16
All tRNA	19	39.18%	0.36	0.009	38.40%Leucoraja erinaceus	39.28%	39.73%Dipturus batis	0.37	0.12
12S rRNA	19	41.88%	0.47	0.011	40.99%Beringraja binoculata	41.68%	42.71%Caliraja rhina	0.22	0.37
16S rRNA	19	39.06%	0.56	0.014	38.24%Leucoraja erinaceus	38.96%	40.33%Okamejei kenojei	0.30	0.21
D-loop	16	34.44%	0.90	0.026	32.40%Raja undulata	34.47%	36.48%Leucoraja naevus	0.02	0.95
ND1	19	43.64%	1.11	0.025	41.33%Leucoraja erinaceus	43.79%	45.44%Okamejei kenojei	0.21	0.4
ND2	19	42.73%	1.08	0.025	40.11%Raja undulata	42.64%	44.74%Leucoraja naevus	0.03	0.89
COX1	19	43.01%	0.90	0.021	41.36%Raja undulata	43.10%	44.83%Okamejei kenojei	0.13	0.58
COX2	19	38.90%	0.72	0.019	37.63%Leucoraja erinaceus	38.93%	40.38%Beringraja binoculata	0.06	0.79
ATP8	19	36.78%	1.31	0.036	35.12%Leucoraja erinaceus	36.31%	39.29%Dipturus trachyderma	0.35	0.14
ATP6	19	41.36%	1.12	0.027	39.04%Amblyraja radiata	41.37%	44.15%Beringraja binoculata	0.41	0.08
COX3	19	46.22%	1.07	0.023	44.02%Leucoraja erinaceus	46.44%	47.96%Leucoraja naevus	0.09	0.72
ND3	19	45.61%	1.03	0.023	43.84%Raja undulata	45.27%	47.85%Beringraja binoculata	0.27	0.26
ND4L	19	45.03%	1.46	0.032	41.75%Raja undulata	45.45%	46.80%Dipturus trachyderma	0.38	0.11
ND4	19	42.17%	0.98	0.023	39.75%Raja undulata	42.29%	43.98%Okamejei kenojei	0.02	0.93
ND5	19	41.09%	0.98	0.024	39.05%Amblyraja radiata	41.12%	42.97%Okamejei kenojei	−0.11	0.64
ND6	19	38.21%	0.81	0.021	37.19%Raja miraletus	38.34%	40.46%Leucoraja naevus	0.23	0.34
CYTB	19	43.52%	1.22	0.028	40.51%Leucoraja erinaceus	43.74%	45.93%Okamejei kenojei	−0.11	0.66

Genera of Rajidae

GC content of the whole genome, % of A + C + G + T

Region

Parameter

Chart

Genera of Rajidae

Raja	6	40.78%	0.64	0.016	39.60%Raja undulata	41.02%	41.25%Raja asterias	−0.51	0.3
Dipturus	4	41.37%	0.23	0.006	41.06%Dipturus batis	41.39%	41.63%Dipturus trachyderma	–	–
Leucoraja	2	41.22%	1.37	0.033	40.25%Leucoraja erinaceus	41.22%	42.19%Leucoraja naevus	–	–
Caliraja	2	41.56%	0.16	0.004	41.44%Caliraja rhina	41.56%	41.67%Caliraja stellulata	–	–
Zearaja	2	41.16%	0.11	0.003	41.08%Zearaja chilensis	41.16%	41.24%Zearaja nasuta	–	–
Amblyraja	1	40.28%	–	–	40.28%Amblyraja radiata	40.28%	40.28%Amblyraja radiata	–	–
Okamejei	1	42.39%	–	–	42.39%Okamejei kenojei	42.39%	42.39%Okamejei kenojei	–	–
Beringraja	1	41.72%	–	–	41.72%Beringraja binoculata	41.72%	41.72%Beringraja binoculata	–	–

Codon usage

Share of each codon in all 13 protein-coding genes, across Rajidae

Gene

Loading codon usage…

Every species, region by region

Each region's page lists the value of every species, with the same statistics by class, order or family and a CSV download.

Whole genome Protein-coding All rRNA All tRNA 12S rRNA 16S rRNA D-loop ND1 ND2 COX1 COX2 ATP8 ATP6 COX3 ND3 ND4L ND4 ND5 ND6 CYTB

Rajidae taxon page All data downloads

The charts

Each chart draws the rows of the table under it, in the table's order: sort a column to reorder the chart.Chart sets its axis.
Distribution: the range (line), mean ± SD (bar), median (tick) and mean (dot). Lengths of the regions are on a log scale.
Variation: the coefficient of variation, or the SD for the skews, which vary around zero.
Lifespan r: r with its 95% confidence interval (Fisher z). Lifespan map: r of every parameter in every region at once, bold where the Benjamini–Hochberg q-value over the map is below 0.05.

What the numbers are

Species: species with the region annotated. SD is the sample standard deviation, CV = SD / mean.
Base percentages are over A + C + G + T, so GC % + AT % = 100. Skews are on the L strand as deposited in RefSeq: GC skew = (G − C) / (G + C), AT skew = (A − T) / (A + T).
Min and Max name the species with the extreme value.

Lifespan columns

r is the Pearson correlation of the parameter with log₁₀ maximum lifespan within the group (5 or more species), and p its two-tailed p-value, as on the original MitoAge. They are not corrected for multiple testing or for shared ancestry: the plot shows Benjamini–Hochberg q-values and phylogenetic contrasts.

The original site labelled the base columns with their complements, so its skews have the opposite sign. Seemethods.