class · mtDNA statistics

Echinoidea

Sea urchins: 4 species in 2 orders. Every region of their mitochondrial genomes, side by side.

Group

species

40.9%

mean GC, whole genome

SD 0.2, range 40.6–41.1%

15,676

median genome length, bp

Range 15,649–15,717 bp

orders

Regions

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

Parameter

Chart

GC % of every region
Region
Whole genome	4	40.94%	0.24	0.006	40.59%Mesocentrotus franciscanus	41.04%	41.11%Heliocidaris crassispina	–	–
Protein-coding	4	41.52%	0.31	0.007	41.10%Mesocentrotus franciscanus	41.57%	41.84%Heliocidaris crassispina	–	–
All rRNA	4	39.64%	0.45	0.011	39.21%Mesocentrotus franciscanus	39.64%	40.07%Strongylocentrotus droebachiensis	–	–
All tRNA	4	39.69%	0.23	0.006	39.51%Strongylocentrotus droebachiensis	39.61%	40.01%Mesocentrotus franciscanus	–	–
12S rRNA	4	42.28%	1.52	0.036	40.91%Mesocentrotus franciscanus	42.07%	44.08%Strongylocentrotus purpuratus	–	–
16S rRNA	4	38.11%	0.31	0.008	37.65%Strongylocentrotus purpuratus	38.22%	38.35%Strongylocentrotus droebachiensis	–	–
D-loop	2	50.41%	2.34	0.046	48.76%Heliocidaris crassispina	50.41%	52.07%Strongylocentrotus purpuratus	–	–
ND1	4	40.44%	1.02	0.025	39.30%Heliocidaris crassispina	40.34%	41.77%Strongylocentrotus droebachiensis	–	–
ND2	4	39.31%	0.27	0.007	39.09%Strongylocentrotus purpuratus	39.24%	39.66%Heliocidaris crassispina	–	–
COX1	4	44.00%	0.52	0.012	43.50%Mesocentrotus franciscanus	43.92%	44.66%Heliocidaris crassispina	–	–
COX2	4	42.83%	0.45	0.011	42.32%Mesocentrotus franciscanus	42.83%	43.33%Strongylocentrotus droebachiensis	–	–
ATP8	4	35.44%	0.60	0.017	34.55%Strongylocentrotus droebachiensis	35.74%	35.76%Heliocidaris crassispina	–	–
ATP6	4	39.89%	1.24	0.031	38.26%Mesocentrotus franciscanus	40.12%	41.08%Strongylocentrotus droebachiensis	–	–
COX3	4	42.98%	0.61	0.014	42.15%Strongylocentrotus purpuratus	43.10%	43.55%Strongylocentrotus droebachiensis	–	–
ND3	4	43.80%	0.94	0.021	42.45%Strongylocentrotus droebachiensis	44.16%	44.44%Strongylocentrotus purpuratus	–	–
ND4L	4	38.69%	0.89	0.023	37.42%Heliocidaris crassispina	38.95%	39.46%Mesocentrotus franciscanus	–	–
ND4	4	41.99%	0.69	0.016	41.18%Mesocentrotus franciscanus	41.97%	42.84%Heliocidaris crassispina	–	–
ND5	4	41.05%	0.27	0.006	40.67%Mesocentrotus franciscanus	41.14%	41.25%Strongylocentrotus droebachiensis	–	–
ND6	4	39.23%	1.83	0.047	37.55%Strongylocentrotus droebachiensis	38.81%	41.77%Heliocidaris crassispina	–	–
CYTB	4	42.06%	0.86	0.020	41.38%Strongylocentrotus droebachiensis	41.84%	43.17%Strongylocentrotus purpuratus	–	–

Orders of Echinoidea

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

Region

Parameter

Chart

Orders of Echinoidea

Camarodonta	3	40.92%	0.28	0.007	40.59%Mesocentrotus franciscanus	41.05%	41.11%Heliocidaris crassispina	–	–
Echinoida	1	41.02%	–	–	41.02%Strongylocentrotus purpuratus	41.02%	41.02%Strongylocentrotus purpuratus	–	–

Codon usage

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

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

Echinoidea 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.