Strongylocentrotus purpuratus

Purple sea urchin

Maximum lifespan

50 yr

AnAge record

mtDNA size

15,650 bp

RefSeq NC_001453.1

GC content

41.02%

Whole genome

Non-coding

243 bp

D-loop 121 bp

Where Purple sea urchin sits among 2,335 species

Whole-genome GC content against maximum lifespan. Purple sea urchin has the 142nd longest lifespan of them.

This species
All other species

Plot other mtDNA features with this species highlighted

Base composition

Whole genome15,650 bp

GC skew (G − C) / (G + C): −0.105
AT skew (A − T) / (A + T): −0.025

Life history

Maximum lifespan: 50 years
Female sexual maturity: 2 years
Male sexual maturity: 2 years

Lifespan from AnAge · AnAge record · other traits from AnAge Build 15 (HAGRID 04605)

About this record

Lifespan source: AnAge build 15
Based on: an observed animal, origin not stated
Data quality: questionable, medium sample
Licence: Free to use, subject to the Human Ageing Genomic Resources conditions of use
Status: Updated in build 2
In the database since: build 1 (2015-07-01)
Last changed: build 2 (2026-11-13)

Every change against the 2015 build is in the changelog download.

Composition by region

Reference (L) strand as deposited in RefSeq

Whole genome15,650 bp

Protein-coding11,487 bp

12S rRNA878 bp

16S rRNA1,530 bp

All tRNA1,541 bp

D-loop121 bp

Genes and regions

Select a column to sort; select a gene to compare it across species

Base composition of Strongylocentrotus purpuratus genes

ND1NADH dehydrogenase subunit 1	969 bp	24.7%	35.1%	18.2%	22.1%	40.25%	−0.097	−0.174
ND2NADH dehydrogenase subunit 2	1,059 bp	25.6%	35.3%	17.2%	21.9%	39.09%	−0.121	−0.160
COX1Cytochrome c oxidase subunit I	1,554 bp	24.4%	31.9%	19.2%	24.5%	43.69%	−0.119	−0.134
COX2Cytochrome c oxidase subunit II	690 bp	26.4%	30.6%	18.3%	24.8%	43.04%	−0.152	−0.074
ATP8ATP synthase F0 subunit 8	168 bp	31.0%	33.3%	11.9%	23.8%	35.71%	−0.333	−0.037
ATP6ATP synthase F0 subunit 6	696 bp	26.7%	33.6%	16.1%	23.6%	39.66%	−0.188	−0.114
COX3Cytochrome c oxidase subunit III	783 bp	26.7%	31.2%	19.5%	22.6%	42.15%	−0.073	−0.077
ND3NADH dehydrogenase subunit 3	351 bp	23.4%	32.2%	19.9%	24.5%	44.44%	−0.103	−0.159
ND4LNADH dehydrogenase subunit 4L	294 bp	27.9%	33.0%	16.0%	23.1%	39.12%	−0.183	−0.084
ND4NADH dehydrogenase subunit 4	1,389 bp	27.8%	30.1%	17.8%	24.3%	42.12%	−0.156	−0.040
ND5NADH dehydrogenase subunit 5	1,914 bp	28.3%	30.7%	17.1%	24.0%	41.07%	−0.168	−0.041
ND6NADH dehydrogenase subunit 6	498 bp	40.8%	20.9%	15.7%	22.7%	38.35%	−0.183	+0.322
CYTBCytochrome b	1,142 bp	25.7%	31.1%	17.5%	25.7%	43.17%	−0.189	−0.094
12S rRNA12S ribosomal RNA	878 bp	32.7%	23.2%	22.4%	21.6%	44.08%	+0.018	+0.169
16S rRNA16S ribosomal RNA	1,530 bp	36.7%	25.7%	19.2%	18.5%	37.65%	+0.017	+0.176
D-loopControl region (D-loop)	121 bp	21.5%	26.4%	26.4%	25.6%	52.07%	+0.016	−0.103

Codon usage

Counts per codon, darker is more frequent

Gene

3,835 codons in all protein-coding genes. Grouped with the Echinoderm and flatworm mitochondrial code (NCBI table 9).

Phe F8.2%

UUU199

UUC115

Leu L15.7%

UUA149

UUG67

CUU118

CUC77

CUA151

CUG41

Ile I9.2%

AUU145

AUC66

AUA141

Met M2.8%

AUG106

Val V6.8%

GUU93

GUC46

GUA81

GUG41

Ser S10.1%

UCU88

UCC88

UCA74

UCG16

AGU17

AGC25

AGA55

AGG25

Pro P4.7%

CCU54

CCC58

CCA57

CCG11

Thr T5.8%

ACU57

ACC69

ACA87

ACG11

Ala A7.4%

GCU69

GCC109

GCA90

GCG17

Tyr Y2.8%

UAU49

UAC60

His H2.1%

CAU24

CAC55

Gln Q2.2%

CAA61

CAG25

Asn N4.5%

AAU41

AAC55

AAA75

Lys K1.5%

AAG57

Asp D1.7%

GAU31

GAC36

Glu E2.4%

GAA50

GAG42

Cys C0.8%

UGU10

UGC21

Trp W2.8%

UGA72

UGG34

Arg R1.9%

CGU7

CGC9

CGA44

CGG14

Gly G6.2%

GGU35

GGC50

GGA104

GGG49

Stop 0.3%

UAA10

UAG2

Genome map

38 annotated features in NC_001453.1

Hover, tap or tab to a feature to see its position, length, strand and GC content. Genes and rRNAs open their own pages.

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 (41.0%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

All 38 features as a table

Annotated features of Strongylocentrotus purpuratus (NC_001453.1)
Feature	Type	Start	End	Length	Strand	GC
tRNA-Phe	Transfer RNA	1	73	73 bp	+	–
12S rRNA	Ribosomal RNA	74	951	878 bp	+	44.1%
tRNA-Glu	Transfer RNA	939	1,009	71 bp	+	–
tRNA-Thr	Transfer RNA	1,014	1,084	71 bp	+	–
D-loop	Control region	1,085	1,205	121 bp	–	52.1%
tRNA-Pro	Transfer RNA	1,206	1,275	70 bp	+	–
tRNA-Gln	Transfer RNA	1,277	1,347	71 bp	−	–
tRNA-Asn	Transfer RNA	1,354	1,425	72 bp	+	–
tRNA-Leu (CUN)	Transfer RNA	1,426	1,497	72 bp	+	–
tRNA-Ala	Transfer RNA	1,497	1,567	71 bp	−	–
tRNA-Trp	Transfer RNA	1,570	1,639	70 bp	+	–
tRNA-Cys	Transfer RNA	1,640	1,706	67 bp	+	–
tRNA-Val	Transfer RNA	1,704	1,777	74 bp	−	–
tRNA-Met	Transfer RNA	1,794	1,867	74 bp	+	–
tRNA-Asp	Transfer RNA	1,868	1,937	70 bp	−	–
tRNA-Tyr	Transfer RNA	1,944	2,014	71 bp	+	–
tRNA-Gly	Transfer RNA	2,020	2,087	68 bp	+	–
tRNA-Leu (UUR)	Transfer RNA	2,088	2,158	71 bp	+	–
ND1	Protein-coding gene	2,162	3,130	969 bp	+	40.3%
tRNA-Ile	Transfer RNA	3,132	3,200	69 bp	+	–
ND2	Protein-coding gene	3,201	4,259	1,059 bp	+	39.1%
16S rRNA	Ribosomal RNA	4,260	5,789	1,530 bp	+	37.7%
COX1	Protein-coding gene	5,785	7,338	1,554 bp	+	43.7%
tRNA-Arg	Transfer RNA	7,349	7,415	67 bp	+	–
ND4L	Protein-coding gene	7,418	7,711	294 bp	+	39.1%
COX2	Protein-coding gene	7,711	8,400	690 bp	+	43.0%
tRNA-Lys	Transfer RNA	8,405	8,475	71 bp	+	–
ATP8	Protein-coding gene	8,476	8,643	168 bp	+	35.7%
ATP6	Protein-coding gene	8,634	9,329	696 bp	+	39.7%
COX3	Protein-coding gene	9,333	10,115	783 bp	+	42.2%
tRNA-Ser (UCN)	Transfer RNA	10,120	10,184	65 bp	−	–
ND3	Protein-coding gene	10,201	10,551	351 bp	+	44.4%
ND4	Protein-coding gene	10,567	11,955	1,389 bp	+	42.1%
tRNA-His	Transfer RNA	11,945	12,013	69 bp	+	–
tRNA-Ser (AGY)	Transfer RNA	12,014	12,081	68 bp	+	–
ND5	Protein-coding gene	12,082	13,995	1,914 bp	+	41.1%
ND6	Protein-coding gene	13,987	14,484	498 bp	−	38.4%
CYTB	Protein-coding gene	14,509	15,650	1,142 bp	+	43.2%