Heliocidaris crassispina
Purple sea urchin
GC content
41.11%
Whole genome
Non-coding
252 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 1,527th longest lifespan of them.
- This species
- All other species
Base composition
Whole genome15,702 bp
- GC skew (G − C) / (G + C)
- −0.186
- AT skew (A − T) / (A + T)
- +0.054
About this record
- Lifespan source
- SeaLifeBase v26.06
- Based on
- an animal in the wild
- Data quality
- acceptable
- Licence
- CC BY-NC 4.0
- Status
- New in build 2
- In the database since
- build 2 (2026-11-13)
The lifespan value is for non-commercial use only; the genome data is not restricted by it.
Every change against the 2015 build is in the changelog download.
Composition by region
Reference (L) strand as deposited in RefSeqWhole genome15,702 bp
Protein-coding11,484 bp
12S rRNA892 bp
16S rRNA1,536 bp
All tRNA1,549 bp
D-loop121 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 972 bp | 39.30% | −0.168 | −0.054 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,059 bp | 39.66% | −0.276 | −0.005 | |||||
| COX1Cytochrome c oxidase subunit I | 1,554 bp | 44.66% | −0.164 | −0.042 | |||||
| COX2Cytochrome c oxidase subunit II | 690 bp | 42.61% | −0.190 | +0.035 | |||||
| ATP8ATP synthase F0 subunit 8 | 165 bp | 35.76% | −0.322 | +0.094 | |||||
| ATP6ATP synthase F0 subunit 6 | 690 bp | 40.58% | −0.307 | −0.015 | |||||
| COX3Cytochrome c oxidase subunit III | 783 bp | 43.30% | −0.174 | −0.018 | |||||
| ND3NADH dehydrogenase subunit 3 | 351 bp | 43.88% | −0.338 | −0.025 | |||||
| ND4LNADH dehydrogenase subunit 4L | 294 bp | 37.42% | −0.327 | +0.043 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,389 bp | 42.84% | −0.284 | +0.005 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,917 bp | 41.21% | −0.230 | +0.070 | |||||
| ND6NADH dehydrogenase subunit 6 | 498 bp | 41.77% | −0.317 | +0.448 | |||||
| CYTBCytochrome b | 1,142 bp | 42.29% | −0.259 | −0.026 | |||||
| 12S rRNA12S ribosomal RNA | 892 bp | 41.14% | −0.025 | +0.253 | |||||
| 16S rRNA16S ribosomal RNA | 1,536 bp | 38.22% | −0.029 | +0.178 | |||||
| D-loopControl region (D-loop) | 121 bp | 48.76% | −0.119 | −0.226 |
Codon usage
Counts per codon, darker is more frequent3,834 codons in all protein-coding genes. Grouped with the Echinoderm and flatworm mitochondrial code (NCBI table 9).
Phe F8.0%
UUU129
UUC179
Leu L16.0%
UUA116
UUG30
CUU84
CUC81
CUA263
CUG41
Ile I9.7%
AUU125
AUC101
AUA144
Met M2.6%
AUG99
Val V6.3%
GUU63
GUC50
GUA94
GUG33
Ser S10.1%
UCU71
UCC82
UCA99
UCG17
AGU20
AGC24
AGA67
AGG6
Pro P4.3%
CCU26
CCC36
CCA88
CCG16
Thr T6.5%
ACU54
ACC89
ACA100
ACG6
Ala A7.6%
GCU70
GCC104
GCA101
GCG15
Tyr Y3.1%
UAU45
UAC72
His H2.1%
CAU18
CAC62
Gln Q2.2%
CAA74
CAG9
Asn N4.2%
AAU22
AAC66
AAA73
Lys K1.4%
AAG54
Asp D1.7%
GAU20
GAC46
Glu E2.6%
GAA77
GAG21
Cys C0.8%
UGU8
UGC24
Trp W2.8%
UGA84
UGG22
Arg R1.9%
CGU3
CGC10
CGA53
CGG7
Gly G6.0%
GGU28
GGC39
GGA124
GGG38
Stop 0.3%
UAA8
UAG4
Genome map
38 annotated features in NC_023774.1Hover, 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 (41.1%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).
All 38 features as a table
| Feature | Type | Start | End | Length | Strand | GC |
|---|---|---|---|---|---|---|
| tRNA-Phe | Transfer RNA | 1 | 73 | 73 bp | + | – |
| 12S rRNA | Ribosomal RNA | 74 | 965 | 892 bp | + | 41.1% |
| tRNA-Glu | Transfer RNA | 966 | 1,034 | 69 bp | + | – |
| tRNA-Thr | Transfer RNA | 1,045 | 1,117 | 73 bp | + | – |
| D-loop | Control region | 1,118 | 1,238 | 121 bp | – | 48.8% |
| tRNA-Pro | Transfer RNA | 1,239 | 1,308 | 70 bp | + | – |
| tRNA-Gln | Transfer RNA | 1,310 | 1,381 | 72 bp | − | – |
| tRNA-Asn | Transfer RNA | 1,385 | 1,456 | 72 bp | + | – |
| tRNA-Leu | Transfer RNA | 1,457 | 1,528 | 72 bp | + | – |
| tRNA-Ala | Transfer RNA | 1,528 | 1,598 | 71 bp | − | – |
| tRNA-Trp | Transfer RNA | 1,600 | 1,668 | 69 bp | + | – |
| tRNA-Cys | Transfer RNA | 1,669 | 1,736 | 68 bp | + | – |
| tRNA-Val | Transfer RNA | 1,736 | 1,805 | 70 bp | − | – |
| tRNA-Met | Transfer RNA | 1,827 | 1,899 | 73 bp | + | – |
| tRNA-Asp | Transfer RNA | 1,901 | 1,970 | 70 bp | − | – |
| tRNA-Tyr | Transfer RNA | 1,979 | 2,049 | 71 bp | + | – |
| tRNA-Gly | Transfer RNA | 2,056 | 2,123 | 68 bp | + | – |
| tRNA-Leu | Transfer RNA | 2,124 | 2,196 | 73 bp | + | – |
| ND1 | Protein-coding gene | 2,199 | 3,170 | 972 bp | + | 39.3% |
| tRNA-Ile | Transfer RNA | 3,171 | 3,241 | 71 bp | + | – |
| ND2 | Protein-coding gene | 3,242 | 4,300 | 1,059 bp | + | 39.7% |
| 16S rRNA | Ribosomal RNA | 4,301 | 5,836 | 1,536 bp | + | 38.2% |
| COX1 | Protein-coding gene | 5,837 | 7,390 | 1,554 bp | + | 44.7% |
| tRNA-Arg | Transfer RNA | 7,402 | 7,470 | 69 bp | + | – |
| ND4L | Protein-coding gene | 7,472 | 7,765 | 294 bp | + | 37.4% |
| COX2 | Protein-coding gene | 7,765 | 8,454 | 690 bp | + | 42.6% |
| tRNA-Lys | Transfer RNA | 8,459 | 8,528 | 70 bp | + | – |
| ATP8 | Protein-coding gene | 8,529 | 8,693 | 165 bp | + | 35.8% |
| ATP6 | Protein-coding gene | 8,684 | 9,373 | 690 bp | + | 40.6% |
| COX3 | Protein-coding gene | 9,377 | 10,159 | 783 bp | + | 43.3% |
| tRNA-Ser | Transfer RNA | 10,159 | 10,228 | 70 bp | − | – |
| ND3 | Protein-coding gene | 10,245 | 10,595 | 351 bp | + | 43.9% |
| ND4 | Protein-coding gene | 10,615 | 12,003 | 1,389 bp | + | 42.8% |
| tRNA-His | Transfer RNA | 11,994 | 12,062 | 69 bp | + | – |
| tRNA-Ser | Transfer RNA | 12,064 | 12,131 | 68 bp | + | – |
| ND5 | Protein-coding gene | 12,132 | 14,048 | 1,917 bp | + | 41.2% |
| ND6 | Protein-coding gene | 14,040 | 14,537 | 498 bp | − | 41.8% |
| CYTB | Protein-coding gene | 14,561 | 15,702 | 1,142 bp | + | 42.3% |