Ruditapes philippinarum

Japanese carpet shell

Maximum lifespan

14 yr

SeaLifeBase record

mtDNA size

22,089 bp

RefSeq NC_031332.1

GC content

30.38%

Whole genome

Non-coding

3,799 bp

Including the D-loop

Where Japanese carpet shell sits among 2,335 species

Whole-genome GC content against maximum lifespan. Japanese carpet shell has the 1,305th longest lifespan of them.

This species
All other species

Plot other mtDNA features with this species highlighted

Base composition

Whole genome22,089 bp

GC skew (G − C) / (G + C): +0.356
AT skew (A − T) / (A + T): −0.138

Life history

Maximum lifespan: 14 years

Lifespan from SeaLifeBase · SeaLifeBase record

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 RefSeq

Whole genome22,089 bp

Protein-coding14,256 bp

12S rRNA1,249 bp

16S rRNA1,408 bp

All tRNA1,522 bp

Genes and regions

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

Base composition of Ruditapes philippinarum genes

ND1NADH dehydrogenase subunit 1	930 bp	23.9%	44.0%	22.0%	10.1%	32.15%	+0.371	−0.296
ND2NADH dehydrogenase subunit 2	1,017 bp	26.8%	43.0%	22.1%	8.1%	30.19%	+0.466	−0.231
COX1Cytochrome c oxidase subunit I	1,719 bp	25.2%	39.3%	22.5%	12.5%	35.17%	+0.285	−0.218
COX2Cytochrome c oxidase subunit II	1,569 bp	30.6%	35.9%	23.5%	10.0%	33.46%	+0.402	−0.080
ATP6ATP synthase F0 subunit 6	738 bp	25.5%	45.4%	19.5%	9.5%	29.04%	+0.346	−0.281
COX3Cytochrome c oxidase subunit III	774 bp	24.3%	43.3%	21.6%	10.9%	32.43%	+0.331	−0.281
ND3NADH dehydrogenase subunit 3	405 bp	34.1%	38.5%	18.0%	9.4%	27.41%	+0.315	−0.061
ND4LNADH dehydrogenase subunit 4L	408 bp	30.4%	46.1%	15.4%	8.1%	23.53%	+0.313	−0.205
ND4NADH dehydrogenase subunit 4	1,359 bp	25.9%	42.2%	22.1%	9.6%	31.79%	+0.392	−0.239
ND5NADH dehydrogenase subunit 5	1,626 bp	28.0%	42.6%	20.4%	8.7%	29.18%	+0.404	−0.206
ND6NADH dehydrogenase subunit 6	492 bp	28.0%	40.9%	24.2%	6.9%	31.10%	+0.556	−0.186
CYTBCytochrome b	1,248 bp	25.2%	42.4%	19.6%	12.9%	32.45%	+0.205	−0.255
12S rRNA12S ribosomal RNA	1,249 bp	35.6%	35.1%	19.1%	9.8%	29.05%	+0.320	+0.007
16S rRNA16S ribosomal RNA	1,408 bp	34.2%	38.1%	18.0%	8.8%	27.03%	+0.342	−0.055

Codon usage

Counts per codon, darker is more frequent

Gene

4,076 codons in all protein-coding genes. Grouped with the Invertebrate mitochondrial code (NCBI table 5).

Phe F9.3%

UUU338

UUC43

Leu L14.0%

UUA343

UUG96

CUU75

CUC1

CUA43

CUG11

Ile I5.5%

AUU202

AUC22

Met M6.5%

AUA198

AUG66

Val V9.9%

GUU180

GUC21

GUA148

GUG56

Ser S10.8%

UCU107

UCC8

UCA39

UCG10

AGU91

AGC12

AGA112

AGG63

Pro P3.0%

CCU69

CCC11

CCA36

CCG8

Thr T3.1%

ACU79

ACC5

ACA35

ACG8

Ala A3.9%

GCU108

GCC10

GCA33

GCG8

Tyr Y4.0%

UAU136

UAC28

His H1.7%

CAU62

CAC7

Gln Q1.1%

CAA28

CAG18

Asn N3.0%

AAU102

AAC20

Lys K3.7%

AAA112

AAG40

Asp D2.3%

GAU76

GAC16

Glu E3.1%

GAA57

GAG69

Cys C2.2%

UGU77

UGC13

Trp W2.7%

UGA56

UGG56

Arg R1.6%

CGU28

CGC0

CGA26

CGG11

Gly G8.1%

GGU146

GGC11

GGA75

GGG99

Stop 0.3%

UAA7

UAG5

Genome map

39 annotated features in NC_031332.1

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
tRNA24

Outer ring: + strand, arrows run clockwise. Inner ring: − strand.
Middle ring: GC% of each gene against the whole genome (30.4%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

All 39 features as a table

Annotated features of Ruditapes philippinarum (NC_031332.1)
Feature	Type	Start	End	Length	Strand	GC
COX2	Protein-coding gene	1,762	3,330	1,569 bp	+	33.5%
tRNA-Pro	Transfer RNA	3,397	3,461	65 bp	+	–
CYTB	Protein-coding gene	3,438	4,685	1,248 bp	+	32.5%
16S rRNA	Ribosomal RNA	4,686	6,093	1,408 bp	+	27.0%
ND4	Protein-coding gene	6,094	7,452	1,359 bp	+	31.8%
tRNA-His	Transfer RNA	7,453	7,514	62 bp	+	–
tRNA-Glu	Transfer RNA	7,515	7,573	59 bp	+	–
tRNA-Ser	Transfer RNA	7,570	7,638	69 bp	+	–
ATP6	Protein-coding gene	7,640	8,377	738 bp	+	29.0%
ND3	Protein-coding gene	8,400	8,804	405 bp	+	27.4%
ND5	Protein-coding gene	8,895	10,520	1,626 bp	+	29.2%
tRNA-Tyr	Transfer RNA	10,535	10,594	60 bp	+	–
tRNA-Met	Transfer RNA	10,603	10,668	66 bp	+	–
tRNA-Met	Transfer RNA	10,677	10,742	66 bp	+	–
tRNA-Asp	Transfer RNA	10,751	10,812	62 bp	+	–
tRNA-Val	Transfer RNA	10,833	10,892	60 bp	+	–
ND6	Protein-coding gene	10,912	11,403	492 bp	+	31.1%
tRNA-Lys	Transfer RNA	11,412	11,474	63 bp	+	–
tRNA-Val	Transfer RNA	11,475	11,538	64 bp	+	–
tRNA-Phe	Transfer RNA	11,539	11,603	65 bp	+	–
tRNA-Trp	Transfer RNA	11,606	11,667	62 bp	+	–
tRNA-Arg	Transfer RNA	11,667	11,729	63 bp	+	–
tRNA-Leu	Transfer RNA	11,744	11,805	62 bp	+	–
tRNA-Gly	Transfer RNA	11,804	11,867	64 bp	+	–
tRNA-Gln	Transfer RNA	11,871	11,938	68 bp	+	–
tRNA-Asn	Transfer RNA	11,941	12,005	65 bp	+	–
tRNA-Thr	Transfer RNA	12,006	12,068	63 bp	+	–
tRNA-Cys	Transfer RNA	12,069	12,128	60 bp	+	–
tRNA-Ala	Transfer RNA	12,148	12,210	63 bp	+	–
tRNA-Ser	Transfer RNA	12,210	12,278	69 bp	+	–
COX3	Protein-coding gene	12,368	13,141	774 bp	+	32.4%
12S rRNA	Ribosomal RNA	13,142	14,390	1,249 bp	+	29.1%
COX1	Protein-coding gene	14,271	15,989	1,719 bp	+	35.2%
tRNA-Leu	Transfer RNA	15,989	16,052	64 bp	+	–
ND1	Protein-coding gene	16,053	16,982	930 bp	+	32.2%
ND2	Protein-coding gene	17,004	18,020	1,017 bp	+	30.2%
ND4L	Protein-coding gene	19,162	19,569	408 bp	+	23.5%
tRNA-Ile	Transfer RNA	21,431	21,496	66 bp	+	–
COX2	Protein-coding gene	21,551	1,432	1,971 bp	+	33.5%