Scomber japonicus

Chub mackerel

Maximum lifespan

18 yr

AnAge record

mtDNA size

16,568 bp

RefSeq NC_013723.1

GC content

46.99%

Whole genome

Non-coding

930 bp

D-loop 865 bp

Where Chub mackerel sits among 2,335 species

Whole-genome GC content against maximum lifespan. Chub mackerel has the 1,033rd longest lifespan of them.

This species
Other ray-finned fishes
Other classes

Plot other mtDNA features with this species highlighted

Base composition

Whole genome16,568 bp

GC skew (G − C) / (G + C): −0.272
AT skew (A − T) / (A + T): +0.038

Life history

Maximum lifespan: 18 years
Adult weight: 1.6 kg
Female sexual maturity: 2.2 years
Male sexual maturity: 2.2 years

Lifespan from AnAge · AnAge record · other traits from AnAge Build 15 (HAGRID 04355)

About this record

Lifespan source: AnAge build 15
Based on: an animal in the wild
Data quality: acceptable, medium sample
Licence: Free to use, subject to the Human Ageing Genomic Resources conditions of use
Status: Unchanged since build 1
In the database since: build 1 (2015-07-01)

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

Composition by region

Reference (L) strand as deposited in RefSeq

Whole genome16,568 bp

Protein-coding11,416 bp

12S rRNA962 bp

16S rRNA1,714 bp

All tRNA1,555 bp

D-loop865 bp

Genes and regions

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

Base composition of Scomber japonicus genes

ND1NADH dehydrogenase subunit 1	975 bp	24.2%	25.7%	16.4%	33.6%	50.05%	−0.344	−0.031
ND2NADH dehydrogenase subunit 2	1,046 bp	25.3%	24.1%	14.7%	35.9%	50.57%	−0.418	+0.025
COX1Cytochrome c oxidase subunit I	1,560 bp	23.7%	27.6%	19.7%	29.0%	48.72%	−0.189	−0.075
COX2Cytochrome c oxidase subunit II	691 bp	27.2%	26.6%	16.8%	29.4%	46.17%	−0.273	+0.011
ATP8ATP synthase F0 subunit 8	168 bp	29.8%	21.4%	14.3%	34.5%	48.81%	−0.415	+0.163
ATP6ATP synthase F0 subunit 6	684 bp	25.1%	29.5%	13.0%	32.3%	45.32%	−0.426	−0.080
COX3Cytochrome c oxidase subunit III	785 bp	26.0%	26.4%	17.2%	30.4%	47.64%	−0.278	−0.007
ND3NADH dehydrogenase subunit 3	349 bp	18.6%	31.5%	15.2%	34.7%	49.86%	−0.391	−0.257
ND4LNADH dehydrogenase subunit 4L	297 bp	21.9%	26.3%	15.8%	36.0%	51.85%	−0.390	−0.091
ND4NADH dehydrogenase subunit 4	1,381 bp	26.5%	26.6%	14.7%	32.2%	46.85%	−0.372	−0.003
ND5NADH dehydrogenase subunit 5	1,839 bp	26.5%	27.0%	14.6%	32.0%	46.55%	−0.374	−0.009
ND6NADH dehydrogenase subunit 6	522 bp	38.5%	16.1%	15.1%	30.3%	45.40%	−0.333	+0.411
CYTBCytochrome b	1,141 bp	24.1%	27.9%	15.8%	32.3%	48.03%	−0.343	−0.073
12S rRNA12S ribosomal RNA	962 bp	30.6%	21.6%	21.3%	26.5%	47.82%	−0.109	+0.171
16S rRNA16S ribosomal RNA	1,714 bp	32.9%	21.1%	20.7%	25.3%	45.97%	−0.102	+0.218
D-loopControl region (D-loop)	865 bp	33.6%	29.1%	14.9%	22.3%	37.23%	−0.199	+0.072

Codon usage

Counts per codon, darker is more frequent

Gene

3,810 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).

Phe F6.1%

UUU82

UUC150

Leu L17.5%

UUA60

UUG18

CUU159

CUC173

CUA198

CUG58

Ile I6.7%

AUU149

AUC105

Met M4.0%

AUA75

AUG78

Val V6.1%

GUU73

GUC69

GUA66

GUG26

Ser S6.4%

UCU42

UCC78

UCA59

UCG8

AGU8

AGC50

Pro P5.8%

CCU58

CCC97

CCA58

CCG9

Thr T7.7%

ACU45

ACC121

ACA115

ACG13

Ala A9.3%

GCU57

GCC162

GCA119

GCG15

Tyr Y3.0%

UAU32

UAC81

His H2.8%

CAU28

CAC78

Gln Q2.3%

CAA71

CAG18

Asn N3.1%

AAU24

AAC94

Lys K1.9%

AAA64

AAG8

Asp D2.0%

GAU16

GAC61

Glu E2.8%

GAA76

GAG31

Cys C0.8%

UGU11

UGC18

Trp W3.1%

UGA103

UGG17

Arg R2.1%

CGU8

CGC16

CGA42

CGG13

Gly G6.3%

GGU31

GGC90

GGA76

GGG43

Stop 0.2%

UAA5

UAG1

AGA0

AGG1

Genome map

38 annotated features in NC_013723.1

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 (47.0%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

All 38 features as a table

Annotated features of Scomber japonicus (NC_013723.1)
Feature	Type	Start	End	Length	Strand	GC
tRNA-Phe	Transfer RNA	1	69	69 bp	+	–
12S rRNA	Ribosomal RNA	70	1,031	962 bp	+	47.8%
tRNA-Val	Transfer RNA	1,032	1,103	72 bp	+	–
16S rRNA	Ribosomal RNA	1,104	2,817	1,714 bp	+	46.0%
tRNA-Leu (UUR)	Transfer RNA	2,818	2,891	74 bp	+	–
ND1	Protein-coding gene	2,892	3,866	975 bp	+	50.1%
tRNA-Ile	Transfer RNA	3,871	3,941	71 bp	+	–
tRNA-Gln	Transfer RNA	3,941	4,011	71 bp	−	–
tRNA-Met	Transfer RNA	4,011	4,080	70 bp	+	–
ND2	Protein-coding gene	4,081	5,126	1,046 bp	+	50.6%
tRNA-Trp	Transfer RNA	5,127	5,199	73 bp	+	–
tRNA-Ala	Transfer RNA	5,202	5,270	69 bp	−	–
tRNA-Asn	Transfer RNA	5,272	5,344	73 bp	−	–
tRNA-Cys	Transfer RNA	5,381	5,448	68 bp	−	–
tRNA-Tyr	Transfer RNA	5,449	5,515	67 bp	−	–
COX1	Protein-coding gene	5,517	7,076	1,560 bp	+	48.7%
tRNA-Ser (UCN)	Transfer RNA	7,068	7,139	72 bp	−	–
tRNA-Asp	Transfer RNA	7,143	7,214	72 bp	+	–
COX2	Protein-coding gene	7,223	7,913	691 bp	+	46.2%
tRNA-Lys	Transfer RNA	7,914	7,987	74 bp	+	–
ATP8	Protein-coding gene	7,989	8,156	168 bp	+	48.8%
ATP6	Protein-coding gene	8,147	8,830	684 bp	+	45.3%
COX3	Protein-coding gene	8,830	9,614	785 bp	+	47.6%
tRNA-Gly	Transfer RNA	9,615	9,686	72 bp	+	–
ND3	Protein-coding gene	9,687	10,035	349 bp	+	49.9%
tRNA-Arg	Transfer RNA	10,036	10,104	69 bp	+	–
ND4L	Protein-coding gene	10,105	10,401	297 bp	+	51.9%
ND4	Protein-coding gene	10,395	11,775	1,381 bp	+	46.9%
tRNA-His	Transfer RNA	11,776	11,846	71 bp	+	–
tRNA-Ser (AGY)	Transfer RNA	11,847	11,914	68 bp	+	–
tRNA-Leu (CUN)	Transfer RNA	11,919	11,991	73 bp	+	–
ND5	Protein-coding gene	11,993	13,831	1,839 bp	+	46.6%
ND6	Protein-coding gene	13,828	14,349	522 bp	−	45.4%
tRNA-Glu	Transfer RNA	14,350	14,418	69 bp	−	–
CYTB	Protein-coding gene	14,423	15,563	1,141 bp	+	48.0%
tRNA-Thr	Transfer RNA	15,564	15,635	72 bp	+	–
tRNA-Pro	Transfer RNA	15,635	15,703	69 bp	−	–
D-loop	Control region	15,704	16,568	865 bp	–	37.2%