Oryzias latipes

Japanese medaka

Maximum lifespan

5 yr

AnAge record

mtDNA size

16,714 bp

RefSeq NC_004387.1

GC content

44.47%

Whole genome

Non-coding

1,136 bp

D-loop 1,073 bp

Where Japanese medaka sits among 2,335 species

Whole-genome GC content against maximum lifespan. Japanese medaka has the 1,980th longest lifespan of them.

This species
Other ray-finned fishes
Other classes

Plot other mtDNA features with this species highlighted

Base composition

Whole genome16,714 bp

GC skew (G − C) / (G + C): −0.193
AT skew (A − T) / (A + T): −0.018

Life history

Maximum lifespan: 5 years
Gestation or incubation: 10 days

Lifespan from AnAge · AnAge record · other traits from AnAge Build 15 (HAGRID 03810)

About this record

Lifespan source: AnAge build 15
Based on: an animal in captivity
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 genome16,714 bp

Protein-coding11,416 bp

12S rRNA942 bp

16S rRNA1,674 bp

All tRNA1,546 bp

D-loop1,073 bp

Genes and regions

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

Base composition of Oryzias latipes genes

ND1NADH dehydrogenase subunit 1	975 bp	23.3%	30.4%	16.4%	29.9%	46.36%	−0.292	−0.132
ND2NADH dehydrogenase subunit 2	1,051 bp	23.7%	29.9%	16.0%	30.4%	46.43%	−0.311	−0.115
COX1Cytochrome c oxidase subunit I	1,557 bp	24.7%	30.6%	19.3%	25.4%	44.77%	−0.136	−0.107
COX2Cytochrome c oxidase subunit II	691 bp	27.2%	30.0%	17.5%	25.3%	42.84%	−0.182	−0.048
ATP8ATP synthase F0 subunit 8	168 bp	30.4%	29.8%	11.3%	28.6%	39.88%	−0.433	+0.010
ATP6ATP synthase F0 subunit 6	683 bp	25.9%	32.5%	15.1%	26.5%	41.58%	−0.275	−0.113
COX3Cytochrome c oxidase subunit III	784 bp	23.7%	30.5%	18.1%	27.7%	45.79%	−0.209	−0.125
ND3NADH dehydrogenase subunit 3	349 bp	20.9%	32.1%	17.2%	29.8%	46.99%	−0.268	−0.211
ND4LNADH dehydrogenase subunit 4L	297 bp	22.2%	34.0%	17.8%	25.9%	43.77%	−0.185	−0.210
ND4NADH dehydrogenase subunit 4	1,381 bp	24.5%	29.5%	16.0%	30.1%	46.05%	−0.305	−0.093
ND5NADH dehydrogenase subunit 5	1,839 bp	26.5%	29.2%	16.1%	28.2%	44.26%	−0.273	−0.048
ND6NADH dehydrogenase subunit 6	522 bp	37.9%	15.3%	15.9%	30.8%	46.74%	−0.320	+0.424
CYTBCytochrome b	1,141 bp	24.3%	30.9%	16.1%	28.7%	44.79%	−0.280	−0.121
12S rRNA12S ribosomal RNA	942 bp	33.4%	22.8%	21.3%	22.4%	43.74%	−0.024	+0.189
16S rRNA16S ribosomal RNA	1,674 bp	34.8%	24.3%	20.5%	20.3%	40.86%	+0.006	+0.178
D-loopControl region (D-loop)	1,073 bp	25.4%	29.1%	20.4%	25.1%	45.48%	−0.102	−0.067

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 F6.5%

UUU145

UUC103

Leu L17.4%

UUA139

UUG41

CUU159

CUC115

CUA143

CUG65

Ile I6.7%

AUU157

AUC99

Met M4.4%

AUA103

AUG64

Val V6.4%

GUU74

GUC57

GUA77

GUG37

Ser S7.1%

UCU52

UCC76

UCA72

UCG13

AGU16

AGC41

Pro P5.6%

CCU68

CCC87

CCA45

CCG13

Thr T7.0%

ACU56

ACC102

ACA93

ACG16

Ala A8.8%

GCU74

GCC128

GCA103

GCG29

Tyr Y2.8%

UAU50

UAC56

His H2.7%

CAU33

CAC69

Gln Q2.6%

CAA77

CAG22

Asn N3.1%

AAU41

AAC78

Lys K2.1%

AAA55

AAG24

Asp D2.0%

GAU28

GAC47

Glu E2.6%

GAA76

GAG22

Cys C0.8%

UGU11

UGC18

Trp W3.1%

UGA77

UGG40

Arg R1.9%

CGU10

CGC11

CGA37

CGG16

Gly G6.4%

GGU55

GGC69

GGA51

GGG69

Stop 0.2%

UAA5

UAG0

AGA1

AGG0

Genome map

38 annotated features in NC_004387.1

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 (44.5%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

All 38 features as a table

Annotated features of Oryzias latipes (NC_004387.1)
Feature	Type	Start	End	Length	Strand	GC
tRNA-Phe	Transfer RNA	1	69	69 bp	+	–
12S rRNA	Ribosomal RNA	70	1,011	942 bp	+	43.7%
tRNA-Val	Transfer RNA	1,012	1,083	72 bp	+	–
16S rRNA	Ribosomal RNA	1,084	2,757	1,674 bp	+	40.9%
tRNA-Leu (UUR)	Transfer RNA	2,758	2,831	74 bp	+	–
ND1	Protein-coding gene	2,832	3,806	975 bp	+	46.4%
tRNA-Ile	Transfer RNA	3,810	3,877	68 bp	+	–
tRNA-Gln	Transfer RNA	3,877	3,947	71 bp	−	–
tRNA-Met	Transfer RNA	3,947	4,016	70 bp	+	–
ND2	Protein-coding gene	4,017	5,067	1,051 bp	+	46.4%
tRNA-Trp	Transfer RNA	5,068	5,139	72 bp	+	–
tRNA-Ala	Transfer RNA	5,140	5,208	69 bp	−	–
tRNA-Asn	Transfer RNA	5,210	5,282	73 bp	−	–
tRNA-Cys	Transfer RNA	5,319	5,384	66 bp	−	–
tRNA-Tyr	Transfer RNA	5,384	5,453	70 bp	−	–
COX1	Protein-coding gene	5,455	7,011	1,557 bp	+	44.8%
tRNA-Ser (UCN)	Transfer RNA	7,013	7,083	71 bp	−	–
tRNA-Asp	Transfer RNA	7,094	7,163	70 bp	+	–
COX2	Protein-coding gene	7,167	7,857	691 bp	+	42.8%
tRNA-Lys	Transfer RNA	7,858	7,930	73 bp	+	–
ATP8	Protein-coding gene	7,932	8,099	168 bp	+	39.9%
ATP6	Protein-coding gene	8,090	8,772	683 bp	+	41.6%
COX3	Protein-coding gene	8,773	9,556	784 bp	+	45.8%
tRNA-Gly	Transfer RNA	9,557	9,625	69 bp	+	–
ND3	Protein-coding gene	9,626	9,974	349 bp	+	47.0%
tRNA-Arg	Transfer RNA	9,975	10,043	69 bp	+	–
ND4L	Protein-coding gene	10,044	10,340	297 bp	+	43.8%
ND4	Protein-coding gene	10,334	11,714	1,381 bp	+	46.1%
tRNA-His	Transfer RNA	11,715	11,785	71 bp	+	–
tRNA-Ser (AGY)	Transfer RNA	11,786	11,854	69 bp	+	–
tRNA-Leu (CUN)	Transfer RNA	11,859	11,931	73 bp	+	–
ND5	Protein-coding gene	11,932	13,770	1,839 bp	+	44.3%
ND6	Protein-coding gene	13,766	14,287	522 bp	−	46.7%
tRNA-Glu	Transfer RNA	14,288	14,355	68 bp	−	–
CYTB	Protein-coding gene	14,359	15,499	1,141 bp	+	44.8%
tRNA-Thr	Transfer RNA	15,500	15,572	73 bp	+	–
tRNA-Pro	Transfer RNA	15,572	15,641	70 bp	−	–
D-loop	Control region	15,642	16,714	1,073 bp	–	45.5%