Danio rerio

Zebra danio or zebrafish

Maximum lifespan

5.5 yr

AnAge record

mtDNA size

16,596 bp

RefSeq NC_002333.2

GC content

39.93%

Whole genome

Non-coding

1,020 bp

D-loop 950 bp

Where Zebra danio or zebrafish sits among 2,335 species

Whole-genome GC content against maximum lifespan. Zebra danio or zebrafish has the 1,962nd longest lifespan of them.

This species
Other ray-finned fishes
Other classes

Plot other mtDNA features with this species highlighted

Base composition

Whole genome16,596 bp

GC skew (G − C) / (G + C): −0.198
AT skew (A − T) / (A + T): +0.064

Life history

Maximum lifespan: 5.5 years

Lifespan from AnAge · AnAge record

About this record

Lifespan source: AnAge build 15
Based on: an animal in captivity
Data quality: high, large 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 genome16,596 bp

Protein-coding11,390 bp

12S rRNA952 bp

16S rRNA1,683 bp

All tRNA1,556 bp

D-loop950 bp

Genes and regions

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

Base composition of Danio rerio genes

ND1NADH dehydrogenase subunit 1	975 bp	30.7%	29.0%	15.5%	24.8%	40.31%	−0.232	+0.027
ND2NADH dehydrogenase subunit 2	1,047 bp	32.2%	27.4%	13.9%	26.5%	40.40%	−0.310	+0.080
COX1Cytochrome c oxidase subunit I	1,551 bp	28.1%	32.0%	17.5%	22.4%	39.85%	−0.123	−0.065
COX2Cytochrome c oxidase subunit II	691 bp	31.0%	29.1%	16.2%	23.7%	39.94%	−0.188	+0.031
ATP8ATP synthase F0 subunit 8	165 bp	35.8%	30.9%	9.1%	24.2%	33.33%	−0.455	+0.073
ATP6ATP synthase F0 subunit 6	684 bp	29.1%	31.4%	12.1%	27.3%	39.47%	−0.385	−0.039
COX3Cytochrome c oxidase subunit III	786 bp	27.1%	30.5%	17.7%	24.7%	42.37%	−0.165	−0.060
ND3NADH dehydrogenase subunit 3	351 bp	29.1%	32.8%	16.0%	22.2%	38.18%	−0.164	−0.060
ND4LNADH dehydrogenase subunit 4L	297 bp	30.0%	29.6%	13.8%	26.6%	40.40%	−0.317	+0.006
ND4NADH dehydrogenase subunit 4	1,381 bp	31.8%	29.8%	14.3%	24.1%	38.38%	−0.257	+0.032
ND5NADH dehydrogenase subunit 5	1,821 bp	32.6%	30.2%	13.1%	24.1%	37.18%	−0.294	+0.038
ND6NADH dehydrogenase subunit 6	519 bp	42.6%	17.1%	12.3%	27.9%	40.27%	−0.388	+0.426
CYTBCytochrome b	1,141 bp	28.9%	32.0%	14.8%	24.3%	39.09%	−0.242	−0.050
12S rRNA12S ribosomal RNA	952 bp	34.0%	20.4%	21.2%	24.4%	45.59%	−0.069	+0.251
16S rRNA16S ribosomal RNA	1,683 bp	37.7%	21.2%	19.5%	21.6%	41.12%	−0.052	+0.280
D-loopControl region (D-loop)	950 bp	33.7%	34.2%	13.6%	18.5%	32.11%	−0.154	−0.008

Codon usage

Counts per codon, darker is more frequent

Gene

3,802 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).

Phe F6.2%

UUU148

UUC88

Leu L15.8%

UUA181

UUG26

CUU146

CUC38

CUA179

CUG29

Ile I8.1%

AUU201

AUC107

Met M5.0%

AUA139

AUG52

Val V5.9%

GUU69

GUC21

GUA111

GUG22

Ser S6.4%

UCU57

UCC19

UCA108

UCG9

AGU14

AGC38

Pro P5.5%

CCU40

CCC40

CCA115

CCG13

Thr T7.7%

ACU63

ACC77

ACA140

ACG13

Ala A8.6%

GCU87

GCC96

GCA132

GCG13

Tyr Y3.0%

UAU55

UAC58

His H2.7%

CAU34

CAC68

Gln Q2.5%

CAA84

CAG10

Asn N3.2%

AAU56

AAC65

Lys K2.3%

AAA81

AAG8

Asp D2.2%

GAU30

GAC54

Glu E2.6%

GAA80

GAG20

Cys C0.8%

UGU14

UGC15

Trp W3.1%

UGA107

UGG11

Arg R2.0%

CGU9

CGC4

CGA53

CGG9

Gly G6.2%

GGU36

GGC39

GGA116

GGG45

Stop 0.3%

UAA7

UAG3

AGA0

AGG0

Genome map

38 annotated features in NC_002333.2

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 (39.9%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

All 38 features as a table

Annotated features of Danio rerio (NC_002333.2)
Feature	Type	Start	End	Length	Strand	GC
D-loop	Control region	1	950	950 bp	–	32.1%
tRNA-Phe	Transfer RNA	951	1,019	69 bp	+	–
12S rRNA	Ribosomal RNA	1,020	1,971	952 bp	+	45.6%
tRNA-Val	Transfer RNA	1,972	2,042	71 bp	+	–
16S rRNA	Ribosomal RNA	2,043	3,725	1,683 bp	+	41.1%
tRNA-Leu (UUR)	Transfer RNA	3,726	3,802	77 bp	+	–
ND1	Protein-coding gene	3,803	4,777	975 bp	+	40.3%
tRNA-Ile	Transfer RNA	4,781	4,854	74 bp	+	–
tRNA-Gln	Transfer RNA	4,852	4,922	71 bp	−	–
tRNA-Met	Transfer RNA	4,924	4,992	69 bp	+	–
ND2	Protein-coding gene	4,993	6,039	1,047 bp	+	40.4%
tRNA-Trp	Transfer RNA	6,038	6,107	70 bp	+	–
tRNA-Ala	Transfer RNA	6,109	6,176	68 bp	−	–
tRNA-Asn	Transfer RNA	6,178	6,250	73 bp	−	–
tRNA-Cys	Transfer RNA	6,283	6,354	72 bp	−	–
tRNA-Tyr	Transfer RNA	6,353	6,423	71 bp	−	–
COX1	Protein-coding gene	6,425	7,975	1,551 bp	+	39.9%
tRNA-Ser (UCN)	Transfer RNA	7,976	8,046	71 bp	−	–
tRNA-Asp	Transfer RNA	8,049	8,117	69 bp	+	–
COX2	Protein-coding gene	8,130	8,820	691 bp	+	39.9%
tRNA-Lys	Transfer RNA	8,821	8,893	73 bp	+	–
ATP8	Protein-coding gene	8,894	9,058	165 bp	+	33.3%
ATP6	Protein-coding gene	9,052	9,735	684 bp	+	39.5%
COX3	Protein-coding gene	9,735	10,520	786 bp	+	42.4%
tRNA-Gly	Transfer RNA	10,520	10,589	70 bp	+	–
ND3	Protein-coding gene	10,590	10,940	351 bp	+	38.2%
tRNA-Arg	Transfer RNA	10,939	11,008	70 bp	+	–
ND4L	Protein-coding gene	11,009	11,305	297 bp	+	40.4%
ND4	Protein-coding gene	11,299	12,679	1,381 bp	+	38.4%
tRNA-His	Transfer RNA	12,681	12,750	70 bp	+	–
tRNA-Ser (AGY)	Transfer RNA	12,750	12,819	70 bp	+	–
tRNA-Leu (CUN)	Transfer RNA	12,823	12,895	73 bp	+	–
ND5	Protein-coding gene	12,897	14,717	1,821 bp	+	37.2%
ND6	Protein-coding gene	14,714	15,232	519 bp	−	40.3%
tRNA-Glu	Transfer RNA	15,233	15,301	69 bp	−	–
CYTB	Protein-coding gene	15,308	16,448	1,141 bp	+	39.1%
tRNA-Thr	Transfer RNA	16,449	16,520	72 bp	+	–
tRNA-Pro	Transfer RNA	16,527	16,596	70 bp	−	–