Pelomedusa subrufa

Helmeted turtle

Maximum lifespan

20.1 yr

AnAge record

mtDNA size

16,787 bp

RefSeq NC_001947.1

GC content

38.70%

Whole genome

Non-coding

1,337 bp

D-loop 1,194 bp

Where Helmeted turtle sits among 2,335 species

Whole-genome GC content against maximum lifespan. Helmeted turtle has the 889th longest lifespan of them.

This species
Other reptiles
Other classes

Plot other mtDNA features with this species highlighted

Base composition

Whole genome16,787 bp

GC skew (G − C) / (G + C): −0.375
AT skew (A − T) / (A + T): +0.107

Life history

Maximum lifespan: 20.1 years
Adult weight: 2.3 kg

Lifespan from AnAge · AnAge record · other traits from AnAge Build 15 (HAGRID 03757)

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 genome16,787 bp

Protein-coding11,367 bp

12S rRNA968 bp

16S rRNA1,604 bp

All tRNA1,526 bp

D-loop1,194 bp

Genes and regions

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

Base composition of Pelomedusa subrufa genes

ND1NADH dehydrogenase subunit 1	968 bp	29.8%	30.8%	11.6%	27.9%	39.46%	−0.414	−0.017
ND2NADH dehydrogenase subunit 2	1,040 bp	34.4%	27.3%	10.0%	28.3%	38.27%	−0.477	+0.115
COX1Cytochrome c oxidase subunit I	1,545 bp	30.0%	29.1%	14.7%	26.3%	40.97%	−0.283	+0.015
COX2Cytochrome c oxidase subunit II	688 bp	35.2%	27.3%	11.9%	25.6%	37.50%	−0.364	+0.126
ATP8ATP synthase F0 subunit 8	168 bp	38.1%	31.0%	3.6%	27.4%	30.95%	−0.769	+0.103
ATP6ATP synthase F0 subunit 6	687 bp	32.8%	30.1%	7.4%	29.7%	37.12%	−0.600	+0.042
COX3Cytochrome c oxidase subunit III	784 bp	30.7%	29.2%	12.6%	27.4%	40.05%	−0.369	+0.026
ND3NADH dehydrogenase subunit 3	352 bp	35.5%	30.1%	9.4%	25.0%	34.38%	−0.455	+0.082
ND4LNADH dehydrogenase subunit 4L	299 bp	31.4%	29.1%	9.4%	30.1%	39.47%	−0.525	+0.039
ND4NADH dehydrogenase subunit 4	1,378 bp	33.2%	27.8%	9.6%	29.4%	38.97%	−0.508	+0.089
ND5NADH dehydrogenase subunit 5	1,818 bp	33.8%	26.8%	10.3%	29.0%	39.38%	−0.475	+0.114
ND6NADH dehydrogenase subunit 6	522 bp	43.5%	15.1%	7.7%	33.7%	41.38%	−0.630	+0.484
CYTBCytochrome b	1,143 bp	30.4%	26.4%	11.4%	31.8%	43.22%	−0.474	+0.069
12S rRNA12S ribosomal RNA	968 bp	35.1%	22.4%	17.9%	24.6%	42.46%	−0.158	+0.221
16S rRNA16S ribosomal RNA	1,604 bp	37.3%	22.7%	17.0%	23.1%	40.03%	−0.153	+0.243
D-loopControl region (D-loop)	1,194 bp	37.9%	34.8%	8.6%	18.7%	27.30%	−0.368	+0.041

Codon usage

Counts per codon, darker is more frequent

Gene

3,794 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).

Phe F5.9%

UUU95

UUC127

Leu L15.9%

UUA168

UUG19

CUU91

CUC95

CUA211

CUG18

Ile I8.6%

AUU147

AUC179

Met M6.1%

AUA215

AUG18

Val V3.7%

GUU29

GUC30

GUA61

GUG19

Ser S7.6%

UCU52

UCC74

UCA102

UCG5

AGU19

AGC36

Pro P5.5%

CCU50

CCC34

CCA124

CCG2

Thr T9.8%

ACU81

ACC140

ACA145

ACG7

Ala A6.5%

GCU53

GCC109

GCA80

GCG6

Tyr Y3.4%

UAU57

UAC71

His H3.0%

CAU50

CAC65

Gln Q2.4%

CAA85

CAG7

Asn N4.1%

AAU54

AAC101

Lys K2.7%

AAA94

AAG8

Asp D1.6%

GAU23

GAC37

Glu E2.0%

GAA72

GAG5

Cys C0.8%

UGU15

UGC15

Trp W2.8%

UGA97

UGG8

Arg R1.7%

CGU6

CGC16

CGA41

CGG3

Gly G5.4%

GGU38

GGC35

GGA95

GGG35

Stop 0.5%

UAA5

UAG3

AGA6

AGG6

Genome map

38 annotated features in NC_001947.1

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 (38.7%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).

All 38 features as a table

Annotated features of Pelomedusa subrufa (NC_001947.1)
Feature	Type	Start	End	Length	Strand	GC
tRNA-Phe	Transfer RNA	1	71	71 bp	+	–
12S rRNA	Ribosomal RNA	72	1,039	968 bp	+	42.5%
tRNA-Val	Transfer RNA	1,040	1,104	65 bp	+	–
16S rRNA	Ribosomal RNA	1,105	2,708	1,604 bp	+	40.0%
tRNA-Leu (UUR)	Transfer RNA	2,709	2,784	76 bp	+	–
ND1	Protein-coding gene	2,785	3,752	968 bp	+	39.5%
tRNA-Ile	Transfer RNA	3,753	3,823	71 bp	+	–
tRNA-Gln	Transfer RNA	3,824	3,893	70 bp	−	–
tRNA-Met	Transfer RNA	3,894	3,962	69 bp	+	–
ND2	Protein-coding gene	3,963	5,002	1,040 bp	+	38.3%
tRNA-Trp	Transfer RNA	5,003	5,077	75 bp	+	–
tRNA-Ala	Transfer RNA	5,079	5,147	69 bp	−	–
tRNA-Asn	Transfer RNA	5,149	5,221	73 bp	−	–
tRNA-Cys	Transfer RNA	5,225	5,294	70 bp	−	–
tRNA-Tyr	Transfer RNA	5,296	5,366	71 bp	−	–
COX1	Protein-coding gene	5,368	6,912	1,545 bp	+	41.0%
tRNA-Ser (UCN)	Transfer RNA	6,908	6,978	71 bp	−	–
tRNA-Asp	Transfer RNA	6,980	7,047	68 bp	+	–
COX2	Protein-coding gene	7,049	7,736	688 bp	+	37.5%
tRNA-Lys	Transfer RNA	7,737	7,806	70 bp	+	–
ATP8	Protein-coding gene	7,808	7,975	168 bp	+	31.0%
ATP6	Protein-coding gene	7,966	8,652	687 bp	+	37.1%
COX3	Protein-coding gene	8,645	9,428	784 bp	+	40.1%
tRNA-Gly	Transfer RNA	9,429	9,495	67 bp	+	–
ND3	Protein-coding gene	9,496	9,847	352 bp	+	34.4%
tRNA-Arg	Transfer RNA	9,846	9,914	69 bp	+	–
ND4L	Protein-coding gene	9,917	10,215	299 bp	+	39.5%
ND4	Protein-coding gene	10,209	11,586	1,378 bp	+	39.0%
tRNA-His	Transfer RNA	11,587	11,656	70 bp	+	–
tRNA-Ser (AGY)	Transfer RNA	11,658	11,714	57 bp	+	–
tRNA-Leu (CUN)	Transfer RNA	11,715	11,786	72 bp	+	–
ND5	Protein-coding gene	11,789	13,606	1,818 bp	+	39.4%
ND6	Protein-coding gene	13,731	14,252	522 bp	−	41.4%
tRNA-Glu	Transfer RNA	14,256	14,323	68 bp	−	–
CYTB	Protein-coding gene	14,316	15,458	1,143 bp	+	43.2%
tRNA-Thr	Transfer RNA	15,460	15,526	67 bp	+	–
tRNA-Pro	Transfer RNA	15,527	15,593	67 bp	−	–
D-loop	Control region	15,594	16,787	1,194 bp	–	27.3%