Cyprinodon macularius
Desert pupfish
GC content
46.90%
Whole genome
Non-coding
916 bp
D-loop 834 bp
Where Desert pupfish sits among 2,335 species
Whole-genome GC content against maximum lifespan. Desert pupfish has the 2,265th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,500 bp
- GC skew (G − C) / (G + C)
- −0.259
- AT skew (A − T) / (A + T)
- −0.026
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
- New in build 2
- In the database since
- build 2 (2026-11-13)
Every change against the 2015 build is in the changelog download.
Composition by region
Reference (L) strand as deposited in RefSeqWhole genome16,500 bp
Protein-coding11,411 bp
12S rRNA945 bp
16S rRNA1,683 bp
All tRNA1,551 bp
D-loop834 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 51.28% | −0.288 | −0.204 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,047 bp | 48.81% | −0.452 | −0.097 | |||||
| COX1Cytochrome c oxidase subunit I | 1,554 bp | 46.14% | −0.233 | −0.130 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 46.02% | −0.296 | +0.019 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 45.24% | −0.526 | +0.043 | |||||
| ATP6ATP synthase F0 subunit 6 | 684 bp | 46.64% | −0.442 | −0.118 | |||||
| COX3Cytochrome c oxidase subunit III | 786 bp | 48.60% | −0.272 | −0.079 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 46.71% | −0.313 | −0.312 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 51.52% | −0.373 | −0.153 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 46.85% | −0.311 | −0.095 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,839 bp | 46.44% | −0.344 | −0.062 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 52.30% | −0.399 | +0.301 | |||||
| CYTBCytochrome b | 1,140 bp | 46.75% | −0.261 | −0.120 | |||||
| 12S rRNA12S ribosomal RNA | 945 bp | 49.10% | −0.103 | +0.177 | |||||
| 16S rRNA16S ribosomal RNA | 1,683 bp | 45.16% | −0.079 | +0.185 | |||||
| D-loopControl region (D-loop) | 834 bp | 38.61% | −0.174 | −0.059 |
Codon usage
Counts per codon, darker is more frequent3,810 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.2%
UUU107
UUC128
Leu L17.6%
UUA76
UUG31
CUU196
CUC175
CUA142
CUG52
Ile I6.9%
AUU152
AUC109
Met M3.8%
AUA71
AUG75
Val V6.0%
GUU71
GUC69
GUA59
GUG31
Ser S6.7%
UCU48
UCC83
UCA53
UCG19
AGU15
AGC39
Pro P5.7%
CCU67
CCC97
CCA41
CCG13
Thr T7.6%
ACU64
ACC106
ACA97
ACG21
Ala A9.1%
GCU65
GCC159
GCA103
GCG21
Tyr Y2.8%
UAU38
UAC69
His H3.0%
CAU36
CAC78
Gln Q2.6%
CAA73
CAG26
Asn N2.9%
AAU45
AAC67
Lys K1.9%
AAA46
AAG26
Asp D2.0%
GAU22
GAC55
Glu E2.6%
GAA72
GAG27
Cys C0.7%
UGU11
UGC17
Trp W3.2%
UGA97
UGG24
Arg R2.0%
CGU12
CGC21
CGA31
CGG12
Gly G6.3%
GGU27
GGC99
GGA60
GGG54
Stop 0.3%
UAA9
UAG1
AGA0
AGG0
Genome map
38 annotated features in NC_056955.1Hover, 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 (46.9%, dashed): out is GC-richer, in is AT-richer (full height = 6 points).
All 38 features as a table
| Feature | Type | Start | End | Length | Strand | GC |
|---|---|---|---|---|---|---|
| tRNA-Phe | Transfer RNA | 1 | 68 | 68 bp | + | – |
| 12S rRNA | Ribosomal RNA | 69 | 1,013 | 945 bp | + | 49.1% |
| tRNA-Val | Transfer RNA | 1,014 | 1,086 | 73 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,087 | 2,769 | 1,683 bp | + | 45.2% |
| tRNA-Leu (UUR) | Transfer RNA | 2,770 | 2,843 | 74 bp | + | – |
| ND1 | Protein-coding gene | 2,844 | 3,818 | 975 bp | + | 51.3% |
| tRNA-Ile | Transfer RNA | 3,824 | 3,893 | 70 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,893 | 3,963 | 71 bp | − | – |
| tRNA-Met | Transfer RNA | 3,963 | 4,031 | 69 bp | + | – |
| ND2 | Protein-coding gene | 4,032 | 5,078 | 1,047 bp | + | 48.8% |
| tRNA-Trp | Transfer RNA | 5,078 | 5,149 | 72 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,152 | 5,220 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,223 | 5,294 | 72 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,332 | 5,397 | 66 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,399 | 5,468 | 70 bp | − | – |
| COX1 | Protein-coding gene | 5,470 | 7,023 | 1,554 bp | + | 46.1% |
| tRNA-Ser (UCN) | Transfer RNA | 7,036 | 7,106 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,110 | 7,179 | 70 bp | + | – |
| COX2 | Protein-coding gene | 7,184 | 7,874 | 691 bp | + | 46.0% |
| tRNA-Lys | Transfer RNA | 7,875 | 7,948 | 74 bp | + | – |
| ATP8 | Protein-coding gene | 7,950 | 8,117 | 168 bp | + | 45.2% |
| ATP6 | Protein-coding gene | 8,108 | 8,791 | 684 bp | + | 46.6% |
| COX3 | Protein-coding gene | 8,791 | 9,576 | 786 bp | + | 48.6% |
| tRNA-Gly | Transfer RNA | 9,576 | 9,647 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,648 | 9,996 | 349 bp | + | 46.7% |
| tRNA-Arg | Transfer RNA | 9,997 | 10,065 | 69 bp | + | – |
| ND4L | Protein-coding gene | 10,066 | 10,362 | 297 bp | + | 51.5% |
| ND4 | Protein-coding gene | 10,356 | 11,736 | 1,381 bp | + | 46.9% |
| tRNA-His | Transfer RNA | 11,737 | 11,805 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,806 | 11,873 | 68 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,883 | 11,956 | 74 bp | + | – |
| ND5 | Protein-coding gene | 11,956 | 13,794 | 1,839 bp | + | 46.4% |
| ND6 | Protein-coding gene | 13,791 | 14,312 | 522 bp | − | 52.3% |
| tRNA-Glu | Transfer RNA | 14,310 | 14,380 | 71 bp | − | – |
| CYTB | Protein-coding gene | 14,385 | 15,524 | 1,140 bp | + | 46.8% |
| tRNA-Thr | Transfer RNA | 15,526 | 15,597 | 72 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,597 | 15,666 | 70 bp | − | – |
| D-loop | Control region | 15,667 | 16,500 | 834 bp | – | 38.6% |