Hypomesus olidus
Pond smelt
GC content
48.34%
Whole genome
Non-coding
1,170 bp
D-loop 1,103 bp
Where Pond smelt sits among 2,335 species
Whole-genome GC content against maximum lifespan. Pond smelt has the 1,987th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,786 bp
- GC skew (G − C) / (G + C)
- −0.208
- AT skew (A − T) / (A + T)
- −0.057
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 RefSeqWhole genome16,786 bp
Protein-coding11,412 bp
12S rRNA945 bp
16S rRNA1,706 bp
All tRNA1,553 bp
D-loop1,103 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 49.85% | −0.255 | −0.231 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,051 bp | 51.48% | −0.301 | −0.180 | |||||
| COX1Cytochrome c oxidase subunit I | 1,551 bp | 46.94% | −0.129 | −0.183 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 46.17% | −0.204 | −0.048 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 45.83% | −0.325 | −0.033 | |||||
| ATP6ATP synthase F0 subunit 6 | 684 bp | 46.49% | −0.346 | −0.186 | |||||
| COX3Cytochrome c oxidase subunit III | 785 bp | 50.06% | −0.247 | −0.138 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 51.29% | −0.218 | −0.306 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 54.21% | −0.280 | −0.191 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 47.36% | −0.278 | −0.136 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,839 bp | 47.53% | −0.318 | −0.109 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 51.53% | −0.323 | +0.415 | |||||
| CYTBCytochrome b | 1,141 bp | 46.98% | −0.239 | −0.187 | |||||
| 12S rRNA12S ribosomal RNA | 945 bp | 51.64% | −0.033 | +0.120 | |||||
| 16S rRNA16S ribosomal RNA | 1,706 bp | 47.89% | −0.045 | +0.179 | |||||
| D-loopControl region (D-loop) | 1,103 bp | 45.78% | −0.228 | −0.003 |
Codon usage
Counts per codon, darker is more frequent3,809 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.3%
UUU113
UUC126
Leu L16.6%
UUA71
UUG33
CUU216
CUC148
CUA99
CUG64
Ile I7.0%
AUU143
AUC122
Met M3.9%
AUA53
AUG97
Val V6.6%
GUU82
GUC71
GUA66
GUG34
Ser S6.9%
UCU69
UCC84
UCA36
UCG19
AGU9
AGC46
Pro P5.6%
CCU80
CCC77
CCA39
CCG18
Thr T7.2%
ACU69
ACC115
ACA62
ACG28
Ala A9.7%
GCU111
GCC150
GCA82
GCG26
Tyr Y2.8%
UAU40
UAC67
His H2.7%
CAU34
CAC67
Gln Q2.5%
CAA54
CAG40
Asn N2.9%
AAU40
AAC71
Lys K2.0%
AAA52
AAG24
Asp D1.9%
GAU19
GAC54
Glu E2.7%
GAA63
GAG40
Cys C0.8%
UGU14
UGC16
Trp W3.2%
UGA80
UGG42
Arg R2.0%
CGU13
CGC21
CGA31
CGG11
Gly G6.6%
GGU36
GGC87
GGA52
GGG76
Stop 0.2%
UAA6
UAG1
AGA0
AGG0
Genome map
38 annotated features in NC_026566.1Hover, 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 (48.3%, 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 | + | 51.6% |
| tRNA-Val | Transfer RNA | 1,014 | 1,084 | 71 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,085 | 2,790 | 1,706 bp | + | 47.9% |
| tRNA-Leu (UUR) | Transfer RNA | 2,797 | 2,870 | 74 bp | + | – |
| ND1 | Protein-coding gene | 2,871 | 3,845 | 975 bp | + | 49.9% |
| tRNA-Ile | Transfer RNA | 3,849 | 3,920 | 72 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,921 | 3,990 | 70 bp | − | – |
| tRNA-Met | Transfer RNA | 3,990 | 4,058 | 69 bp | + | – |
| ND2 | Protein-coding gene | 4,063 | 5,113 | 1,051 bp | + | 51.5% |
| tRNA-Trp | Transfer RNA | 5,114 | 5,185 | 72 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,187 | 5,255 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,257 | 5,329 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,357 | 5,421 | 65 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,421 | 5,488 | 68 bp | − | – |
| COX1 | Protein-coding gene | 5,491 | 7,041 | 1,551 bp | + | 46.9% |
| tRNA-Ser (UCN) | Transfer RNA | 7,042 | 7,112 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,117 | 7,189 | 73 bp | + | – |
| COX2 | Protein-coding gene | 7,204 | 7,894 | 691 bp | + | 46.2% |
| tRNA-Lys | Transfer RNA | 7,895 | 7,969 | 75 bp | + | – |
| ATP8 | Protein-coding gene | 7,971 | 8,138 | 168 bp | + | 45.8% |
| ATP6 | Protein-coding gene | 8,129 | 8,812 | 684 bp | + | 46.5% |
| COX3 | Protein-coding gene | 8,812 | 9,596 | 785 bp | + | 50.1% |
| tRNA-Gly | Transfer RNA | 9,597 | 9,667 | 71 bp | + | – |
| ND3 | Protein-coding gene | 9,668 | 10,016 | 349 bp | + | 51.3% |
| tRNA-Arg | Transfer RNA | 10,017 | 10,086 | 70 bp | + | – |
| ND4L | Protein-coding gene | 10,087 | 10,383 | 297 bp | + | 54.2% |
| ND4 | Protein-coding gene | 10,377 | 11,757 | 1,381 bp | + | 47.4% |
| tRNA-His | Transfer RNA | 11,758 | 11,826 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,827 | 11,895 | 69 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,896 | 11,969 | 74 bp | + | – |
| ND5 | Protein-coding gene | 11,970 | 13,808 | 1,839 bp | + | 47.5% |
| ND6 | Protein-coding gene | 13,805 | 14,326 | 522 bp | − | 51.5% |
| tRNA-Glu | Transfer RNA | 14,327 | 14,396 | 70 bp | − | – |
| CYTB | Protein-coding gene | 14,401 | 15,541 | 1,141 bp | + | 47.0% |
| tRNA-Thr | Transfer RNA | 15,542 | 15,613 | 72 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,614 | 15,683 | 70 bp | − | – |
| D-loop | Control region | 15,684 | 16,786 | 1,103 bp | – | 45.8% |