Notropis atherinoides
Emerald shiner
GC content
45.73%
Whole genome
Non-coding
1,106 bp
D-loop 1,051 bp
Where Emerald shiner sits among 2,335 species
Whole-genome GC content against maximum lifespan. Emerald shiner has the 2,099th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,710 bp
- GC skew (G − C) / (G + C)
- −0.183
- AT skew (A − T) / (A + T)
- +0.015
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 genome16,710 bp
Protein-coding11,403 bp
12S rRNA957 bp
16S rRNA1,682 bp
All tRNA1,562 bp
D-loop1,051 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 48.51% | −0.218 | −0.108 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,045 bp | 48.90% | −0.260 | −0.037 | |||||
| COX1Cytochrome c oxidase subunit I | 1,551 bp | 43.59% | −0.169 | −0.074 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 42.84% | −0.176 | +0.028 | |||||
| ATP8ATP synthase F0 subunit 8 | 165 bp | 38.18% | −0.492 | +0.137 | |||||
| ATP6ATP synthase F0 subunit 6 | 683 bp | 44.66% | −0.292 | −0.069 | |||||
| COX3Cytochrome c oxidase subunit III | 784 bp | 46.56% | −0.184 | −0.079 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 47.28% | −0.176 | −0.109 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 43.77% | −0.277 | −0.078 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,382 bp | 46.09% | −0.246 | −0.071 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,836 bp | 46.08% | −0.244 | −0.022 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 50.00% | −0.318 | +0.326 | |||||
| CYTBCytochrome b | 1,141 bp | 46.54% | −0.247 | −0.072 | |||||
| 12S rRNA12S ribosomal RNA | 957 bp | 49.95% | −0.054 | +0.215 | |||||
| 16S rRNA16S ribosomal RNA | 1,682 bp | 45.42% | −0.031 | +0.229 | |||||
| D-loopControl region (D-loop) | 1,051 bp | 37.01% | −0.177 | +0.012 |
Codon usage
Counts per codon, darker is more frequent3,804 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.0%
UUU99
UUC130
Leu L16.5%
UUA116
UUG38
CUU131
CUC117
CUA159
CUG66
Ile I6.8%
AUU171
AUC87
Met M4.6%
AUA88
AUG86
Val V6.6%
GUU69
GUC53
GUA86
GUG42
Ser S6.3%
UCU40
UCC57
UCA66
UCG23
AGU12
AGC41
Pro P5.7%
CCU49
CCC59
CCA90
CCG17
Thr T7.8%
ACU73
ACC99
ACA96
ACG28
Ala A9.4%
GCU53
GCC152
GCA105
GCG46
Tyr Y3.0%
UAU50
UAC63
His H2.7%
CAU32
CAC72
Gln Q2.6%
CAA64
CAG34
Asn N3.0%
AAU44
AAC71
Lys K2.1%
AAA52
AAG26
Asp D1.9%
GAU28
GAC46
Glu E2.7%
GAA64
GAG37
Cys C0.7%
UGU8
UGC19
Trp W3.2%
UGA97
UGG23
Arg R2.0%
CGU13
CGC11
CGA39
CGG14
Gly G6.5%
GGU34
GGC65
GGA84
GGG64
Stop 0.2%
UAA5
UAG1
AGA0
AGG0
Genome map
38 annotated features in NC_033925.1Hover, 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 (45.7%, 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 | 69 | 69 bp | + | – |
| 12S rRNA | Ribosomal RNA | 70 | 1,026 | 957 bp | + | 50.0% |
| tRNA-Val | Transfer RNA | 1,027 | 1,098 | 72 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,099 | 2,780 | 1,682 bp | + | 45.4% |
| tRNA-Leu (UUR) | Transfer RNA | 2,781 | 2,856 | 76 bp | + | – |
| ND1 | Protein-coding gene | 2,858 | 3,832 | 975 bp | + | 48.5% |
| tRNA-Ile | Transfer RNA | 3,837 | 3,908 | 72 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,907 | 3,977 | 71 bp | − | – |
| tRNA-Met | Transfer RNA | 3,979 | 4,047 | 69 bp | + | – |
| ND2 | Protein-coding gene | 4,048 | 5,092 | 1,045 bp | + | 48.9% |
| tRNA-Trp | Transfer RNA | 5,093 | 5,163 | 71 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,165 | 5,233 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,235 | 5,307 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,338 | 5,405 | 68 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,406 | 5,476 | 71 bp | − | – |
| COX1 | Protein-coding gene | 5,478 | 7,028 | 1,551 bp | + | 43.6% |
| tRNA-Ser (UCN) | Transfer RNA | 7,029 | 7,099 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,103 | 7,175 | 73 bp | + | – |
| COX2 | Protein-coding gene | 7,183 | 7,873 | 691 bp | + | 42.8% |
| tRNA-Lys | Transfer RNA | 7,874 | 7,949 | 76 bp | + | – |
| ATP8 | Protein-coding gene | 7,951 | 8,115 | 165 bp | + | 38.2% |
| ATP6 | Protein-coding gene | 8,109 | 8,791 | 683 bp | + | 44.7% |
| COX3 | Protein-coding gene | 8,792 | 9,575 | 784 bp | + | 46.6% |
| tRNA-Gly | Transfer RNA | 9,576 | 9,647 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,648 | 9,996 | 349 bp | + | 47.3% |
| tRNA-Arg | Transfer RNA | 9,997 | 10,065 | 69 bp | + | – |
| ND4L | Protein-coding gene | 10,066 | 10,362 | 297 bp | + | 43.8% |
| ND4 | Protein-coding gene | 10,356 | 11,737 | 1,382 bp | + | 46.1% |
| tRNA-His | Transfer RNA | 11,738 | 11,806 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,807 | 11,875 | 69 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,877 | 11,949 | 73 bp | + | – |
| ND5 | Protein-coding gene | 11,950 | 13,785 | 1,836 bp | + | 46.1% |
| ND6 | Protein-coding gene | 13,782 | 14,303 | 522 bp | − | 50.0% |
| tRNA-Glu | Transfer RNA | 14,304 | 14,372 | 69 bp | − | – |
| CYTB | Protein-coding gene | 14,377 | 15,517 | 1,141 bp | + | 46.5% |
| tRNA-Thr | Transfer RNA | 15,518 | 15,589 | 72 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,589 | 15,659 | 71 bp | − | – |
| D-loop | Control region | 15,660 | 16,710 | 1,051 bp | – | 37.0% |