Cymatogaster aggregata
Shiner perch
GC content
43.88%
Whole genome
Non-coding
887 bp
D-loop 820 bp
Where Shiner perch sits among 2,335 species
Whole-genome GC content against maximum lifespan. Shiner perch has the 1,725th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,533 bp
- GC skew (G − C) / (G + C)
- −0.259
- AT skew (A − T) / (A + T)
- −0.008
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 genome16,533 bp
Protein-coding11,452 bp
12S rRNA946 bp
16S rRNA1,693 bp
All tRNA1,555 bp
D-loop820 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 42.67% | −0.313 | −0.134 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,046 bp | 45.89% | −0.454 | −0.032 | |||||
| COX1Cytochrome c oxidase subunit I | 1,596 bp | 46.12% | −0.209 | −0.102 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 43.27% | −0.231 | −0.046 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 41.67% | −0.400 | +0.041 | |||||
| ATP6ATP synthase F0 subunit 6 | 683 bp | 44.22% | −0.404 | −0.118 | |||||
| COX3Cytochrome c oxidase subunit III | 785 bp | 45.73% | −0.226 | −0.108 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 46.99% | −0.329 | −0.243 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 47.14% | −0.329 | −0.134 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 45.33% | −0.364 | −0.052 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,839 bp | 41.71% | −0.364 | −0.045 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 45.02% | −0.421 | +0.352 | |||||
| CYTBCytochrome b | 1,141 bp | 42.77% | −0.311 | −0.145 | |||||
| 12S rRNA12S ribosomal RNA | 946 bp | 47.04% | −0.061 | +0.178 | |||||
| 16S rRNA16S ribosomal RNA | 1,693 bp | 43.65% | −0.083 | +0.212 | |||||
| D-loopControl region (D-loop) | 820 bp | 35.12% | −0.139 | −0.026 |
Codon usage
Counts per codon, darker is more frequent3,821 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.6%
UUU155
UUC98
Leu L16.9%
UUA98
UUG23
CUU195
CUC128
CUA164
CUG38
Ile I7.1%
AUU159
AUC111
Met M4.2%
AUA123
AUG39
Val V5.9%
GUU74
GUC53
GUA75
GUG24
Ser S6.4%
UCU48
UCC67
UCA61
UCG16
AGU21
AGC30
Pro P5.7%
CCU66
CCC94
CCA47
CCG9
Thr T7.9%
ACU76
ACC108
ACA107
ACG9
Ala A9.1%
GCU95
GCC141
GCA99
GCG13
Tyr Y2.9%
UAU46
UAC64
His H2.7%
CAU42
CAC60
Gln Q2.6%
CAA88
CAG11
Asn N3.1%
AAU48
AAC69
Lys K2.0%
AAA65
AAG10
Asp D2.1%
GAU33
GAC48
Glu E2.7%
GAA83
GAG21
Cys C0.7%
UGU9
UGC16
Trp W3.2%
UGA98
UGG23
Arg R2.0%
CGU13
CGC19
CGA33
CGG10
Gly G6.3%
GGU41
GGC93
GGA61
GGG47
Stop 0.2%
UAA4
UAG2
AGA0
AGG0
Genome map
38 annotated features in NC_009059.1Hover, 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 (43.9%, 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 | 69 | 69 bp | + | – |
| 12S rRNA | Ribosomal RNA | 70 | 1,015 | 946 bp | + | 47.0% |
| tRNA-Val | Transfer RNA | 1,016 | 1,087 | 72 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,088 | 2,780 | 1,693 bp | + | 43.7% |
| tRNA-Leu (UUR) | Transfer RNA | 2,781 | 2,854 | 74 bp | + | – |
| ND1 | Protein-coding gene | 2,855 | 3,829 | 975 bp | + | 42.7% |
| tRNA-Ile | Transfer RNA | 3,834 | 3,903 | 70 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,903 | 3,974 | 72 bp | − | – |
| tRNA-Met | Transfer RNA | 3,974 | 4,042 | 69 bp | + | – |
| ND2 | Protein-coding gene | 4,043 | 5,088 | 1,046 bp | + | 45.9% |
| tRNA-Trp | Transfer RNA | 5,089 | 5,159 | 71 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,161 | 5,229 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,232 | 5,304 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,339 | 5,406 | 68 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,407 | 5,474 | 68 bp | − | – |
| COX1 | Protein-coding gene | 5,476 | 7,071 | 1,596 bp | + | 46.1% |
| tRNA-Ser (UCN) | Transfer RNA | 7,072 | 7,142 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,146 | 7,219 | 74 bp | + | – |
| COX2 | Protein-coding gene | 7,228 | 7,918 | 691 bp | + | 43.3% |
| tRNA-Lys | Transfer RNA | 7,919 | 7,992 | 74 bp | + | – |
| ATP8 | Protein-coding gene | 7,994 | 8,161 | 168 bp | + | 41.7% |
| ATP6 | Protein-coding gene | 8,152 | 8,834 | 683 bp | + | 44.2% |
| COX3 | Protein-coding gene | 8,835 | 9,619 | 785 bp | + | 45.7% |
| tRNA-Gly | Transfer RNA | 9,620 | 9,691 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,692 | 10,040 | 349 bp | + | 47.0% |
| tRNA-Arg | Transfer RNA | 10,041 | 10,109 | 69 bp | + | – |
| ND4L | Protein-coding gene | 10,110 | 10,406 | 297 bp | + | 47.1% |
| ND4 | Protein-coding gene | 10,400 | 11,780 | 1,381 bp | + | 45.3% |
| tRNA-His | Transfer RNA | 11,781 | 11,849 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,850 | 11,917 | 68 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,925 | 11,997 | 73 bp | + | – |
| ND5 | Protein-coding gene | 11,998 | 13,836 | 1,839 bp | + | 41.7% |
| ND6 | Protein-coding gene | 13,833 | 14,354 | 522 bp | − | 45.0% |
| tRNA-Glu | Transfer RNA | 14,355 | 14,422 | 68 bp | − | – |
| CYTB | Protein-coding gene | 14,428 | 15,568 | 1,141 bp | + | 42.8% |
| tRNA-Thr | Transfer RNA | 15,569 | 15,641 | 73 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,643 | 15,713 | 71 bp | − | – |
| D-loop | Control region | 15,714 | 16,533 | 820 bp | – | 35.1% |