Cyprinella lutrensis
Red shiner
GC content
45.06%
Whole genome
Non-coding
1,106 bp
D-loop 1,050 bp
Where Red shiner sits among 2,335 species
Whole-genome GC content against maximum lifespan. Red shiner has the 2,254th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,706 bp
- GC skew (G − C) / (G + C)
- −0.185
- AT skew (A − T) / (A + T)
- +0.010
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
- Updated in build 2
- In the database since
- build 1 (2015-07-01)
- Last changed
- 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 genome16,706 bp
Protein-coding11,400 bp
12S rRNA956 bp
16S rRNA1,683 bp
All tRNA1,561 bp
D-loop1,050 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 49.74% | −0.204 | −0.167 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,045 bp | 48.80% | −0.298 | −0.009 | |||||
| COX1Cytochrome c oxidase subunit I | 1,551 bp | 43.46% | −0.154 | −0.090 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 43.27% | −0.151 | +0.010 | |||||
| ATP8ATP synthase F0 subunit 8 | 162 bp | 40.12% | −0.446 | +0.155 | |||||
| ATP6ATP synthase F0 subunit 6 | 684 bp | 40.50% | −0.307 | −0.066 | |||||
| COX3Cytochrome c oxidase subunit III | 784 bp | 46.17% | −0.149 | −0.090 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 42.69% | −0.248 | −0.060 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 45.12% | −0.299 | −0.080 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,382 bp | 44.94% | −0.243 | −0.083 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,836 bp | 44.28% | −0.255 | −0.019 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 46.36% | −0.289 | +0.307 | |||||
| CYTBCytochrome b | 1,141 bp | 46.28% | −0.273 | −0.090 | |||||
| 12S rRNA12S ribosomal RNA | 956 bp | 50.00% | −0.054 | +0.213 | |||||
| 16S rRNA16S ribosomal RNA | 1,683 bp | 45.40% | −0.029 | +0.230 | |||||
| D-loopControl region (D-loop) | 1,050 bp | 36.29% | −0.197 | +0.007 |
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 F6.1%
UUU101
UUC132
Leu L16.4%
UUA123
UUG46
CUU147
CUC105
CUA154
CUG50
Ile I6.9%
AUU165
AUC96
Met M4.4%
AUA108
AUG61
Val V6.6%
GUU66
GUC55
GUA96
GUG33
Ser S6.5%
UCU50
UCC57
UCA67
UCG15
AGU11
AGC47
Pro P5.6%
CCU51
CCC67
CCA76
CCG20
Thr T7.8%
ACU68
ACC97
ACA98
ACG34
Ala A9.2%
GCU70
GCC132
GCA124
GCG23
Tyr Y3.0%
UAU50
UAC63
His H2.8%
CAU34
CAC71
Gln Q2.6%
CAA70
CAG29
Asn N2.9%
AAU47
AAC64
Lys K2.1%
AAA50
AAG29
Asp D2.0%
GAU30
GAC47
Glu E2.7%
GAA58
GAG43
Cys C0.7%
UGU12
UGC14
Trp W3.1%
UGA90
UGG29
Arg R2.0%
CGU12
CGC12
CGA35
CGG17
Gly G6.5%
GGU46
GGC60
GGA76
GGG64
Stop 0.2%
UAA7
UAG0
AGA0
AGG0
Genome map
38 annotated features in NC_008643.1Hover, 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 (45.1%, 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 | 1,025 | 956 bp | + | 50.0% |
| tRNA-Val | Transfer RNA | 1,026 | 1,097 | 72 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,098 | 2,780 | 1,683 bp | + | 45.4% |
| tRNA-Leu (UUR) | Transfer RNA | 2,781 | 2,856 | 76 bp | + | – |
| ND1 | Protein-coding gene | 2,858 | 3,832 | 975 bp | + | 49.7% |
| 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 | + | 48.8% |
| 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 | 5,406 | 69 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,407 | 5,477 | 71 bp | − | – |
| COX1 | Protein-coding gene | 5,479 | 7,029 | 1,551 bp | + | 43.5% |
| tRNA-Ser (UCN) | Transfer RNA | 7,030 | 7,100 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,104 | 7,176 | 73 bp | + | – |
| COX2 | Protein-coding gene | 7,183 | 7,873 | 691 bp | + | 43.3% |
| tRNA-Lys | Transfer RNA | 7,874 | 7,949 | 76 bp | + | – |
| ATP8 | Protein-coding gene | 7,951 | 8,112 | 162 bp | + | 40.1% |
| ATP6 | Protein-coding gene | 8,106 | 8,789 | 684 bp | + | 40.5% |
| COX3 | Protein-coding gene | 8,789 | 9,572 | 784 bp | + | 46.2% |
| tRNA-Gly | Transfer RNA | 9,573 | 9,644 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,645 | 9,993 | 349 bp | + | 42.7% |
| tRNA-Arg | Transfer RNA | 9,994 | 10,062 | 69 bp | + | – |
| ND4L | Protein-coding gene | 10,063 | 10,359 | 297 bp | + | 45.1% |
| ND4 | Protein-coding gene | 10,353 | 11,734 | 1,382 bp | + | 44.9% |
| tRNA-His | Transfer RNA | 11,735 | 11,803 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,805 | 11,872 | 68 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,874 | 11,946 | 73 bp | + | – |
| ND5 | Protein-coding gene | 11,947 | 13,782 | 1,836 bp | + | 44.3% |
| ND6 | Protein-coding gene | 13,779 | 14,300 | 522 bp | − | 46.4% |
| tRNA-Glu | Transfer RNA | 14,301 | 14,369 | 69 bp | − | – |
| CYTB | Protein-coding gene | 14,375 | 15,515 | 1,141 bp | + | 46.3% |
| tRNA-Thr | Transfer RNA | 15,516 | 15,586 | 71 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,586 | 15,656 | 71 bp | − | – |
| D-loop | Control region | 15,657 | 16,706 | 1,050 bp | – | 36.3% |