Menidia menidia
Atlantic silverside
GC content
49.35%
Whole genome
Non-coding
852 bp
D-loop 789 bp
Where Atlantic silverside sits among 2,335 species
Whole-genome GC content against maximum lifespan. Atlantic silverside has the 2,252nd longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,456 bp
- GC skew (G − C) / (G + C)
- −0.230
- AT skew (A − T) / (A + T)
- −0.031
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 genome16,456 bp
Protein-coding11,406 bp
12S rRNA949 bp
16S rRNA1,690 bp
All tRNA1,559 bp
D-loop789 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% | −0.300 | −0.211 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,045 bp | 52.34% | −0.342 | −0.161 | |||||
| COX1Cytochrome c oxidase subunit I | 1,551 bp | 49.52% | −0.180 | −0.121 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 46.74% | −0.226 | +0.005 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 48.81% | −0.463 | +0.047 | |||||
| ATP6ATP synthase F0 subunit 6 | 684 bp | 47.95% | −0.421 | −0.079 | |||||
| COX3Cytochrome c oxidase subunit III | 785 bp | 50.45% | −0.268 | −0.111 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 49.86% | −0.276 | −0.189 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 54.88% | −0.399 | −0.104 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 52.72% | −0.316 | −0.139 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,839 bp | 48.94% | −0.287 | −0.127 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 52.49% | −0.263 | +0.298 | |||||
| CYTBCytochrome b | 1,141 bp | 48.20% | −0.284 | −0.161 | |||||
| 12S rRNA12S ribosomal RNA | 949 bp | 51.21% | −0.045 | +0.214 | |||||
| 16S rRNA16S ribosomal RNA | 1,690 bp | 50.06% | −0.085 | +0.192 | |||||
| D-loopControl region (D-loop) | 789 bp | 39.04% | −0.156 | +0.019 |
Codon usage
Counts per codon, darker is more frequent3,807 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.3%
UUU89
UUC152
Leu L17.3%
UUA44
UUG25
CUU177
CUC193
CUA122
CUG96
Ile I6.8%
AUU153
AUC104
Met M3.9%
AUA54
AUG96
Val V6.2%
GUU77
GUC68
GUA52
GUG38
Ser S6.6%
UCU49
UCC74
UCA52
UCG23
AGU17
AGC36
Pro P5.8%
CCU49
CCC100
CCA53
CCG18
Thr T7.6%
ACU58
ACC144
ACA61
ACG26
Ala A9.5%
GCU67
GCC184
GCA77
GCG33
Tyr Y2.9%
UAU46
UAC66
His H2.8%
CAU24
CAC83
Gln Q2.7%
CAA57
CAG44
Asn N2.9%
AAU37
AAC73
Lys K1.9%
AAA40
AAG33
Asp D1.9%
GAU29
GAC45
Glu E2.7%
GAA62
GAG39
Cys C0.7%
UGU6
UGC19
Trp W3.1%
UGA85
UGG32
Arg R2.0%
CGU9
CGC20
CGA28
CGG20
Gly G6.4%
GGU37
GGC93
GGA60
GGG52
Stop 0.2%
UAA5
UAG2
AGA0
AGG0
Genome map
38 annotated features in NC_011174.1Hover, 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 (49.4%, 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 | 1,018 | 949 bp | + | 51.2% |
| tRNA-Val | Transfer RNA | 1,019 | 1,091 | 73 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,092 | 2,781 | 1,690 bp | + | 50.1% |
| tRNA-Leu (UUR) | Transfer RNA | 2,782 | 2,855 | 74 bp | + | – |
| ND1 | Protein-coding gene | 2,856 | 3,830 | 975 bp | + | 49.9% |
| tRNA-Ile | Transfer RNA | 3,835 | 3,904 | 70 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,904 | 3,974 | 71 bp | − | – |
| tRNA-Met | Transfer RNA | 3,974 | 4,043 | 70 bp | + | – |
| ND2 | Protein-coding gene | 4,044 | 5,088 | 1,045 bp | + | 52.3% |
| tRNA-Trp | Transfer RNA | 5,089 | 5,160 | 72 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,162 | 5,230 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,234 | 5,306 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,344 | 5,409 | 66 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,410 | 5,480 | 71 bp | − | – |
| COX1 | Protein-coding gene | 5,482 | 7,032 | 1,551 bp | + | 49.5% |
| tRNA-Ser (UCN) | Transfer RNA | 7,039 | 7,109 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,113 | 7,184 | 72 bp | + | – |
| COX2 | Protein-coding gene | 7,188 | 7,878 | 691 bp | + | 46.7% |
| tRNA-Lys | Transfer RNA | 7,879 | 7,952 | 74 bp | + | – |
| ATP8 | Protein-coding gene | 7,954 | 8,121 | 168 bp | + | 48.8% |
| ATP6 | Protein-coding gene | 8,112 | 8,795 | 684 bp | + | 48.0% |
| COX3 | Protein-coding gene | 8,795 | 9,579 | 785 bp | + | 50.5% |
| tRNA-Gly | Transfer RNA | 9,580 | 9,650 | 71 bp | + | – |
| ND3 | Protein-coding gene | 9,651 | 9,999 | 349 bp | + | 49.9% |
| tRNA-Arg | Transfer RNA | 10,000 | 10,068 | 69 bp | + | – |
| ND4L | Protein-coding gene | 10,069 | 10,365 | 297 bp | + | 54.9% |
| ND4 | Protein-coding gene | 10,359 | 11,739 | 1,381 bp | + | 52.7% |
| tRNA-His | Transfer RNA | 11,740 | 11,808 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,809 | 11,879 | 71 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,880 | 11,952 | 73 bp | + | – |
| ND5 | Protein-coding gene | 11,953 | 13,791 | 1,839 bp | + | 48.9% |
| ND6 | Protein-coding gene | 13,788 | 14,309 | 522 bp | − | 52.5% |
| tRNA-Glu | Transfer RNA | 14,310 | 14,379 | 70 bp | − | – |
| CYTB | Protein-coding gene | 14,384 | 15,524 | 1,141 bp | + | 48.2% |
| tRNA-Thr | Transfer RNA | 15,525 | 15,598 | 74 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,599 | 15,667 | 69 bp | − | – |
| D-loop | Control region | 15,668 | 16,456 | 789 bp | – | 39.0% |