Trinectes maculatus
Hogchoker
GC content
46.53%
Whole genome
Non-coding
954 bp
D-loop 880 bp
Where Hogchoker sits among 2,335 species
Whole-genome GC content against maximum lifespan. Hogchoker has the 1,903rd longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,553 bp
- GC skew (G − C) / (G + C)
- −0.327
- AT skew (A − T) / (A + T)
- +0.070
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 genome16,553 bp
Protein-coding11,399 bp
12S rRNA959 bp
16S rRNA1,701 bp
All tRNA1,540 bp
D-loop880 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 50.26% | −0.400 | +0.002 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,053 bp | 49.00% | −0.535 | +0.073 | |||||
| COX1Cytochrome c oxidase subunit I | 1,549 bp | 47.00% | −0.250 | −0.065 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 45.15% | −0.276 | +0.071 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 43.45% | −0.671 | +0.137 | |||||
| ATP6ATP synthase F0 subunit 6 | 684 bp | 45.32% | −0.419 | −0.070 | |||||
| COX3Cytochrome c oxidase subunit III | 785 bp | 49.43% | −0.309 | −0.028 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 49.28% | −0.360 | −0.107 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 47.81% | −0.423 | −0.058 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 46.56% | −0.418 | +0.005 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,830 bp | 45.03% | −0.434 | +0.036 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 45.98% | −0.467 | +0.454 | |||||
| CYTBCytochrome b | 1,133 bp | 48.10% | −0.369 | −0.054 | |||||
| 12S rRNA12S ribosomal RNA | 959 bp | 47.97% | −0.165 | +0.279 | |||||
| 16S rRNA16S ribosomal RNA | 1,701 bp | 46.86% | −0.200 | +0.283 | |||||
| D-loopControl region (D-loop) | 880 bp | 37.20% | −0.174 | +0.004 |
Codon usage
Counts per codon, darker is more frequent3,803 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F5.9%
UUU93
UUC132
Leu L17.5%
UUA76
UUG22
CUU131
CUC179
CUA213
CUG46
Ile I7.4%
AUU139
AUC144
Met M3.9%
AUA101
AUG46
Val V5.7%
GUU53
GUC72
GUA64
GUG27
Ser S6.5%
UCU34
UCC75
UCA69
UCG13
AGU11
AGC44
Pro P5.9%
CCU51
CCC109
CCA56
CCG10
Thr T8.4%
ACU51
ACC141
ACA109
ACG18
Ala A8.6%
GCU59
GCC150
GCA108
GCG10
Tyr Y2.9%
UAU38
UAC73
His H2.8%
CAU20
CAC88
Gln Q2.6%
CAA84
CAG15
Asn N3.5%
AAU33
AAC101
Lys K2.1%
AAA69
AAG10
Asp D1.8%
GAU18
GAC52
Glu E2.4%
GAA62
GAG28
Cys C0.6%
UGU6
UGC17
Trp W3.1%
UGA93
UGG26
Arg R2.0%
CGU8
CGC14
CGA49
CGG6
Gly G6.0%
GGU34
GGC97
GGA61
GGG38
Stop 0.2%
UAA6
UAG1
AGA0
AGG0
Genome map
38 annotated features in NC_023769.1Hover, 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 (46.5%, 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 | 1,028 | 959 bp | + | 48.0% |
| tRNA-Val | Transfer RNA | 1,029 | 1,101 | 73 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,102 | 2,802 | 1,701 bp | + | 46.9% |
| tRNA-Leu (UUR) | Transfer RNA | 2,803 | 2,876 | 74 bp | + | – |
| ND1 | Protein-coding gene | 2,877 | 3,851 | 975 bp | + | 50.3% |
| tRNA-Ile | Transfer RNA | 3,854 | 3,922 | 69 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,922 | 3,992 | 71 bp | − | – |
| tRNA-Met | Transfer RNA | 3,992 | 4,061 | 70 bp | + | – |
| ND2 | Protein-coding gene | 4,062 | 5,114 | 1,053 bp | + | 49.0% |
| tRNA-Trp | Transfer RNA | 5,119 | 5,189 | 71 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,191 | 5,259 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,261 | 5,333 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,372 | 5,436 | 65 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,437 | 5,503 | 67 bp | − | – |
| COX1 | Protein-coding gene | 5,505 | 7,053 | 1,549 bp | + | 47.0% |
| tRNA-Ser (UCN) | Transfer RNA | 7,056 | 7,126 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,130 | 7,198 | 69 bp | + | – |
| COX2 | Protein-coding gene | 7,204 | 7,894 | 691 bp | + | 45.2% |
| tRNA-Lys | Transfer RNA | 7,895 | 7,969 | 75 bp | + | – |
| ATP8 | Protein-coding gene | 7,972 | 8,139 | 168 bp | + | 43.5% |
| ATP6 | Protein-coding gene | 8,130 | 8,813 | 684 bp | + | 45.3% |
| COX3 | Protein-coding gene | 8,813 | 9,597 | 785 bp | + | 49.4% |
| tRNA-Gly | Transfer RNA | 9,598 | 9,669 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,670 | 10,018 | 349 bp | + | 49.3% |
| tRNA-Arg | Transfer RNA | 10,019 | 10,089 | 71 bp | + | – |
| ND4L | Protein-coding gene | 10,092 | 10,388 | 297 bp | + | 47.8% |
| ND4 | Protein-coding gene | 10,382 | 11,762 | 1,381 bp | + | 46.6% |
| tRNA-His | Transfer RNA | 11,763 | 11,831 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,832 | 11,899 | 68 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,905 | 11,977 | 73 bp | + | – |
| ND5 | Protein-coding gene | 11,978 | 13,807 | 1,830 bp | + | 45.0% |
| ND6 | Protein-coding gene | 13,812 | 14,333 | 522 bp | − | 46.0% |
| tRNA-Glu | Transfer RNA | 14,335 | 14,403 | 69 bp | − | – |
| CYTB | Protein-coding gene | 14,406 | 15,538 | 1,133 bp | + | 48.1% |
| tRNA-Thr | Transfer RNA | 15,540 | 15,615 | 76 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,602 | 15,673 | 72 bp | − | – |
| D-loop | Control region | 15,674 | 16,553 | 880 bp | – | 37.2% |