Clupea pallasii
Pacific herring
GC content
47.37%
Whole genome
Non-coding
1,109 bp
D-loop 1,047 bp
Where Pacific herring sits among 2,335 species
Whole-genome GC content against maximum lifespan. Pacific herring has the 975th longest lifespan of them.
- This species
- Other ray-finned fishes
- Other classes
Base composition
Whole genome16,700 bp
- GC skew (G − C) / (G + C)
- −0.192
- AT skew (A − T) / (A + T)
- +0.022
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 genome16,700 bp
Protein-coding11,403 bp
12S rRNA953 bp
16S rRNA1,685 bp
All tRNA1,550 bp
D-loop1,047 bp
Genes and regions
Select a column to sort; select a gene to compare it across species| Composition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| ND1NADH dehydrogenase subunit 1 | 975 bp | 49.64% | −0.198 | −0.153 | |||||
| ND2NADH dehydrogenase subunit 2 | 1,045 bp | 50.05% | −0.300 | −0.050 | |||||
| COX1Cytochrome c oxidase subunit I | 1,551 bp | 46.10% | −0.152 | −0.072 | |||||
| COX2Cytochrome c oxidase subunit II | 691 bp | 45.01% | −0.196 | +0.026 | |||||
| ATP8ATP synthase F0 subunit 8 | 168 bp | 42.26% | −0.352 | +0.052 | |||||
| ATP6ATP synthase F0 subunit 6 | 683 bp | 46.12% | −0.352 | −0.076 | |||||
| COX3Cytochrome c oxidase subunit III | 785 bp | 48.79% | −0.196 | −0.065 | |||||
| ND3NADH dehydrogenase subunit 3 | 349 bp | 46.71% | −0.190 | −0.151 | |||||
| ND4LNADH dehydrogenase subunit 4L | 297 bp | 48.49% | −0.319 | −0.059 | |||||
| ND4NADH dehydrogenase subunit 4 | 1,381 bp | 49.60% | −0.226 | −0.034 | |||||
| ND5NADH dehydrogenase subunit 5 | 1,836 bp | 46.51% | −0.253 | −0.012 | |||||
| ND6NADH dehydrogenase subunit 6 | 522 bp | 50.19% | −0.282 | +0.385 | |||||
| CYTBCytochrome b | 1,141 bp | 46.36% | −0.202 | −0.092 | |||||
| 12S rRNA12S ribosomal RNA | 953 bp | 50.26% | −0.094 | +0.215 | |||||
| 16S rRNA16S ribosomal RNA | 1,685 bp | 47.36% | −0.098 | +0.276 | |||||
| D-loopControl region (D-loop) | 1,047 bp | 39.06% | −0.125 | −0.006 |
Codon usage
Counts per codon, darker is more frequent3,805 codons in all protein-coding genes. Grouped with the Vertebrate mitochondrial code (NCBI table 2).
Phe F6.3%
UUU97
UUC142
Leu L16.1%
UUA79
UUG26
CUU130
CUC99
CUA182
CUG96
Ile I6.6%
AUU160
AUC93
Met M4.5%
AUA63
AUG109
Val V6.7%
GUU69
GUC60
GUA83
GUG43
Ser S6.0%
UCU40
UCC62
UCA53
UCG20
AGU10
AGC45
Pro P5.8%
CCU60
CCC89
CCA49
CCG21
Thr T8.0%
ACU70
ACC118
ACA80
ACG35
Ala A9.7%
GCU57
GCC153
GCA123
GCG37
Tyr Y3.0%
UAU43
UAC72
His H2.7%
CAU19
CAC82
Gln Q2.6%
CAA59
CAG39
Asn N3.2%
AAU47
AAC73
Lys K2.0%
AAA51
AAG25
Asp D1.9%
GAU28
GAC45
Glu E2.5%
GAA68
GAG28
Cys C0.8%
UGU11
UGC20
Trp W3.1%
UGA96
UGG22
Arg R2.0%
CGU7
CGC10
CGA45
CGG15
Gly G6.3%
GGU32
GGC45
GGA78
GGG86
Stop 0.2%
UAA3
UAG3
AGA0
AGG0
Genome map
38 annotated features in NC_009578.1Hover, 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 (47.4%, 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 | 1,022 | 953 bp | + | 50.3% |
| tRNA-Val | Transfer RNA | 1,023 | 1,093 | 71 bp | + | – |
| 16S rRNA | Ribosomal RNA | 1,094 | 2,778 | 1,685 bp | + | 47.4% |
| tRNA-Leu (UUR) | Transfer RNA | 2,779 | 2,853 | 75 bp | + | – |
| ND1 | Protein-coding gene | 2,854 | 3,828 | 975 bp | + | 49.6% |
| tRNA-Ile | Transfer RNA | 3,835 | 3,906 | 72 bp | + | – |
| tRNA-Gln | Transfer RNA | 3,906 | 3,976 | 71 bp | − | – |
| tRNA-Met | Transfer RNA | 3,976 | 4,044 | 69 bp | + | – |
| ND2 | Protein-coding gene | 4,045 | 5,089 | 1,045 bp | + | 50.1% |
| tRNA-Trp | Transfer RNA | 5,090 | 5,161 | 72 bp | + | – |
| tRNA-Ala | Transfer RNA | 5,163 | 5,231 | 69 bp | − | – |
| tRNA-Asn | Transfer RNA | 5,233 | 5,305 | 73 bp | − | – |
| tRNA-Cys | Transfer RNA | 5,337 | 5,402 | 66 bp | − | – |
| tRNA-Tyr | Transfer RNA | 5,404 | 5,474 | 71 bp | − | – |
| COX1 | Protein-coding gene | 5,476 | 7,026 | 1,551 bp | + | 46.1% |
| tRNA-Ser (UCN) | Transfer RNA | 7,027 | 7,097 | 71 bp | − | – |
| tRNA-Asp | Transfer RNA | 7,102 | 7,171 | 70 bp | + | – |
| COX2 | Protein-coding gene | 7,184 | 7,874 | 691 bp | + | 45.0% |
| tRNA-Lys | Transfer RNA | 7,875 | 7,949 | 75 bp | + | – |
| ATP8 | Protein-coding gene | 7,951 | 8,118 | 168 bp | + | 42.3% |
| ATP6 | Protein-coding gene | 8,109 | 8,791 | 683 bp | + | 46.1% |
| COX3 | Protein-coding gene | 8,792 | 9,576 | 785 bp | + | 48.8% |
| tRNA-Gly | Transfer RNA | 9,577 | 9,648 | 72 bp | + | – |
| ND3 | Protein-coding gene | 9,649 | 9,997 | 349 bp | + | 46.7% |
| tRNA-Arg | Transfer RNA | 9,998 | 10,067 | 70 bp | + | – |
| ND4L | Protein-coding gene | 10,068 | 10,364 | 297 bp | + | 48.5% |
| ND4 | Protein-coding gene | 10,358 | 11,738 | 1,381 bp | + | 49.6% |
| tRNA-His | Transfer RNA | 11,739 | 11,807 | 69 bp | + | – |
| tRNA-Ser (AGY) | Transfer RNA | 11,808 | 11,875 | 68 bp | + | – |
| tRNA-Leu (CUN) | Transfer RNA | 11,875 | 11,945 | 71 bp | + | – |
| ND5 | Protein-coding gene | 11,946 | 13,781 | 1,836 bp | + | 46.5% |
| ND6 | Protein-coding gene | 13,778 | 14,299 | 522 bp | − | 50.2% |
| tRNA-Glu | Transfer RNA | 14,300 | 14,368 | 69 bp | − | – |
| CYTB | Protein-coding gene | 14,373 | 15,513 | 1,141 bp | + | 46.4% |
| tRNA-Thr | Transfer RNA | 15,514 | 15,584 | 71 bp | + | – |
| tRNA-Pro | Transfer RNA | 15,584 | 15,653 | 70 bp | − | – |
| D-loop | Control region | 15,654 | 16,700 | 1,047 bp | – | 39.1% |