DDBJ
CODON USAGE DATABASE

Classical Codon Table by CUTD

Compartment
Source
All counts each unique CDS once.
Exploratory datasetNot a formal CUTD release

fields: triplet · amino acid · fraction · ‰ · (count)

Swipe the table to see all 64 codons →

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DATA & METHODS

Every table has a provenance.

Updated from ddbj-sc on 2026-11-05. This site contains preliminary Raw CDS v3 analysis alongside historical tables. Neither snapshot is a formal CUTD Release V1.0.0.

Coverage & snapshots
Latest completed codon aggregates
Raw CDS v3 (2026-10-24), source library sfl-20261024-001, DDBJ source snapshot observed 2026-10-24 / RefSeq 237. Precomputed analysis completed 2026-11-03. Updated taxa: 9606, 4932, 83333, 1423 and 2097. Counts were retrieved from ddbj-sc and verified against the existing 64-codon aggregate. Later protein-level analysis provides no replacement codon vector. SARS-CoV-2 retains its historical table because the newer codon aggregate is a hash slice rather than the full set.
v3 CDS set & counting
S2 (All) counts each distinct clean nuclear cds_hash once across DDBJ TRA, TSA, WGS and RefSeq. S3 tables count hashes present in the selected source. TRA means traditional DDBJ records, excluding the independent TSA source; TSA is included in All. Clean records exclude partial CDS, pseudogenes, ambiguous bases, exceptions, slippage, artificial locations and lengths not divisible by 3. “Clean nuclear records” is the corresponding S1 count, before sequence deduplication; it is not an unfiltered raw-record count.
Compartment & genetic code
v3 excludes organelles using replicon_type and, for human and yeast, additional organelle-code exclusions. Codons are interpreted under each target’s stated genetic code; v3 is not split by every per-record transl_table. Historical tables retain their previous code-inferred compartment labels and minor-code tables. The exact filter and interpretation policy are included in JSON exports.
Historical tables
Unique (TaxID, CDS sequence), using the prior exploratory filter. Raw record counts are unavailable. Existing mitochondrial, minority-code and other historical tables retain their data and provenance. Each table displays its own snapshot.
Values & comparison
Frequency = count / total codons × 1,000, including stops. Fraction is the within-amino-acid share; RSCU = fraction × synonymous codons. Overall difference = half the L1 distance across all 64 frequencies. Δ pp uses shares rounded to one decimal place. Comparisons require the same genetic code and source; different snapshots and filters are explicitly labelled.
Heatmap & prototype conventions
Fixed reversed RdBu palette on log₂(RSCU), clipped to ⅓–3. Met, Trp and stops are grey; original values remain in tooltips and exports. Rankings show share; small-sample warnings use <100 CDS; one comparison taxon. Final release rules remain subject to data-side confirmation.
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