Prime Elementology Gene Genome Atlas: A Prime-Z Atlas of Genes, Codon–Protein Bridges, Mutation Shadows, and Genome Boundaries

# D05 Prime Elementology Gene-Genome Atlas v2.0 **Dataset title:** Prime Elementology Gene-Genome Atlas **Module:** D05 **Version:** 2.0 **Author:** Phan Thành Trung **ORCID:** 0009-0000-7520-6781 **DOI basis:** 10.5281/zenodo.21201470 **Release date:** 2026-07-09 ## 1. Purpose D05 v2.0 is a layered gene-code atlas for Prime Elementology. It treats a gene not as a single flat DNA string, but as a **layered code-locking structure** in which alphabet, codon, reading frame, region, transcript, protein bridge, regulatory motif, variant shadow, and Prime-TB boundary all participate in biological meaning. The central interpretive statement is: > A gene is not merely a sequence of nucleotides. It is a layered code-locking structure in which alphabet, codon, frame, region, transcript, protein bridge, regulatory motif, variant shadow, and boundary all participate in the production of biological meaning. Prime-TB Cut does not cut the gene once; it cuts the gene across its code layers. ## 2. v2.0 Main Change Version 1 used the prime basis `{2,3,5,7}`, but several rows collapsed most information into the `v2` axis. Version 2.0 corrects this by assigning one prime to each DNA base: | Base | Prime | |---|---:| | A | 2 | | T | 3 | | G | 5 | | C | 7 | The corrected prime-base vector is: `V_base(G) = (#A, #T, #G, #C)` The corrected prime-base signature is: `Π_base(G) = 2^#A · 3^#T · 5^#G · 7^#C` Example: `ATGGCCGCTGAA` has `V_base = (3,2,4,3)` and `Π_base = 2^3 · 3^2 · 5^4 · 7^3`. ## 3. Dataset Scope This release is a **synthetic seed / schema atlas**, not a complete empirical genome database. It is designed to demonstrate the D05 schema and Prime-TB cutting logic before expansion to real gene catalogs. | Metric | Count | |---|---:| | Total rows | 205 | | Total columns | 140 | | Active seed records | 48 | | Schema field rows | 140 | | Schema record-type rows | 16 | | Seed genes | 3 | ## 4. Active Record Types | Record type | Count | Meaning | |---|---:|---| | `boundary_region` | 3 | Prime-TB boundary displacement row. | | `cds` | 3 | Coding sequence row with codon and protein bridge descriptors. | | `codon_profile` | 11 | Individual codon row with amino-acid bridge. | | `exon` | 6 | Retained sequence-region row. | | `gene` | 3 | Gene-level prime-base passport row. | | `intron` | 3 | Spliced/removed region row. | | `motif_region` | 3 | Regulatory motif row. | | `mutation_shadow` | 3 | Reference-to-variant shadow row. | | `prime_tb_cutsite` | 3 | Prime-TB representational cutsite row. | | `protein_bridge` | 3 | DNA-to-protein bridge row. | | `regulatory_region` | 1 | Standalone regulatory seed row. | | `transcript` | 3 | Transcript-level sequence and frame row. | | `variant` | 3 | Symbolic variant row. | ## 5. Gene-Level Seed Examples | Gene | Sequence | Prime-base vector | Prime-base signature | Frame-0 codons | Frame-0 AA | |---|---|---|---|---|---| | PEGA1 | `ATGGCCGCTGAA` | `(3,2,4,3)` | `2^3 · 3^2 · 5^4 · 7^3` | `ATG|GCC|GCT|GAA` | `MAAE` | | PEGB1 | `ATGCGCGCCTAA` | `(3,2,3,4)` | `2^3 · 3^2 · 5^3 · 7^4` | `ATG|CGC|GCC|TAA` | `MRA*` | | PEGG1 | `ATGATATATGA` | `(5,4,2,0)` | `2^5 · 3^4 · 5^2` | `ATG|ATA|TAT` | `MIY` | ## 6. Mutation Shadow Logic Mutation shadows are corrected as vector displacements in the order `(A,T,G,C)`. | Mutation | Prime ratio | Vector shadow | |---|---|---| | G → A | 2/5 | (+1,+0,-1,+0) | | C → T | 3/7 | (+0,+1,+0,-1) | | A → G | 5/2 | (-1,+0,+1,+0) | This avoids collapsing a mutation into a single abstract scalar axis. Instead, each mutation is represented as a movement between prime-coded base axes. ## 7. Prime-TB Boundary Logic Boundary rows with a split motif such as: `ATGGCC|GCTGAA` are recalculated as a right-minus-left ATGC displacement: `Δ_boundary = V_right - V_left` The `tb_score` is the L1 magnitude of that displacement: `tb_score = |ΔA| + |ΔT| + |ΔG| + |ΔC|` This makes the Prime-TB cutsite a boundary descriptor rather than merely a visual split. ## 8. Interpretation Policy D05 v2.0 is a **descriptor/proxy layer**. It should not be interpreted as claiming that prime numbers are direct biological causes of genes, proteins, mutations, or regulation. The intended use is: - structural description, - schema design, - explainable feature construction, - Prime-TB boundary analysis, - gene-to-protein bridge representation, - variant-shadow modeling, - and future benchmark expansion. ## 9. Recommended Citation Wording > D05 Prime Elementology Gene-Genome Atlas v2.0 defines a layered gene-code schema in which DNA bases are mapped to prime-base axes A→2, T→3, G→5, C→7. The atlas represents gene sequences through prime-base vectors, codon frames, protein bridges, regulatory motifs, variant shadows, and Prime-TB boundary cuts as a descriptive XAI/proxy layer rather than a direct causal biological model. ## 10. Files - `D05_Prime_Elementology_Gene_Genome_Atlas_v2_0.csv` — full CSV dataset. - `D05_Prime_Elementology_Gene_Genome_Atlas_v2_0.xlsx` — workbook version with README, summary, data, and column dictionary sheets. - `D05_Prime_Elementology_Gene_Genome_Atlas_v2_0_README.md` — this README. ## 11. Version Note D05 v2.0 supersedes the earlier seed CSV where `v2`, `v3`, `v5`, and `v7` did not fully encode the intended DNA-base prime axes. Legacy values are preserved in: - `legacy_v2` - `legacy_v3` - `legacy_v5` - `legacy_v7` - `legacy_prime_signature` The corrected fields are: - `v2 = #A` - `v3 = #T` - `v5 = #G` - `v7 = #C` - `prime_signature = 2^#A · 3^#T · 5^#G · 7^#C`