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

Introduction A gene is a multi-layered biological unit. It may be described through genomic coordinates, transcripts, exon–intron structure, coding sequence, codons, protein products, variants, regulatory regions, and functional annotations. In modern genomic datasets, genes are commonly represented through gene IDs, gene symbols, chromosomes, strands, start and end positions, transcript IDs, protein IDs, exon counts, intron counts, CDS regions, UTRs, variants, and functional annotation fields. The Prime Elementology Gene–Genome Atlas introduces an additional reading layer: the Prime-Z layer. This layer does not begin with the biological function of a gene. Instead, it begins with the material substrate of DNA sequence. Each DNA base has a Prime-Z signature derived from the chemical formula of its nucleobase. When bases form codons, motifs, genes, or genome regions, the base-level Prime-Z vectors are aggregated to form higher-level Prime-Z signatures. Therefore, a gene in this atlas is not only an A/T/G/C sequence or a coordinate interval on a chromosome. It is also an entity with: Prime-Z gene signaturecodon Prime-Z profilemutation-shadow profileboundary-region profilePrime-TB Cutsite candidate D05 is designed as a continuation of D04: D04 reads the chemistry of DNA units.D05 reads the Prime-Z structure of genes and genome regions. Within the atlas system, D04 functions as the Prime-Z alphabet of DNA, while D05 functions as a map of biological words, regions, and structured genomic text.