Hierarchical territorial organization of IL1B intron 3 reveals compartmentalized intronic regulatory architectures

This repository contains the computational datasets generated and analyzed in support of the manuscript: “Hierarchical territorial organization of IL1B intron 3 reveals compartmentalized intronic regulatory architectures.” The repository includes: • Computationally reconstructed IL1B intron 3 FASTA sequence and selected territorial microdomains (Z4C2, Z2C4, and Z2C6)• TFBS analyses generated using FIMO and JASPAR• RNA-binding protein interaction analyses• RNAfold and RNAstructure outputs• trRosettaRNA structural predictions• Computational three-dimensional RNA models (*.pdb)• Supplementary tables• Python scripts and associated computational materials• Manuscript and associated figures Sequence provenance: The deposited FASTA files do not represent newly generated or experimentally determined DNA or RNA sequences. They were computationally derived from the publicly available human GRCh38/hg38 reference genome. The IL1B locus corresponds to NCBI Gene ID 3553; the genomic reference corresponds to GRCh38.p14 (assembly accession GCF_000001405.40), chromosome 2 RefSeq accession NC_000002.12. The microdomain FASTA files represent computationally extracted subsequences of the reconstructed IL1B intron 3 sequence. Structural model provenance: The deposited PDB files are computational RNA structure predictions generated using trRosettaRNA and do not represent experimentally determined macromolecular structures. No X-ray crystallography, NMR, cryo-electron microscopy, or other experimental structural determination was performed. These materials are provided to document the exact computational inputs and outputs used in the study and to support full reproducibility and downstream computational analysis.