Intron–mRNA Matching Patterns in Differentially Expressed Genes in Cervical Cancer

Cervical cancer (CC) is characterized by widespread transcriptomic dysregulation, yet sequence matching patterns between mRNAs and their corresponding introns remain insufficiently characterized in differentially expressed genes (DEGs). This study aimed to describe computationally predicted intron–mRNA matching features in the reference sequences of CC DEGs. DEGs were identified using Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, and the corresponding mRNA and intron sequences were retrieved from the Ensembl human reference genome. Reverse complementation combined with Smith–Waterman local alignment was used to analyze the positional distributions of predicted matching fragments across full-length mRNAs and within translation initiation and termination regions. Descriptive analyses were further stratified by the GC content of the matching fragments. On normalized full-length mRNA coordinates, high-GC fragments exhibited higher matching frequencies in certain segments near the 5′ end, whereas matching frequencies of low-GC fragments increased toward the 3′ end. Within the translation initiation region, predicted matching frequencies were generally higher upstream than downstream of the AUG codon, and the low-GC group exhibited a local peak near the initiation codon. Within the translation termination region, the low-GC group exhibited a pronounced peak downstream of the stop codon, whereas the high-GC group showed no similarly pronounced downstream peak and displayed greater positional fluctuations in matching frequency. Overall, the predicted matching distributions differed across the analyzed regions and GC groups. This study provides a sequence-level description of intron–mRNA matching patterns within this reference sequence collection of CC DEGs; their biological significance requires further validation.