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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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Human messenger RNA harbors widespread noncoding splice isoforms.

Qili Shi1, Haochen Li1, Junjiao Song1

  • 1Fudan University Shanghai Cancer Center and Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, 270 Dong An Road, Xuhui District, Shanghai 200032, China.

Briefings in Bioinformatics
|February 16, 2026
PubMed
Summary
This summary is machine-generated.

Human mRNA contains numerous noncoding splice isoforms, generated by alternative splicing and polyadenylation. These regulatory isoforms are prevalent in cancer and can predict patient survival, revealing mRNA

Keywords:
mRNAmRNA translation–noncoding dualitynoncoding splice isoformprotein-coding isoform

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Premessenger RNA from protein-coding genes commonly undergoes alternative splicing, producing diverse protein isoforms.
  • The existence of noncoding splice isoforms within human mRNA derived from protein-coding genes was previously unexplored.

Purpose of the Study:

  • To investigate the prevalence and characteristics of noncoding splice isoforms in human mRNA.
  • To explore the role of these noncoding isoforms in tissue specificity, RNA processing, and cancer.

Main Methods:

  • Bioinformatic analysis of human transcriptomic data.
  • Identification and characterization of mRNA noncoding isoforms.
  • Analysis of tissue distribution, association with RNA processing pathways, and cancer relevance.

Main Results:

  • Discovery of 15,836 mRNA noncoding isoforms across 7,298 human protein-coding genes.
  • These isoforms are primarily produced via alternative splicing and polyadenylation, exhibiting tissue-specific expression.
  • Upregulation of mRNA noncoding isoforms in cancer, association with cancer hallmarks, and predictive value for patient survival.

Conclusions:

  • Human mRNA harbors widespread noncoding splice isoforms, in addition to protein-coding ones.
  • These noncoding isoforms play regulatory roles and are implicated in cancer progression.
  • Highlights the functional duality of mRNA, accommodating both protein translation and regulatory noncoding functions.