Structural and compositional features of untranslated regions of eukaryotic mRNAs
Abstract
The important role of 5' and 3' untranslated regions of eukaryotic mRNAs in gene regulation and expression is now widely accepted. In order to study the general structural and compositional features of these sequences we developed UTRdb, a specialized database of 5' and 3'-UTR sequences from seven different taxonomic groups of eukaryotic mRNAs cleaned of redundancy. The analysis of the UTR sequences contained in this database showed that 5'-UTR sequences, on average 200 nucleotides long, are 1.5-3 times shorter than the corresponding 3'-UTR sequences in the various taxonomic groups considered here. As to their compositional properties on average 5'-UTR sequences resulted in all cases GC richer than 3'-UTR sequences, and significant correlations were found between the GC content of 5' and 3'-UTR sequences and the GC content of the third silent codon positions of the corresponding protein coding genes. The dinucleotide analysis showed a differential depletion of CpG in vertebrate 5' and 3'-UTR, with 5'-UTR sequences being more CpG-rich, and a generalized depletion of TpA in both 5' and 3'-UTR was observed in all eukaryotic sequence collections.
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The mRNA 5 ́ region is known to have a composition bias.
“Finally, mRNA 5´ region is known to have a composition bias [53] and a better delimitation of this sequence may be necessary [54].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [53]
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- Authors
- Pesole, G., Liuni, S., Grillo, G., & Saccone, C.
- Affiliations
- University of Basilicata (IT)
- University of Bari Aldo Moro (IT)
- Corresponding author
- Pesole, Graziano
- Venue
- Gene
- Publisher
- Elsevier BV
- Published
- 1997-12
- Volume
- 205
- Issue
- 1-2
- Pages
- 95-102
- ISSN
- 0378-1119 (ISSN-L)
- OpenAlex
- W1977396924
- Cited by
- 108
- References
- 20
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 1 · 2021: 3 · 2019: 3 · 2018: 1 · 2017: 3 · 2015: 5 · 2014: 2 · 2013: 4 · 2012: 6
- FWCI
- 1.77
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Gene (publishedVersion)
- PubMed (publishedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- 5' untranslated region, 3' untranslated region, eukaryotic mRNA, sequence databases, GC content, CpG depletion, dinucleotide composition, third codon position, gene expression regulation, taxonomic comparison
- MeSH terms
- Base Composition, Introns, RNA, Messenger, Protein Biosynthesis
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