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Computational prediction of SEG (single exon gene) function in humans
Meena K Sakharkar1, Vincent T K Chow, Kingshuk Ghosh
1School of Mechanical and Production Engineering, Nanyang Center for Supercomputing and Visualization, Nanyang Technological University, Singapore 639798.
Frontiers in Bioscience : a Journal and Virtual Library
|March 17, 2005
Summary
Single exon genes (SEGs) constitute 12% of the human genome. Genome-wide analysis reveals SEGs function in DNA binding, phosphorylation, and acetylation, with potential roles in cellular processes.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Human genes typically contain introns, dividing them into exons and introns, resulting in multi-exon genes (MEGs).
- A significant portion of the human genome, approximately 12%, comprises single exon genes (SEGs), whose functions remain underexplored.
Purpose of the Study:
- To perform a comprehensive, genome-wide functional assignment for 3750 human single exon gene sequences.
- To elucidate the molecular functions and cellular roles of SEGs using multiple bioinformatics databases.
Main Methods:
- Utilized PFAM for protein family assignment, identifying 13% of SEGs in the G-protein coupled receptor (GPCR) family and prevalent DNA binding functions.
- Employed PROSITE to detect 336 unique motifs, revealing widespread phosphorylation and acetylation signals, accounting for 25% of known patterns.
- Applied SUPERFAMILY to assign 33% of SEGs to the membrane alpha-helical protein structural class.
Main Results:
- Functional annotation across sequence signals, families, and 3D structures suggests SEGs predominantly act as DNA binders, phosphorylating, and acetylating agents.
- Analysis indicated SEG expression and retro-transposition events, hinting at dynamic genomic roles.
- The study identified SEGs with DNA binding, phosphorylation, and acetylation functions, suggesting roles as house-keeping agents.
Conclusions:
- Functional assignment of SEGs using PFAM, PROSITE, and SUPERFAMILY highlights their specific and predominant molecular functions.
- The intriguing functions of SEGs as DNA binding, phosphorylating, and acetylating agents warrant further investigation.
- A deeper understanding of SEG function is crucial for fully exploring their role in cellular biology and the broader cellular environment.