Transgene-design

Transgene-design designs mammalian transgenes by optimizing exonic synonymous-site GC content and modulating exonic splice enhancer (ESE) density to improve expression of human intronless transgenes and native retrogenes.

Key Features:

• GC optimization: Optimizes GC content at exonic synonymous sites to increase expression efficiency of human intronless transgenes and native retrogenes.
• ESE manipulation: Identifies and adjusts exonic splice enhancers (ESEs), allowing modulation of ESE density for intronless versus intron-containing contexts.
• Input flexibility: Accepts native gene sequences or commercially optimized sequences as input for redesign.
• First intron retention: Provides an option to retain the first intron within the gene sequence.
• Motif protection and avoidance: Allows protection or avoidance of specified sequence motifs that may influence gene expression or stability.

Scientific Applications:

• Gene expression regulation: Designs transgenes for experiments investigating determinants of mammalian gene expression.
• Functional genomics: Enables construction of transgenes for functional genomics assays in mammalian systems.
• Genetic engineering: Supports generation of optimized constructs for genetic engineering in mammalian cells.
• Therapeutic development: Facilitates design of transgenes relevant to development of novel therapeutic strategies.

Methodology:

Optimizes exonic synonymous-site GC content, identifies and adjusts exonic splice enhancers (ESEs), offers first intron retention, protects or avoids specified motifs, and accepts native or commercially optimized input sequences.