IsoPrimer

IsoPrimer designs PCR primer pairs targeting the specific set of expressed splicing variants of genes of interest for quantitative PCR and RNA-seq validation experiments.

Key Features:

• Isoform Identification: Identifies the most expressed gene isoforms based on expression levels of splicing variants derived from an RNA-seq dataset.
• Junction-Spanning Primer Design: Designs primer pairs overlapping exon-exon junctions common to the expressed variants.
• Specificity Verification: Verifies the specificity of the designed primer pairs.

Scientific Applications:

• Gene Expression Quantification: Enables accurate quantification of gene expression in specific conditions by targeting all expressed alternative transcripts.
• RNA-seq Validation: Supports validation experiments for RNA-seq data through targeted quantitative PCR.
• Alternative Splicing Analysis: Facilitates functional assessment of eukaryotic genes that generate multiple transcripts through alternative splicing.

Methodology:

IsoPrimer processes expression levels of splicing variants from an RNA-seq dataset to identify highly expressed isoforms, then designs primer pairs overlapping shared exon-exon junctions and verifies their specificity.