SpliceV

SpliceV visualizes and analyzes RNA splicing events from next-generation RNA-seq data to characterize forward- and back-splice junctions, exon-level and single-nucleotide coverage, and linear and circular RNA features.

Key Features:

• Splice junction plotting: Plots forward- and back-splice junctions derived from RNA-seq to represent splice connectivity.
• Coverage visualization: Displays exon-level and single-nucleotide coverage across transcripts to assess expression and splice site usage.
• Circular RNA analysis: Identifies and visualizes back-splice junctions and features of circRNAs formed by downstream splice donors and upstream splice acceptors.
• Regulatory element integration: Displays predicted RNA binding protein sites and repetitive elements along primary transcripts to relate regulatory features to splicing.
• Input data support: Operates on next-generation sequencing (RNA-seq) data and associated splice junction information.

Scientific Applications:

• Alternative splicing analysis: Characterizes isoform diversity and exon usage by visualizing splice junctions and coverage.
• circRNA research: Identifies and inspects circular RNA back-splice junctions to study circRNA biogenesis and occurrence.
• Transcriptome diversity and annotation: Assists in interpreting transcriptome complexity by linking junction and coverage patterns to transcript models.
• Splicing regulation studies: Correlates predicted RNA binding protein sites and repetitive elements with observed splicing patterns to investigate regulatory mechanisms.

Methodology:

Processes next-generation RNA-seq data to plot forward- and back-splice junctions and exon-level/single-nucleotide coverage, and overlays predicted RNA binding protein sites and repetitive elements for integrated analysis.