ScanExitronLR

ScanExitronLR identifies and annotates exitron splicing events from long-read RNA-seq data to characterize their transcript-level occurrence and potential impacts on protein function.

Key Features:

• Long-Read RNA-seq Compatibility: Processes long-read RNA-seq data to capture full-length transcript isoforms and complex splicing events.
• Comprehensive Exitron Detection: Processes BAM alignment files with a reference genome and gene annotation to identify exitron events at the individual transcript level.
• Detailed Annotation Outputs: Annotates exitrons for truncation or frameshift types, nonsense-mediated decay (NMD) status, and interruptions of Pfam domains.
• Robust Performance: Demonstrated effective detection in noisy long-read data compared with methods developed for short-read datasets.
• Facilitation of Downstream Analyses: Produces outputs suitable for downstream analyses such as differential exitron splicing studies.

Scientific Applications:

• Cancer research: Enables identification and characterization of exitron events that may contribute to tumorigenesis and cancer progression.
• Alternative splicing and proteome plasticity studies: Supports investigations of coding-sequence excision events that alter protein structure and function.

Methodology:

Processes BAM alignment files together with a reference genome and gene annotation to map long-read RNA-seq transcripts, identify exitron splicing events at the transcript level, and annotate consequences (truncation/frameshift, NMD status, Pfam domain interruptions), with methods tolerant to noisy long-read data.