ExTraMapper

ExTraMapper maps exon- and transcript-level orthologs between pairs of orthologous genes to enable fine-scale comparative analysis of exon conservation and transcript correspondence.

Key Features:

• Exon-Level Mapping: Identifies over 350,000 exon mappings between human and mouse genomes using sequence conservation together with gene annotation and sequence data.
• Transcript-Level Mapping: Identifies more than 30,000 transcript mappings between human and mouse, enabling transcript-scale orthology assessment.
• Detection of Splice Variants: Detects exon fusions, splits, and losses resulting from splice site mutations and maps microexons that were previously overlooked.
• Expression Correlation: Reanalysis of RNA-seq data from 13 matched human and mouse tissues yields improved correlation of transcript-specific expression levels between species.
• Cross-Species Applicability: Detects conserved exon and transcript pairs between other organism pairs such as human and rhesus macaque.

Scientific Applications:

• Alternative Splicing Analysis: Enables investigation of exon fusions, splits, microexons, and the impacts of splice site mutations on exon conservation.
• Gene Expression Conservation: Supports cross-species comparison of transcript-specific expression using RNA-seq data.
• Evolutionary Dynamics: Facilitates study of exon and transcript conservation and divergence across species pairs including human, mouse, and rhesus macaque.
• Comparative Genomics and Functional Annotation: Aids functional annotation of conserved and non-coding regions and the exploration of conserved genetic mechanisms.

Methodology:

Leverages sequence conservation between exons and uses gene annotation information alongside sequence data to establish exon- and transcript-level orthology, and reanalyzes RNA-seq from 13 matched human and mouse tissues to assess transcript-specific expression correlation.