The goal of this function is to help understand how changes in splicing profile affect the protein function in the cell. Two lists of genomic regions are expected: one list of regions of interest, and another serves as the control. A typical input can be a list of alternatively spliced exons or junctions identified by an RNA-seq experiments as the "target", and a list of expressed but not alternatively spliced exons or junctions in the same experiment as the "background", although generally any regions meaningful for the user can be used. The tool compares the frequency of predicted protein features overlapping with regions in each list and performs an enrichment analysis.

Please consult the help page for more information.

Target File

Expect human GRCh38 or mouse GRCm39 genomic regions in Bed6 format with Ensembl gene ID in the 4th column. Score column and additional columns are ignored.

An example target file can be downloaded here: human or mouse.

Background File

Expect human GRCh38 or mouse GRCm39 genomic regions in Bed6 format with Ensembl gene ID in the 4th column. Score column and additional columns are ignored.

An example background file can be downloaded here: human or mouse.

Please select the species : :

• Human GRCh38 (hg38)
• Mouse CRCm39 (mm39)

Please select one (recommended) or more prediction tool(s) from the following list. To start exploring, choose only Pfam. :

• Pfam: protein families and domains
• SFLD: protein families
• PANTHER: gene classification by functions
• Hamap: High-quality Automated and Manual Annotation of Microbial Proteomes
• ProSiteProfiles: protein domains, families, functional sites and associated patterns and profiles
• ProSitePatterns: protein domains, families, functional sites and associated patterns and profiles
• SMART: domain architectures
• CDD: protein domains and families
• PRINTS: protein fingerprints (groups of conserved motifs used to characterise protein families)
• TIGRFAM: protein families
• PIRSF: protein families and domains
• SUPERFAMILY: structural and functional annotations
• Gene3D: protein families and domain architectures
• Coils: coiled coil regions
• MobiDBLite: intrinsically disordered regions

Please note that each tool is designed to predict a different set of features of the protein sequence. A detailed description of the tools can be found at InterPro website. Choosing multiple tools may produce redundancy in the result if they are designed to predict similar features.