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Table 1 Terminology and the corresponding definitions used in this manuscript.

From: CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Term Definition
Canonical transcript The splice variant with the lowest isoform number among known transcripts in the current database (e.g. TAIR10). For example, if gene X has two known transcripts X.1 and X.2, as specified in the database, X.1 is defined as the canonical form
Co-spliced transcripts The transcripts containing common RNA-binding motifs that are co-expressed with a specific SF
Differentially spliced Splice variants transcribed from the same gene that are spliced by different SFs.
Peptide ratio The length ratio of a given non-canonical protein isoform to the canonical protein isoform
Protein isoforms The proteins that are synthesized from different splice variants
Ri region (1 ≤ i ≤ 4) R1 (-31:-1 5′ss), R2 (0:30 5′ss), R3 (-30:0 3′ss), and R4 (1:31 3′ss) sequences for each exon in a transcript
Ri ratio The ratio of the number of exons containing a motif in Ri region to the total number of exons
Splice variant (SV) Transcripts that are products of the same precursor mRNA.
Splicing-related proteins (SRPs) Proteins known to be involved in the spliceosome machinery
Splicing factor (SF) SRPs with known RNA-binding domains
Super-cluster Clusters of transcripts with similar expression profiles grouped according to known Arabidopsis seed developmental stages.