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

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.