Table S7. List of hormone-related and splicing factor genes, which have different isoforms after GA was applied. (XLSX 31 kb)

Table S8. List of cis-NATs in moso bamboo, which were classified into head-to-head (5′-5′), tail-to-tail (3′-3′) and fully overlapping. (XLSX 156 kb)

Spliced regions identified by RSR for the Tg sample. This file contains all supplementary results for five test cases for the Tg sample. (XLSX 105 kb)

Table S4. Datasets used in paper including description and relevant figures information plus PubMed ID and SRA ID. (XLSX 54 kb)

Table S7. List of the 158 distinct genes/proteins between E7 and NH under salt stress conditions, as well as PPI information. (XLSX 27938 kb)

Table S1. Genomic and splicing features used in logistic linear regression model. (XLSX 40 kb)

Background The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene...

Background Alternative splicing (AS) is a major source of variability in the transcriptome of eukaryotes. There is an increasing interest in its role in different pathologies....

AbstractRNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show...

Background Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript...

Background Most existing tools for detecting next-generation sequencing-based splicing events focus on generic splicing events. Consequently, special types of non-canonical...

Background In-depth study of the intron retention levels of transcripts provide insights on the mechanisms regulating pre-mRNA splicing efficiency. Additionally, detailed...

Background Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a...

Background Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune...

Excel file with characteristics of the validated events and PCR primers. (XLSX 27 kb)

Table S4. Expression level of all isoforms. (XLSX 16864 kb)

Additional file 1: Table S1. Encoding and expression profiles of transcripts. Table S2. Expression profiles of phosphatase subunit genes. Table S3. Encoding and expression...

Tab delimited text file that includes the differentially retained introns, when comparing the ZRSR2mut samples to the controls using the IntEREst-DESeq2. (TSV 634 kb)

Spliced regions identified by RSR for the Dtt sample. This file contains all supplementary results for five test cases for the Dtt sample. (XLSX 2828 kb)