| Files for download | Description |
|---|---|
| predicted branch sites | Tab separated fields: transcript name, intron #, sequence |
| predicted PPTs and CU tracts | Tab separated fields: transcript name, intron #, sequence |
| predicted UA tracts | Tab separated fields: transcript name, intron #, sequence |
| predicted intronic cis-regulatory elements | Tab separated fields: transcript name, intron #, splice site type (5' or 3'), sequences |
| predicted exonic cis-regulatory elements (intron retention) | Tab separated fields: transcript name, exon #, splice site type (5' or 3'), sequences |
| exonic cis-regulatory elements by Pertea et al. | Tab separated fields: transcript name, exon #, splice site type (5' or 3'), sequences |
| predicted U12 introns | Tab separated fields are as follows: gene name, transcript name, intron #, species, branch site, upstream exonic sequence, intron sequence, downstream exonic sequence |
| orthologs of genes with predicted U12 introns that also contain U12 introns | Tab separated fields: gene name, orthologous genes names (separated with whitespace) |
|
SRP011480_unpollinated_ear_tip.bed.gz SRP011480_seedling_shoot.bed.gz SRP011480_seedling_root.bed.gz SRP011480_immature_tassel.bed.gz SRP002417_whole_plant.bed.gz SRP002417_aerial_tissue.bed.gz DRS000668_tissue_pool.bed.gz | TopHat2 result files for seven libraries used in the study |
| orthologous gene pairs from Ensembl used in the study | Tab separated fields: gene1, gene2 |
|
MotifSearch.jar README.txt | Java tool used used in the study to search for cis-regulatory exonic and intronic elements in plant splice sites. |