Downloads

From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately:

Arabidopsis thaliana

AS events

• EVENT INFORMATION - Information about AS event coordinates and sequences. TAIR10 asssembly.
• EVENT METRICS - Summary statistics for the usage of each AS event.
• MAIN PSI TABLE - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
• ABIOTIC PSI TABLE - Inclusion patterns of AS events in ABIOTIC stress experiments (special dataset).
• BIOTIC PSI TABLE - Inclusion patterns of AS events in BIOTIC stress experiments (special dataset).
• LIGHT PSI TABLE - Inclusion patterns of AS events in LIGHT experiments (special dataset).
• SPL_FACTORS PSI TABLE - Inclusion patterns of AS events upon SPLICING FACTOR disruption (special dataset).

Event features

• SPLICE SITE INFORMATION - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
• PRIMER SUGGESTIONS - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.

Protein impact

• PROTEIN IMPACT - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
• PROTEIN IMPACT (Legacy) - Predicted effect of the AS event on the open reading frame of the transcript. Version v3, to use with the option --legacy in vast-tools compare.
• PROTEIN ISOFORMS - Mappings of events to Protein IDs.
• DOMAIN OVERLAP (PFAM) - Overlap of AS events with Pfam domains.
• DOMAIN OVERLAP (PROSITE) - Overlap of AS events with PROSITE domains.
• PROTEIN DISORDERED REGIONS - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3.

Genes

• GENE INFORMATION - Information about gene names, descriptions, genomic coordinates and biotypes.
• MAIN EXPRESSION TABLE - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
• ABIOTIC EXPRESSION TABLE - Gene expression in ABIOTIC stress experiments (special dataset).
• BIOTIC EXPRESSION TABLE - Gene expression in BIOTIC stress experiments (special dataset).
• LIGHT EXPRESSION TABLE - Gene expression in LIGHT experiments (special dataset).
• SPL_FACTORS EXPRESSION TABLE - Gene expression upon SPLICING FACTOR disruption (special dataset).
• EVENT_ID-to-GENE_ID - Table relating genes to AS events.

Samples

• SAMPLE INFORMATION - SRA identifiers and other information related to RNA-seq data used in this database.
• SAMPLE CONFIG PLOT - Config file with sample information used for the plot in the main panel.