Difference between revisions of "Downloads"

Revision as of 10:13, 5 November 2020

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

• EVENTS table - Information about AS event coordinates and sequences. TAIR10 asssembly.
• 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 SITES table - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
• PCR VALIDATION table - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.

Protein impact

• PROTEIN IMPACT table - Effect of the AS event in the open reading frame of the transcript. Version v3.
• PROTEIN ISOFORMS - Mappings of events to ProteinIDs.
• DOMAINS table (PFAM) - Mappings to Pfam domains
• DOMAINS table (PROSITE) - Mappings to PROSITE domains.
• PROTEIN DISORDERED REGIONS table - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3.

Genes

• GENES table - 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).
• GENE-EVENTS table - Table relating genes to AS events.

Samples

• SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.