Downloads

From VastDB

From this page you can download tables with the information in VastDB. Tables are split by species, and tables with different features of the database can be downloaded separately:

Human

AS events
  • EVENTS table (hg19) - Information about AS event coordinates and sequences.
  • EVENTS table (hg38) - Information about AS event coordinates and sequences.
  • PSI table - Inclusion patterns of AS events across tissues, cell types and developmental stages.
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 (VastDB) - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website. (NOTE: ORF impact descriptions for Alternative Splice Sites (ALTA/ALTD events) are still under development and are less reliable; see FAQ for further details).
  • PROTEIN IMPACT table (vast-tools) - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library. (NOTE: ORF impact descriptions for Alternative Splice Sites (ALTA/ALTD events) are still under development and are less reliable; see FAQ for further details).
  • 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.
  • PROTEIN DOMAIN IMAGES - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
  • PDB STRUCTURES table - Mappings to protein structures in the Protein Data Bank
  • 3D MODELS table - Mappings to protein structural models generated with Phyre2.
Genes
  • GENES table - Information about gene names, descriptions, genomic coordinates and biotypes.
  • EXPRESSION table - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
  • GENE-EVENTS table - Table relating genes to AS events.
Evolutionary conservation
  • EVENT CONSERVATION table (hg19-mm9) - Conservation relationships detected with LiftOver from the source assembly (hg19, S) to the target assembly (mm9, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
  • EVENT CONSERVATION table (hg19-galGal3) - Conservation relationships detected with LiftOver from the source assembly (hg19, S) to the target assembly (galGal3, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
  • GENE HOMOLOGY table - Homology relationships between genes.
Samples
  • SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.

Mouse

AS events
  • EVENTS table (mm9) - Information about AS event coordinates and sequences.
  • EVENTS table (mm10) - Information about AS event coordinates and sequences.
  • PSI table - Inclusion patterns of AS events across tissues, cell types and developmental stages.
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 (VastDB) - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website. (NOTE: ORF impact descriptions for Alternative Splice Sites (ALTA/ALTD events) are still under development and are less reliable; see FAQ for further details).
  • PROTEIN IMPACT table (vast-tools) - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library. (NOTE: ORF impact descriptions for Alternative Splice Sites (ALTA/ALTD events) are still under development and are less reliable; see FAQ for further details).
  • 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.
  • PROTEIN DOMAIN IMAGES - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
  • PDB STRUCTURES table - Mappings to protein structures in the Protein Data Bank
  • 3D MODELS table - Mappings to protein structural models generated with Phyre2.
Genes
  • GENES table - Information about gene names, descriptions, genomic coordinates and biotypes.
  • EXPRESSION table - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
  • GENE-EVENTS table - Table relating genes to AS events.
Evolutionary conservation
  • EVENT CONSERVATION table (mm9- hg19) - Conservation relationships detected with LiftOver from the source assembly (mm9, S) to the target assembly (hg19, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
  • EVENT CONSERVATION table (mm9- galGal3) - Conservation relationships detected with LiftOver from the source assembly (mm9, S) to the target assembly (galGal3, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
  • GENE HOMOLOGY table - Homology relationships between genes.
Samples
  • SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.

Chicken

AS events
  • EVENTS table (galGal3) - Information about AS event coordinates and sequences.
  • PSI table - Inclusion patterns of AS events across tissues, cell types and developmental stages.
Event features
Protein impact
  • PROTEIN IMPACT table (VastDB) - Effect of the AS event in the open reading frame of the transcript. This table only contains protein impact information for events included in the VastDB website. (NOTE: ORF impact descriptions for Alternative Splice Sites (ALTA/ALTD events) are still under development and are less reliable; see FAQ for further details).
  • PROTEIN IMPACT table (vast-tools) - Effect of the AS event in the open reading frame of the transcript. This table contains protein impact information for all events in the vast-tools library. (NOTE: ORF impact descriptions for Alternative Splice Sites (ALTA/ALTD events) are still under development and are less reliable; see FAQ for further details).
  • 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.
  • PROTEIN DOMAIN IMAGES - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
  • PDB STRUCTURES table - Mappings to protein structures in the Protein Data Bank
  • 3D MODELS table - Mappings to protein structural models generated with Phyre2.
Genes
  • GENES table - Information about gene names, descriptions, genomic coordinates and biotypes.
  • EXPRESSION table - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
  • GENE-EVENTS table - Table relating genes to AS events.
Evolutionary conservation
  • EVENT CONSERVATION table (galGal3-hg19) - Conservation relationships detected with LiftOver from the source assembly (galGal3, S) to the target assembly (hg19, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
  • EVENT CONSERVATION table (galGal3-mm9) - Conservation relationships detected with LiftOver from the source assembly (galGal3, S) to the target assembly (mm9, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
  • GENE HOMOLOGY table - Homology relationships between genes.
Samples
  • SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.