Difference between revisions of "Downloads"

Revision as of 16:30, 16 December 2020

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:

PROTEIN IMPACT - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
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 disopred.

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).
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.

Homo sapiens (hg19)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Mus musculus (mm10)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Mus musculus (mm9)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Bos taurus (bosTau6)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Gallus gallus (galGal4)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Gallus gallus (galGal3)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Danio rerio (danRer10)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

Drosophila melanogaster (dm6)

AS events

EVENT INFORMATION - Information about AS event coordinates and sequences.
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).

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 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 disopred.

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).
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.

@@ Line 1: / Line 1: @@
 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====
+====General files====
+* [{{SERVER}}/downloads/general/EVENT_CONSERVATION.tab.gz EVENT CONSERVATION table]  - Information about the evolutionary conservation for all AS events for all pairwise species comparisons.
+* [{{SERVER}}/downloads/general/GENE_ORTHOLOGY.tab.gz GENE ORTHOLOGY table]  - Information about the orthology relationshipts for all pairwise species comparisons.
+====<i>Homo sapiens (hg38)</i>====
 =====AS events=====
-* [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg19.tab.gz EVENTS table (hg19, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
+* [{{SERVER}}/downloads/hg38/EVENT_INFO-hg38.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
-* [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg19_ALL.tab.gz EVENTS table (hg19, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
+* [{{SERVER}}/downloads/hg38/EVENT_METRICS-hg38.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
-* [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg38.tab.gz EVENTS table (hg38, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website for which genomic coordinates could be determined by LiftOver from hg19.
+* [{{SERVER}}/downloads/hg38/PSI_TABLE-hg38.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
-* [{{SERVER}}/downloads/Human/VASTDB_EVENTS_Hsa108_hg38_ALL.tab.gz EVENTS table (hg38, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1) for which genomic coordinates could be determined by LiftOver from hg19.
-* [{{SERVER}}/downloads/Human/VASTDB_PSI_Hsa108_hg19.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
 =====Event features=====
-* [{{SERVER}}/downloads/Human/VASTDB_SPLICE_SITE_SCORES_Hsa108_hg19.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/hg38/SPLICE_SITE_SCORES-hg38.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
-* [{{SERVER}}/downloads/Human/VASTDB_PCR_VALIDATIONS_Hsa108_hg19.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+* [{{SERVER}}/downloads/hg38/PCR_PRIMERS-hg38.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
 =====Protein impact=====
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_IMPACT_Hsa108_hg19-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/hg38/PROT_IMPACT-hg38-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_IMPACT_Hsa108_hg19_ALL-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/hg38/PROT_ISOFORMS-hg38.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_PFAM_Hsa108_hg19.tab.gz DOMAINS table (PFAM)] - Mappings to Pfam domains
+* [{{SERVER}}/downloads/hg38/PROT_PFAM-hg38.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_PROSITE_Hsa108_hg19.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
+* [{{SERVER}}/downloads/hg38/PROT_PROSITE-hg38.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_DISORDER_Hsa108_hg19.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
+* [{{SERVER}}/downloads/hg38/PROT_DISORDER-hg38.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_DOMAIN_PNG_URLs_Hsa108_hg19.tab.gz PROTEIN DOMAIN IMAGES] - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_STRUCT_PDB_Hsa108_hg19.tab.gz PDB STRUCTURES table] - Mappings to protein structures in the Protein Data Bank
-* [{{SERVER}}/downloads/Human/VASTDB_PROT_STRUCT_PHYRE_Hsa108_hg19.tab.gz 3D MODELS table] - Mappings to protein structural models generated with Phyre2.
 =====Genes=====
-* [{{SERVER}}/downloads/Human/VASTDB_GENES_Hsa108_hg19.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/hg38/GENE_INFO-hg38.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
-* [{{SERVER}}/downloads/Human/VASTDB_EXPRESSION_Hsa108_hg19.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
+* [{{SERVER}}/downloads/hg38/EXPRESSION_TABLE-hg38.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
-* [{{SERVER}}/downloads/Human/VASTDB_EVENTID_to_GENEID_Hsa108_hg19.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
+* [{{SERVER}}/downloads/hg38/EVENTID_to_GENEID-hg38.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
-=====Evolutionary conservation=====
-* [{{SERVER}}/downloads/Human/VASTDB_CONSERVATION_Hsa108_hg19_to_Mmu139_mm9.tab.gz 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.
-* [{{SERVER}}/downloads/Human/VASTDB_CONSERVATION_Hsa108_hg19_to_Gga61_galGal3.tab.gz 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.
-*  [{{SERVER}}/downloads/Human/VASTDB_CONSERVATION_Hsa108_hg19_to_Dre63_danRer10.tab.gz EVENT CONSERVATION table (hg19-danRer10]) - Conservation relationships detected with LiftOver from the source assembly (hg19, S) to the target assembly (danRer10, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
-* [{{SERVER}}/downloads/Human/VASTDB_GENE_HOMOLOGY_Hsa108_hg19.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
 =====Samples=====
-* [{{SERVER}}/downloads/Human/VASTDB_SAMPLE_INFO_Hsa108_hg19.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
+* [{{SERVER}}/downloads/hg38/SAMPLE_INFO-hg38.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
-====Mouse====
+====<i>Homo sapiens (hg19)</i>====
 =====AS events=====
-* [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm9.tab.gz EVENTS table (mm9, VastDB)]  - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
+* [{{SERVER}}/downloads/hg19/EVENT_INFO-hg19.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
-* [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm9_ALL.tab.gz EVENTS table (mm9, vast-tools)]  - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
+* [{{SERVER}}/downloads/hg19/EVENT_METRICS-hg19.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
-* [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm10.tab.gz EVENTS table (mm10, VastDB)] - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website for which genomic coordinates could be determined by LiftOver from mm9.
+* [{{SERVER}}/downloads/hg19/PSI_TABLE-hg19.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
-* [{{SERVER}}/downloads/Mouse/VASTDB_EVENTS_Mmu139_mm10_ALL.tab.gz EVENTS table (mm10, vast-tools)] - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1) for which genomic coordinates could be determined by LiftOver from mm9.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PSI_Mmu139_mm9.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
 =====Event features=====
-* [{{SERVER}}/downloads/Mouse/VASTDB_SPLICE_SITE_SCORES_Mmu139_mm9.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/hg19/SPLICE_SITE_SCORES-hg19.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PCR_VALIDATIONS_Mmu139_mm9.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+* [{{SERVER}}/downloads/hg19/PCR_PRIMERS-hg19.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
 =====Protein impact=====
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_IMPACT_Mmu139_mm9-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/hg19/PROT_IMPACT-hg19-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_IMPACT_Mmu139_mm9_ALL-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/hg19/PROT_ISOFORMS-hg19.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_PFAM_Mmu139_mm9.tab.gz DOMAINS table (PFAM)] -  Mappings to Pfam domains
+* [{{SERVER}}/downloads/hg19/PROT_PFAM-hg19.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_PROSITE_Mmu139_mm9.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
+* [{{SERVER}}/downloads/hg19/PROT_PROSITE-hg19.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_DISORDER_Mmu139_mm9.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
+* [{{SERVER}}/downloads/hg19/PROT_DISORDER-hg19.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_DOMAIN_PNG_URLs_Mmu139_mm9.tab.gz PROTEIN DOMAIN IMAGES] - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_STRUCT_PDB_Mmu139_mm9.tab.gz PDB STRUCTURES table] - Mappings to protein structures in the Protein Data Bank
-* [{{SERVER}}/downloads/Mouse/VASTDB_PROT_STRUCT_PHYRE_Mmu139_mm9.tab.gz 3D MODELS table] - Mappings to protein structural models generated with Phyre2.
 =====Genes=====
-* [{{SERVER}}/downloads/Mouse/VASTDB_GENES_Mmu139_mm9.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/hg19/GENE_INFO-hg19.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
-* [{{SERVER}}/downloads/Mouse/VASTDB_EXPRESSION_Mmu139_mm9.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
+* [{{SERVER}}/downloads/hg19/EXPRESSION_TABLE-hg19.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
-* [{{SERVER}}/downloads/Mouse/VASTDB_EVENTID_to_GENEID_Mmu139_mm9.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
+* [{{SERVER}}/downloads/hg19/EVENTID_to_GENEID-hg19.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
-=====Evolutionary conservation=====
-* [{{SERVER}}/downloads/Mouse/VASTDB_CONSERVATION_Mmu139_mm9_to_Hsa108_hg19.tab.gz  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.
-* [{{SERVER}}/downloads/Mouse/VASTDB_CONSERVATION_Mmu139_mm9_to_Gga61_galGal3.tab.gz 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.
-* [{{SERVER}}/downloads/Mouse/VASTDB_CONSERVATION_Mmu139_mm9_to_Dre63_danRer10.tab.gz EVENT CONSERVATION table (mm9- danRer10)] - Conservation relationships detected with LiftOver from the source assembly (mm9, S) to the target assembly (danRer10, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
-* [{{SERVER}}/downloads/Mouse/VASTDB_GENE_HOMOLOGY_Mmu139_mm9.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
 =====Samples=====
-* [{{SERVER}}/downloads/Mouse/VASTDB_SAMPLE_INFO_Mmu139_mm9.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
+* [{{SERVER}}/downloads/hg19/SAMPLE_INFO-hg19.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
-====Chicken====
+====<i>Mus musculus (mm10)</i>====
 =====AS events=====
-* [{{SERVER}}/downloads/Chicken/VASTDB_EVENTS_Gga61_galGal3.tab.gz EVENTS table (galGal3, VastDB)]  - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
+* [{{SERVER}}/downloads/mm10/EVENT_INFO-mm10.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
-* [{{SERVER}}/downloads/Chicken/VASTDB_EVENTS_Gga61_galGal3_ALL.tab.gz EVENTS table (galGal3, vast-tools)]  - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
+* [{{SERVER}}/downloads/mm10/EVENT_METRICS-mm10.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PSI_Gga61_galGal3.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
+* [{{SERVER}}/downloads/mm10/PSI_TABLE-mm10.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
 =====Event features=====
-* [{{SERVER}}/downloads/Chicken/VASTDB_SPLICE_SITE_SCORES_Gga61_galGal3.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/mm10/SPLICE_SITE_SCORES-mm10.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PCR_VALIDATIONS_Gga61_galGal3.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+* [{{SERVER}}/downloads/mm10/PCR_PRIMERS-mm10.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
 =====Protein impact=====
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_IMPACT_Gga61_galGal3-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/mm10/PROT_IMPACT-mm10-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_IMPACT_Gga61_galGal3_ALL-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/mm10/PROT_ISOFORMS-mm10.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_PFAM_Gga61_galGal3.tab.gz DOMAINS table (PFAM)] -  Mappings to Pfam domains
+* [{{SERVER}}/downloads/mm10/PROT_PFAM-mm10.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_PROSITE_Gga61_galGal3.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
+* [{{SERVER}}/downloads/mm10/PROT_PROSITE-mm10.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_DISORDER_Gga61_galGal3.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
+* [{{SERVER}}/downloads/mm10/PROT_DISORDER-mm10.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_DOMAIN_PNG_URLs_Gga61_galGal3.tab.gz PROTEIN DOMAIN IMAGES] - Images representing the location of AS events relative to the protein domain architecture/disordered regions.
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_STRUCT_PDB_Gga61_galGal3.tab.gz PDB STRUCTURES table] - Mappings to protein structures in the Protein Data Bank
-* [{{SERVER}}/downloads/Chicken/VASTDB_PROT_STRUCT_PHYRE_Gga61_galGal3.tab.gz 3D MODELS table] - Mappings to protein structural models generated with Phyre2.
 =====Genes=====
-* [{{SERVER}}/downloads/Chicken/VASTDB_GENES_Gga61_galGal3.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/mm10/GENE_INFO-mm10.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
-* [{{SERVER}}/downloads/Chicken/VASTDB_EXPRESSION_Gga61_galGal3.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
+* [{{SERVER}}/downloads/mm10/EXPRESSION_TABLE-mm10.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
-* [{{SERVER}}/downloads/Chicken/VASTDB_EVENTID_to_GENEID_Gga61_galGal3.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
+* [{{SERVER}}/downloads/mm10/EVENTID_to_GENEID-mm10.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
-=====Evolutionary conservation=====
-* [{{SERVER}}/downloads/Chicken/VASTDB_CONSERVATION_Gga61_galGal3_to_Hsa108_hg19.tab.gz  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.
-* [{{SERVER}}/downloads/Chicken/VASTDB_CONSERVATION_Gga61_galGal3_to_Mmu139_mm9.tab.gz 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.
-* [{{SERVER}}/downloads/Chicken/VASTDB_CONSERVATION_Gga61_galGal3_to_Dre63_danRer10.tab.gz EVENT CONSERVATION table (galGal3-danRer10)] - Conservation relationships detected with LiftOver from the source assembly (galGal3, S) to the target assembly (danRer10, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
-* [{{SERVER}}/downloads/Chicken/VASTDB_GENE_HOMOLOGY_Gga61_galGal3.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
 =====Samples=====
-* [{{SERVER}}/downloads/Chicken/VASTDB_SAMPLE_INFO_Gga61_galGal3.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
+* [{{SERVER}}/downloads/mm10/SAMPLE_INFO-mm10.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
+====<i>Mus musculus (mm9)</i>====
+=====AS events=====
+* [{{SERVER}}/downloads/mm9/EVENT_INFO-mm9.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
+* [{{SERVER}}/downloads/mm9/EVENT_METRICS-mm9.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
+* [{{SERVER}}/downloads/mm9/PSI_TABLE-mm9.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
+=====Event features=====
+* [{{SERVER}}/downloads/mm9/SPLICE_SITE_SCORES-mm9.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/mm9/PCR_PRIMERS-mm9.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+=====Protein impact=====
+* [{{SERVER}}/downloads/mm9/PROT_IMPACT-mm9-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
+* [{{SERVER}}/downloads/mm9/PROT_ISOFORMS-mm9.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
+* [{{SERVER}}/downloads/mm9/PROT_PFAM-mm9.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
+* [{{SERVER}}/downloads/mm9/PROT_PROSITE-mm9.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
+* [{{SERVER}}/downloads/mm9/PROT_DISORDER-mm9.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
+=====Genes=====
+* [{{SERVER}}/downloads/mm9/GENE_INFO-mm9.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/mm9/EXPRESSION_TABLE-mm9.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
+* [{{SERVER}}/downloads/mm9/EVENTID_to_GENEID-mm9.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
+=====Samples=====
+* [{{SERVER}}/downloads/mm9/SAMPLE_INFO-mm9.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
+====<i>Bos taurus (bosTau6)</i>====
+=====AS events=====
+* [{{SERVER}}/downloads/bosTau6/EVENT_INFO-bosTau6.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
+* [{{SERVER}}/downloads/bosTau6/EVENT_METRICS-bosTau6.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
+* [{{SERVER}}/downloads/bosTau6/PSI_TABLE-bosTau6.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
+=====Event features=====
+* [{{SERVER}}/downloads/bosTau6/SPLICE_SITE_SCORES-bosTau6.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/bosTau6/PCR_PRIMERS-bosTau6.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+=====Protein impact=====
+* [{{SERVER}}/downloads/bosTau6/PROT_IMPACT-bosTau6-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
+* [{{SERVER}}/downloads/bosTau6/PROT_ISOFORMS-bosTau6.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
+* [{{SERVER}}/downloads/bosTau6/PROT_PFAM-bosTau6.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
+* [{{SERVER}}/downloads/bosTau6/PROT_PROSITE-bosTau6.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
+* [{{SERVER}}/downloads/bosTau6/PROT_DISORDER-bosTau6.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
+=====Genes=====
+* [{{SERVER}}/downloads/bosTau6/GENE_INFO-bosTau6.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/bosTau6/EXPRESSION_TABLE-bosTau6.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
+* [{{SERVER}}/downloads/bosTau6/EVENTID_to_GENEID-bosTau6.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
+=====Samples=====
+* [{{SERVER}}/downloads/bosTau6/SAMPLE_INFO-bosTau6.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
+====<i>Gallus gallus (galGal4)</i>====
+=====AS events=====
+* [{{SERVER}}/downloads/galGal4/EVENT_INFO-galGal4.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
+* [{{SERVER}}/downloads/galGal4/EVENT_METRICS-galGal4.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
+* [{{SERVER}}/downloads/galGal4/PSI_TABLE-galGal4.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
+=====Event features=====
+* [{{SERVER}}/downloads/galGal4/SPLICE_SITE_SCORES-galGal4.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/galGal4/PCR_PRIMERS-galGal4.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+=====Protein impact=====
+* [{{SERVER}}/downloads/galGal4/PROT_IMPACT-galGal4-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
+* [{{SERVER}}/downloads/galGal4/PROT_ISOFORMS-galGal4.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
+* [{{SERVER}}/downloads/galGal4/PROT_PFAM-galGal4.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
+* [{{SERVER}}/downloads/galGal4/PROT_PROSITE-galGal4.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
+* [{{SERVER}}/downloads/galGal4/PROT_DISORDER-galGal4.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
+=====Genes=====
+* [{{SERVER}}/downloads/galGal4/GENE_INFO-galGal4.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/galGal4/EXPRESSION_TABLE-galGal4.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
+* [{{SERVER}}/downloads/galGal4/EVENTID_to_GENEID-galGal4.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
+=====Samples=====
+* [{{SERVER}}/downloads/galGal4/SAMPLE_INFO-galGal4.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
+====<i>Gallus gallus (galGal3)</i>====
+=====AS events=====
+* [{{SERVER}}/downloads/galGal3/EVENT_INFO-galGal3.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
+* [{{SERVER}}/downloads/galGal3/EVENT_METRICS-galGal3.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
+* [{{SERVER}}/downloads/galGal3/PSI_TABLE-galGal3.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
+=====Event features=====
+* [{{SERVER}}/downloads/galGal3/SPLICE_SITE_SCORES-galGal3.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/galGal3/PCR_PRIMERS-galGal3.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+=====Protein impact=====
+* [{{SERVER}}/downloads/galGal3/PROT_IMPACT-galGal3-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
+* [{{SERVER}}/downloads/galGal3/PROT_ISOFORMS-galGal3.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
+* [{{SERVER}}/downloads/galGal3/PROT_PFAM-galGal3.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
+* [{{SERVER}}/downloads/galGal3/PROT_PROSITE-galGal3.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
+* [{{SERVER}}/downloads/galGal3/PROT_DISORDER-galGal3.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
+=====Genes=====
+* [{{SERVER}}/downloads/galGal3/GENE_INFO-galGal3.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/galGal3/EXPRESSION_TABLE-galGal3.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
+* [{{SERVER}}/downloads/galGal3/EVENTID_to_GENEID-galGal3.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
+=====Samples=====
+* [{{SERVER}}/downloads/galGal3/SAMPLE_INFO-galGal3.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
+====<i>Danio rerio (danRer10)</i>====
+=====AS events=====
+* [{{SERVER}}/downloads/danRer10/EVENT_INFO-danRer10.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
+* [{{SERVER}}/downloads/danRer10/EVENT_METRICS-danRer10.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
+* [{{SERVER}}/downloads/danRer10/PSI_TABLE-danRer10.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
+=====Event features=====
+* [{{SERVER}}/downloads/danRer10/SPLICE_SITE_SCORES-danRer10.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/danRer10/PCR_PRIMERS-danRer10.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+=====Protein impact=====
+* [{{SERVER}}/downloads/danRer10/PROT_IMPACT-danRer10-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
+* [{{SERVER}}/downloads/danRer10/PROT_ISOFORMS-danRer10.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
+* [{{SERVER}}/downloads/danRer10/PROT_PFAM-danRer10.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
+* [{{SERVER}}/downloads/danRer10/PROT_PROSITE-danRer10.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
+* [{{SERVER}}/downloads/danRer10/PROT_DISORDER-danRer10.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
+=====Genes=====
+* [{{SERVER}}/downloads/danRer10/GENE_INFO-danRer10.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/danRer10/EXPRESSION_TABLE-danRer10.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
+* [{{SERVER}}/downloads/danRer10/EVENTID_to_GENEID-danRer10.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
+=====Samples=====
+* [{{SERVER}}/downloads/danRer10/SAMPLE_INFO-danRer10.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.
-====Zebrafish====
+====<i>Drosophila melanogaster (dm6)</i>====
 =====AS events=====
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_EVENTS_Dre63_danRer10.tab.gz EVENTS table (danRer10, VastDB)]  - Information about AS event coordinates and sequences. This table only contains events included in the VastDB website.
+* [{{SERVER}}/downloads/dm6/EVENT_INFO-dm6.tab.gz EVENT INFORMATION]  - Information about AS event coordinates and sequences.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_EVENTS_Dre63_danRer10_ALL.tab.gz EVENTS table (danRer10, vast-tools)]  - Information about AS event coordinates and sequences. This table contains all events in the vast-tools library (version 1).
+* [{{SERVER}}/downloads/dm6/EVENT_METRICS-dm6.tab.gz EVENT METRICS]  - Summary statistics for the usage of each AS event.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PSI_Dre63_danRer10.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages.
+* [{{SERVER}}/downloads/dm6/PSI_TABLE-dm6.tab.gz MAIN PSI TABLE] - Inclusion patterns of AS events across tissues, cell types and developmental stages (main PSI plot).
 =====Event features=====
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_SPLICE_SITE_SCORES_Dre63_danRer10.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
+* [{{SERVER}}/downloads/dm6/SPLICE_SITE_SCORES-dm6.tab.gz SPLICE SITE INFORMATION] - Sequences and strength scores of 5' and 3' splice sites of alternative exons.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PCR_VALIDATIONS_Dre63_danRer10.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
+* [{{SERVER}}/downloads/dm6/PCR_PRIMERS-dm6.tab.gz PRIMER SUGGESTIONS] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR.
 =====Protein impact=====
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_IMPACT_Dre63_danRer10-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/dm6/PROT_IMPACT-dm6-v3.tab.gz PROTEIN IMPACT] - Predicted effect of the AS event on the open reading frame of the transcript. Version v3.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_IMPACT_Dre63_danRer10_ALL-v1.4.2.tab.gz 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.
+* [{{SERVER}}/downloads/dm6/PROT_ISOFORMS-dm6.tab.gz PROTEIN ISOFORMS] -  Mappings of events to Protein IDs.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_PFAM_Dre63_danRer10.tab.gz DOMAINS table (PFAM)] -  Mappings to Pfam domains
+* [{{SERVER}}/downloads/dm6/PROT_PFAM-dm6.tab.gz DOMAIN OVERLAP (PFAM)] -  Overlap of AS events with Pfam domains.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_PROSITE_Dre63_danRer10.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains.
+* [{{SERVER}}/downloads/dm6/PROT_PROSITE-dm6.tab.gz DOMAIN OVERLAP (PROSITE)] - Overlap of AS events with PROSITE domains.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_PROT_DISORDER_Dre63_danRer10.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons.
+* [{{SERVER}}/downloads/dm6/PROT_DISORDER-dm6.tab.gz PROTEIN DISORDERED REGIONS] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred.
 =====Genes=====
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_GENES_Dre63_danRer10.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes.
+* [{{SERVER}}/downloads/dm6/GENE_INFO-dm6.tab.gz GENE INFORMATION] - Information about gene names, descriptions, genomic coordinates and biotypes.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_EXPRESSION_Dre63_danRer10.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads.
+* [{{SERVER}}/downloads/dm6/EXPRESSION_TABLE-dm6.tab.gz MAIN EXPRESSION TABLE] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads (main GE plot).
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_EVENTID_to_GENEID_Dre63_danRer10.tab.gz GENE-EVENTS table] - Table relating genes to AS events.
+* [{{SERVER}}/downloads/dm6/EVENTID_to_GENEID-dm6.tab.gz EVENT_ID to GENE_ID] - Table relating genes to AS events.
-=====Evolutionary conservation=====
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_CONSERVATION_Dre63_danRer10_to_Hsa108_hg19.tab.gz  EVENT CONSERVATION table (danRer10- hg19)] - Conservation relationships detected with LiftOver from the source assembly (danRer10, S) to the target assembly (hg19, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_CONSERVATION_Dre63_danRer10_to_Mmu139_mm9.tab.gz EVENT CONSERVATION table (danRer10- mm9)] - Conservation relationships detected with LiftOver from the source assembly (danRer10, S) to the target assembly (mm9, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_CONSERVATION_Dre63_danRer10_to_Gga61_galGal3.tab.gz EVENT CONSERVATION table (danRer10- galGal3)] - Conservation relationships detected with LiftOver from the source assembly (danRer10, S) to the target assembly (galGal3, T). Coordinates, splicing pattern and VastDB Event ID (if possible) are listed for the target event.
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_GENE_HOMOLOGY_Dre63_danRer10.tab.gz GENE HOMOLOGY table] - Homology relationships between genes.
 =====Samples=====
-* [{{SERVER}}/downloads/Zebrafish/VASTDB_SAMPLE_INFO_Dre63_danRer10.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database.
+* [{{SERVER}}/downloads/dm6/SAMPLE_INFO-dm6.tab.gz SAMPLE INFORMATION] - SRA identifiers and other information related to RNA-seq data used in this database.

Difference between revisions of "Downloads"

From VastDB

Revision as of 16:30, 16 December 2020

Contents

General files

Homo sapiens (hg38)

AS events

Event features

Protein impact

Genes

Samples

Homo sapiens (hg19)

AS events

Event features

Protein impact

Genes

Samples

Mus musculus (mm10)

AS events

Event features

Protein impact

Genes

Samples

Mus musculus (mm9)

AS events

Event features

Protein impact

Genes

Samples

Bos taurus (bosTau6)

AS events

Event features

Protein impact

Genes

Samples

Gallus gallus (galGal4)

AS events

Event features

Protein impact

Genes

Samples

Gallus gallus (galGal3)

AS events

Event features

Protein impact

Genes

Samples

Danio rerio (danRer10)

AS events

Event features

Protein impact

Genes

Samples

Drosophila melanogaster (dm6)

AS events

Event features

Protein impact

Genes

Samples