Difference between revisions of "Downloads"
From PastDB
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| − | From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately: | + | {{#vardefine:server|http://vastdb.crg.eu}}From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately: |
====<i>Arabidopsis thaliana</i>==== | ====<i>Arabidopsis thaliana</i>==== | ||
=====AS events===== | =====AS events===== | ||
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/EVENT_INFO-araTha10.tab.gz EVENTS table] - Information about AS event coordinates and sequences. TAIR10 asssembly. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PSI_TABLE-araTha10.tab.gz PSI table] - Inclusion patterns of AS events across tissues, cell types and developmental stages. |
=====Event features===== | =====Event features===== | ||
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/SPLICE_SITE_SCORES-araTha10.tab.gz SPLICE SITES table] - Sequences and strength scores of 5' and 3' splice sites of alternative exons. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PCR_PRIMERS-araTha10.tab.gz PCR VALIDATION table] - Suggested primer sequences and expected band lengths for validation of AS events by RT-PCR. |
=====Protein impact===== | =====Protein impact===== | ||
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PROT_IMPACT-araTha10-v2.3.tab.gz PROTEIN IMPACT table] - Effect of the AS event in the open reading frame of the transcript. Version v2.3. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PROT_ISOFORMS-araTha10.tab.gz PROTEIN ISOFORMS] - Mappings of events to ProteinIDs. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PROT_PFAM-araTha10.tab.gz DOMAINS table (PFAM)] - Mappings to Pfam domains |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PROT_PROSITE-araTha10.tab.gz DOMAINS table (PROSITE)] - Mappings to PROSITE domains. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/PROT_DISORDER-araTha10.tab.gz PROTEIN DISORDERED REGIONS table] - Intrinsic disorder rates for A, C1 and C2 exons, using disopred3. |
=====Genes===== | =====Genes===== | ||
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/GENE_INFO-araTha10.tab.gz GENES table] - Information about gene names, descriptions, genomic coordinates and biotypes. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/EXPRESSION_TABLE-araTha10.tab.gz EXPRESSION table] - Gene expression across tissues, cell types and developmental stages. Measured in cRPKM and in raw reads. |
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/EVENTID_to_GENEID-araTha10.tab.gz GENE-EVENTS table] - Table relating genes to AS events. |
=====Samples===== | =====Samples===== | ||
| − | * [{{ | + | * [{{#var:server}}/downloads/araTha10/SAMPLE_INFO-araTha10.tab.gz SAMPLE_INFO table] - SRA identifiers and other information related to RNA-seq data used in this database. |
Revision as of 15:55, 23 June 2020
From this page you can download tables with the information in PastDB. Tables with different features of the database can be downloaded separately:
Contents
Arabidopsis thaliana
AS events
- EVENTS table - Information about AS event coordinates and sequences. TAIR10 asssembly.
- 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 - Effect of the AS event in the open reading frame of the transcript. Version v2.3.
- 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.
- 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.
Samples
- SAMPLE_INFO table - SRA identifiers and other information related to RNA-seq data used in this database.