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Protocols

VastDB specifications

Information


Unique identifier OMICS_20724
Name VastDB
Alternative name Vertebrate Alternative Splicing and Transcription Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.2.0
Maintained Yes

Maintainers


  • person_outline VastDB Team
  • person_outline Manuel Irimia
  • person_outline Benjamin Blencowe

Additional information


http://vastdb.crg.eu/wiki/FAQ

Publication for Vertebrate Alternative Splicing and Transcription Database

VastDB citations

 (3)
library_books

A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation

2018
Sci Rep
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] ific functions.Further, to determine how ociad2 expression varies with respect to ociad1, we compared their transcript levels across different human tissues and cell lines using RNA-seq datasets from VastDB (see Methods). We found that except liver, ociad2 showed reduced transcript-level expression as compared to ociad1 in human tissues such as heart, kidney, spleen, brain, lung, adipose, bone mar […]

call_split

Evolutionary recruitment of flexible Esrp dependent splicing programs into diverse embryonic morphogenetic processes

2017
Nat Commun
PMCID: 5703972
PMID: 29180615
DOI: 10.1038/s41467-017-01961-y
call_split See protocol

[…] splice site choices. It has been extensively used to identify differentially spliced AS events in human, mouse, chicken, and planarians, providing high validation rates in RT-PCR assays,–. Associated VASTDB files to run vast-tools gene expression and AS analyzes on zebrafish (species key “Dre”) and sea urchin (species key “Spu”) can be downloaded at http://vastdb.crg.eu/libs/vastdb.dre.10.03.17.ta […]

library_books

Complex transcriptional regulation and independent evolution of fungal like traits in a relative of animals

2015
eLife
PMCID: 4739763
PMID: 26465111
DOI: 10.7554/eLife.08904.036

[…] etails).The different modules to detect and quantify AS have been integrated into vast-tools (https://github.com/vastgroup/vast-tools; species key “Cfr”). Associated files can be downloaded at http://vastdb.crg.eu/libs/vastdb.cfr.31.1.15.tar.gz.We used a threshold of ≥20 PIR in at least one stage for positive intron retention events. As a threshold for ES events we used skipping rates below 90% (m […]

Citations

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VastDB institution(s)
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Barcelona, Spain
VastDB funding source(s)
Supported by grants from European Research Council (ERC-StG-LS2- 637591); Spanish Ministry of Economy and Competitiveness (‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and BFU2014-55076-P); McLaughlin Foundation; Canadian Institutes of Health Research; and an EMBO LTF fellowship.

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