PastDB is a database of Alternative Splicing (AS) profiles across multiple tissues and environmental conditions of Arabidopsis thaliana. PastDB contains AS events (including exon skipping, alternative 5' and 3' splice sites and retained introns). AS event identification and sequence inclusion level quantification in RNA-seq samples have been performed with [https://github.com/vastgroup/vast-tools VAST-TOOLS].

In addition to AS inclusion levels, PastDB provides general information about the AS events, including genomic and sequence context, impact on the reading frame, overlap with protein domains and disordered regions and primers for AS event validation through RT-PCR. Moreover, it also provides measures of Gene Expression, using the cRPKM metric.

If you see an AS event that you find inconsistent, or you have any questions, comments or suggestions about the database, please do not hesitate to e-mail us to [mailto:vastdb@googlegroups.com vastdb@googlegroups.com].

EventFunction

2020-06-22T11:44:45Z

Mirimia:

{{NAMESPACE}}
==Submit functional annotations for AS events==

Dear PastDB user,

Our goal is to make PastDB (and VastDB) a comprehensive resource for the research community, gathering information about the behaviour of alternative splicing events at many different levels, and displaying it in a concise and intuitive manner. With that in mind, we think that displaying brief annotations of the biological functions described for some of our AS events, together with links to bibliographical evidence, could be a very useful feature for future PastDB releases.

That's why we kindly ask for your help. If you have published references speaking about the effects of an AS event with a ''vast-tools'' ID, you can let us know using this form, and we will include it in our next release, so that other researchers can benefit of your knowledge too.

Thank you very much in advance,

The VastDB/PastDB team

P.S. If you have many annotations, you can also send us a tab-delimited text file to [mailto:vastdb@googlegroups.com vastdb@googlegroups.com], and we will add it to our dataset.

<emailform>
{|
| Name: || <emailform name=40 /> ||
|-
| Email: || <emailform from=40 /> ||
|-
| Event ID: || <emailform event=40 /> || ''(e.g. MmuEX0025260)''
|-
| PubMed ID: || <emailform pmid=40 /> || ''(e.g. [https://www.ncbi.nlm.nih.gov/pubmed/20164337 20164337])''
|-
| Annotation: || <emailform function=60x8 /> || ''(e.g. LSD1 isoforms display in vitro a comparable demethylase activity, yet the inclusion of exon E8a (MmuEX0025260) reduces LSD1 repressor activity on a reporter gene. The knockdown of neurospecific variants in cortical neurons results in the inhibition of neurite maturation, whereas overexpression of the same variants enhances it. Instead, perturbation of LSD1 isoforms that are devoid of the neurospecific exon elicits no morphogenic effect.)''
|-
|| || <emailform submit="Submit Annotation" /> ||
|}
</emailform>
<emailform result>
Thank you for your contribution!

Our data curation team will review this to include it in the next PastDB release.
{| width="300px"
| '''Name:''' <emailform name />
| '''Email:''' <emailform from/>
| '''Event ID:''' <emailform event />
| '''PMID:''' <emailform pmid />
| '''Biological function:''' <emailform function />
|}
</emailform>