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SpliceVault
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   * * Select splice site of interest using Gene Name, Transcript and Exon
       selectors.
     * Customise settings: choose how many and what type of mis-splicing events
       you want to display.
     * More questions? See FAQ

CUSTOMISE SETTINGS

Number of Events: 11000412345678910
Show all Events
Maximum Number of Exons Skipped: 11000212345678910
Show all Exon Skipping
Show Cryptics Within: +/-50 nt+/-1,000 nt00+/-600
nt501502503504505506507508509501,000
Show all Cryptics



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Gene Name:

300K-RNA (hg38) 40K-RNA (hg19)
Transcript:

RefSeq Ensembl
Exon:

Acceptor Donor

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 * FAQ




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What is SpliceVault?

SpliceVault houses our resource of the most common mis-splicing events local to
the exon-intron junction, based on unannotated splice-junctions detected across
335,301 publicly available RNA-Seq samples from GTEx and SRA, and built in
GRCh38 (300K-RNA). It is collectively hosted with an older version of the
database, 40K-RNA.

300K-RNA (top-4 events) is an empirical method which accurately predicts the
nature of variant associated mis-splicing with 90% sensitivity

See Dawes et al. 2022 (link TBC) for details on formation of the 300K-RNA
database

What's the difference between 300K-RNA & 40K-RNA?

300K-RNA is a database of splice-junctions found across 335,663 publicly
available RNA-Seq samples from GTEx and SRA, and built in hg38 (GRCh38). See
Dawes et al. 2022 (link) for details and methods.

40K-RNA is an older version of the database, based on 40,233 RNA-Seq samples
similarly from GTEx and SRA, but built in hg19 (GRCh37). See Dawes et al. 2022
(link TBC) for details and methods. We only recommend using this version of the
database if you can't convert your splice site of interest to hg38 for whatever
reason.

How was the canonical transcript chosen for each gene?
GRCh37
 * Ensembl - Canonical transcript as provided by Ensembl. Ensembl API derives
   this based on legacy canonical transcript selection rules *
 * Refseq - Canonical transcript not provided. Calculated using Ensembl’s legacy
   canonical transcript selection rules *

GRCh38
 * Ensembl - Canonical transcript as provided by Ensembl. Please refer to
   http://www.ensembl.org/info/genome/genebuild/canonical.html for further info
   on how it was derived
 * Refseq - Canonical transcript not provided. Calculated using Ensembl’s legacy
   canonical transcript selection rules *

* The canonical transcript is used in the gene tree analysis in Ensembl and does
not necessarily reflect the most biologically relevant transcript of a gene. For
human, the canonical transcript for a gene is set according to the following
hierarchy:

 1. Longest CCDS translation with no stop codons.
 2. If no (1), choose the longest Ensembl/Havana merged translation with no stop
    codons.
 3. If no (2), choose the longest translation with no stop codons.
 4. If no translation, choose the longest non-protein-coding transcript

(Source:
https://web.archive.org/web/20200928022822/https://m.ensembl.org/Help/Glossary?id=521)



What are GTEx and SRA/Intropolis?

GTEx provide RNA-Seq data from a large set of healthy individuals. SRA (Sequence
Read Arcchive) is an online archive of high-throughput RNA sequencing data.
Intropolis is a set of ~42M exon-exon junctions found across 21,504 human
RNA-seq samples from the Sequence Read Archive (SRA).

How do I read the 'Skipped Exons' column?

The column reports the ids of the exons skipped, for example '2' refers to
skipping of exon 2 in that transcript (not skipping of 2 exons), and '2-3'
denotes skipping of exons 2 and 3.

How is cryptic distance calculated?

We report the maximum number of reads observed in any one sample for each
splicing event, across samples from GTEx. We report only for GTEx samples as
these are all healthy samples unlike SRA/Intropolis which may have misleading
outliers. If the max reads of annotated splicing is low (<250) we recommend not
excluding any events missing from 300K-RNA as it could just be due to poor read
depth.

How were the default settings chosen? (top 4 events, skipping < 2 exons and
cryptics within +/- 600 nt)?

The default settings were chosen as they gave a Sensitivity of 90% and PPV of
31% for predicting exon skipping and cryptic activation events in Dawes et al.
2022 (link TBC). Users are free to customise settings for their own purposes,
however we recommend these thresholds for clinical use.

Can I export the data?

To export the table you've generated, click either copy or download and select
file type. If you are planning to open the file in Excel, we recommend the
'Excel' format so that the 'Exons skipped' column doesn't get converted to
dates.

To download the 300K-RNA database see (Link available in near future), and to
download the 40K-RNA database see (Link available in near future).

How do I open IGV links?

In your IGV desktop app, go to Preferences > Advanced & check Enable Port with
Port number 60151. You may need to restart IGV after enabling

IGV must be open when the link is clicked for it to work, and will open so that
the donor and acceptor used in the splice junction are at both edges of the
screen.

Why does SpliceVault freeze after a few minutes?

We’re hosting SpliceVault on shinyapps.io; which pauses the website if not used
for 10 minutes or more (to save computing costs). You can simply click “reload”
and continue your analysis.

How do I cite SpliceVault?

Dawes et al. 2022 (link TBC)

Disconnected from the server. Reload