Splice Site Prediction
developed by
JSI medical systems GmbH
Tullastr. 18
77955 Ettenheim
GERMANY
phone: +49-7822/4401050-0
fax: +49-7822/440150-20
email: mail@varSEAK.bio
web: www.jsi-medisys.com
The JSI splice site prediction tool predicts changes in the quality of splice sites at and in close proximity to
a site of genetic variation. For this, several scores are calculated, among them scores taking into account not
only the overall quality of the known splice motif but also the probability of the respective sequence being
present as a known splice site throughout the whole genome. The JSI splice site prediction tool has been trained
with approximately 200 000 splice sites, i.e. the known splice sites throughout the whole genome (GRCh37). To
display this web page we recommend the web browsers Firefox
and Chrome. Note: Internet Explorer is not
supported.
Additionally, the MaxEntScan scoring tool for human splice sites has been integrated and the respective scores
are displayed alongside the JSI scores for comparison.
We would like to thank Yeo Gene for his friendly approval to integrate the MaxEntScan scoring algorithm into our
software.
Querying the splice site prediction tool
- Search for your gene of interest
- Change the transcript by clicking the input field and choosing from the list, if required. If you leave this
field empty, the longest transcript will be automatically choosen.
- Enter your variant:
- a) either enter HGVS c. nomenclature
- b) or change the radio button to "Sequence" and enter a genomic sequence (allowed characters are
A,T,G,C, sequence must be between 20 and 50 bases long)
- Click the [Search] button
- To start another query within the same gene, change transcript and variant as preferred and click [Search].
- To start another query on another gene, click the [X] button in the upper right corner of the gene name.
Visible information
- For a short overview and legend, make sure that the Info foldout banner is opened on the lower right of the
screen.
- General information about the gene of interest (gene, chromosome, strand, genomic start, genomic end, number
of exons in transcript, base pairs) is provided within the Search area.
- At the top of the Results area, the variant and its position on the transcript, gene and genomic level is
displayed.
- Below, a bar represents the structure of exons (blue) and introns (yellow). The exons and introns are
numbered.
- Additionally, in the sequence, upper case bold letters are used for exons, lower case letters are used for
introns.
- The upper sequence is the reference, the lower sequence contains your variant. The site of the variant is
marked with an arrow between the sequences.
- Below the sequences, there are two lines, each showing markings for 5' and 3' splice sites, respectively.
- Known splice sites are also marked as boxes between the reference and variant sequence: blue for authentic
splice sites in the selected transcript, red for alternative splice sites from other transcripts.
- For 3' splice sites, more details can be shown. The selected splice site is marked by a red bar, the
corresponding Branch Point is marked by a black bar, and the 5' start point of the AG Exception Zone is
marked by a red triangle.
- Below the chart, there are two tables. The table on the left shows information regarding the 5' splice sites
whilst the table on the right shows information regarding the 3' splice sites. Each table entry shows the
calculated scores in two lines. The upper line is presenting the scores for the reference sequence, the
lower line shows the scores for the sequence including your variant.
- Next to the table header, a short text can be shown, summarizing the predicted splicing effects for the
variant sequence.
- By default, only the most relevant results are displayed. Click [Show All] to see all results from all
possible splice sites within the displayed sequence. Click [Show Positive Scores] to display only results
with a positive Score (i.e. possible splice sites) in the reference or variant sequence.
- Each splice site indicated in the chart is represented by one row in the respective table. Authentic and
alternative splice sites are marked by a correspondingly coloured bar at the beginning of the row. Hovering
over the respective row will highlight the splice site in the chart.
- For 3' splice sites, radio buttons serve to select for which possible splice site the details (position,
Branch Point sequence and AGEZ (AG Exception Zone)) should be shown.
Scores
5' spliceSITE scores |
|
c.pos |
cDNA Position in set transcript. |
Score |
Total score indicating the overall quality of a (possible) splice site.
A positive value predicts a functional splice site.
A negative value predicts that this position is not a functional splice site. Negative values below
-1000 are shown as "neg.".
|
BCS |
Base Consensus Score: summed up likelihood for single bases 3 bp upstream to 4 bp downstream of GT. |
MCS |
Motif Consensus Score: calculation based on the likelihood and frequency of the complete 9mer sequence
of the donor splice site (5'<3bp>GT<4bp>3')
|
5' MaxEntScan scores |
|
ENT |
Maximum Entropy Model by MaxEntScan. |
MDD |
Maximum Dependence Decomposition Model by MaxEntScan. |
MM |
First-order Markov Model by MaxEntScan. |
WMM |
Weight Matrix Model by MaxEntScan. |
3' spliceSITE scores |
|
c.pos |
cDNA Position in set transcript. |
Score |
Total score indicating the overall quality of a (possible) splice site.
A positive value predicts a functional splice site.
A negative value predicts that this position is not a functional splice site.
Negative values below -1000 are shown as "neg.".
|
BCS |
Base Consensus Score: summed up likelihood for single bases upstream AG. |
MCS |
Motif Consensus Score: Sequence upstream of AG is divided to 6mer oligos. The score is calculated based
on the frequency of each 6mer at a given position.
|
CAGG |
Base Consensus Score, indicates the splice site quality by summing up the likelihood of the occurrence
of the bases flanking the AG.
|
BP |
Branch Point: sequence for branch point should match to yTnAy
Branch point must be located in the AGEZ (AG Exception Zone).
|
BPPos |
Branch Point Position: optimum is 23 bp downstream of 3' splice site. |
PPT |
Polypyrimidine tract score, indicates C/T content of the polypyrimidine tract between Branch Point and
3' splice site.
|
U2BE |
U2 binding energy score, indicates the quality of binding capacity of the branch point motif regarding
the U2 splicesosomal unit.
|
3' MaxEntScan scores |
|
ENT |
Maximum Entropy Model by MaxEntScan. |
MM |
First-order Markov Model by MaxEntScan. |
WMM |
Weight Matrix Model by MaxEntScan. |
References:
- Baralle, Marco, Baralle, Francisco Ernesto, The Splicing Code.BioSystems https://doi.org/10.1016/j.biosystems.2017.11.002
- Caminsky NG, Mucaki EJ and Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of
the literature and guidelines for information-theoretical analysis [version 1; referees: 2 approved]
F1000Research 2014, 3:282 (doi: 10.12688/f1000research.5654.1)
- Corvelo A, Hallegger M, Smith CWJ, Eyras E (2010) Genome-Wide Association between Branch Point Properties
and Alternative Splicing. PLoS Comput Biol 6(11): e1001016. doi:10.1371/journal.pcbi.1001016
- Lee, Melissa, Ross, Patrick, Sharma, Neeraj, Atalar, Melis, Evans, Taylor A., Pellicore, Matthew J., Davis,
Emily, Lam, Anh-Thu N., Stanley, Susan E., Khalil, Sara E., Solomon, George, Walker, Doug, Raraigh, Karen
S., Vecchio-Pagan, Briana, Armanios, Mary, Cutting, Garry R., Systematic Computational Identification of
Variants That Activate Exonic and Intronic Cryptic Splice Sites. American Journal of Human Genetics http://dx.doi.org/10.1016/j.ajhg.2017.04.001
- Nabih, Amena, Sobotka, Julia A., Wu, Monica Z., Wedeles, Christopher J., Claycomb, Julie M., Examining the
intersection between splicing, nuclear export and small RNA pathways. Biochimica et Biophysica Acta (BBA)
-General Subjects https://doi.org/10.1016/j.bbagen.2017.05.027
- Pohl, Martin, Bortfeldt, Ralf H., Grützmann, Konrad and Schuster, Stefan, Alternative splicing of mutually
exclusive exons - A review. BioSystems https://doi.org/10.1016/j.biosystems.2013.07.003
- Ratnadiwakara Madara, Mohenska Monika, Änkö Minna-Liisa, Splicing factors as regulators of miRNA biogenesis
- links to human disease. Seminars in Cell & Developmental Biology https://doi.org/10.1016/j.semcdb.2017.10.008
- o Yeo G. and Burge C.B., Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing
Signals, RECOMB 2003 (Journal Comp. Bio in press)