Human Splicing Finder - por 1508 - 3

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23/04/2020

Human Splicing Finder - Version 3.1

Human Splicing Finder

Results POR c.732-36C>T

POR c.831-35C>T

POR c.1508C>T

POR c.1716G>A

Sequences

Reference sequence POR Gene > ENST00000461988 Transcript > Exon number: 13 (271 bp) + 100 intronic nucleotides at exon ends - No SNP related to this sequence found in Ensembl variation database. 1

ggccctgggt gagtggggct ggcctgcaga acgggacttg gggccggggc tgggcaaggg cctcggtgtg gcggtggagc tcacacggcc ctccccacag

101

GTCCACCCCA ACTCTGTGCA CATCTGTGCG GTGGTTGTGG AGTACGAGAC CAAGGCTGGC CGCATCAACA AGGGCGTGGC CACCAACTGG CTGCGGGCCA

201

AGGAGCCTGC CGGGGAGAAC GGCGGCCGTG CGCTGGTGCC CATGTTCGTG CGCAAGTCCC AGTTCCGCCT GCCCTTCAAG GCCACCACGC CTGTCATCAT

301

GGTGGGCCCC GGCACCGGGG TGGCACCCTT CATAGGCTTC ATCCAGGAGC GGGCCTGGCT GCGACAGCAG Ggtgagtggg gtcccatggg ggagaggggg

401

tgacgactgg gagccccgcg ctcaccccgg cccctgccac gcag

Total sequence length: 444 nucleotides

Mutant sequence 1

ggccctgggt gagtggggct ggcctgcaga acgggacttg gggccggggc tgggcaaggg cctcggtgtg gcggtggagc tcacacggcc ctccccacag

101

GTCCACCCCA ACTCTGTGCA CATCTGTGCG GTGGTTGTGG AGTACGAGAC CAAGGCTGGC CGCATCAACA AGGGCGTGGC CACCAACTGG CTGCGGGCCA

201

AGGAGCCTGT CGGGGAGAAC GGCGGCCGTG CGCTGGTGCC CATGTTCGTG CGCAAGTCCC AGTTCCGCCT GCCCTTCAAG GCCACCACGC CTGTCATCAT

301

GGTGGGCCCC GGCACCGGGG TGGCACCCTT CATAGGCTTC ATCCAGGAGC GGGCCTGGCT GCGACAGCAG Ggtgagtggg gtcccatggg ggagaggggg

401

tgacgactgg gagccccgcg ctcaccccgg cccctgccac gcag

Total sequence length: 444 nucleotides The underlined sequences are analyzed by HSF. NB: This color indicates where a SNP is located on the sequence(s).

Interpreted Data This table shows only relevant results related to the mutation position and context. The mutation occurs in the late exonic positions, the following table show results of donor splice sites, ESE and ESS that could be affected by the mutation Predicted signal New Donor Site

Prediction algorithm

cDNA Position

Interpretation

G A G C C T G T C G G G G A G

Activation of an exonic cryptic donor site. Potential alteration of splicing.

1

1 - HSF Matrices 104

ESE Site

1 - ESE-Finder - SC35

www.umd.be/HSF/4DACTION/input_SSF

106

108

110

112

114

116

Alteration of an exonic 1/3

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Human Splicing Finder - Version 3.1

Broken

G G A G C C T G C C G G G G 1

2 - ESR Sequences from Goren et al.

2 102

104

106

108

110

112

ESE site. Potential alteration of splicing.

114

Raw Data Tables In the tables below, positions in sequence for the 5' intron are labeled as negative and as positive for the 3' intron. Variations in the tables below are noted in colored boxes, according to the following scale: Site broken

0% - 25% variation

Potential Splice Sites

26% - 50% variation

51% - 75% variation

Potential Branch Points

76% - 100% variation

Enhancer motifs

New site<

Silencer motifs

Other splicing motifs Silencer motifs from Sironi et al. Threshold values: Motif 1: 60 Motif 2: 60 Motif 3: 60 Variation expresses the difference between reference and mutant values. Wild Type value is taken as reference.

Sequence cDNA Position Position

206

106

208

108

209

109

Sironi Motif Reference

Reference silencer (value 0100)

Motif 3 TCTCCCAA

CCTGCCGG (64.93)

Sironi Mutant motif

Mutant silencer Variation (value 0100) Site broken -6.08

Motif 2 TGCCGGG Motif 2 TGTCGGG +17.31 % [T/G]G[T/A]GGGG (72.47) [T/G]G[T/A]GGGG (85.01) Motif 2 GCCGGGG Motif 2 GTCGGGG 0% [T/G]G[T/A]GGGG (67.64) [T/G]G[T/A]GGGG (67.64)

ESS decamers from Wang et al. No Silencer motif found with this matrice

Fas-ESS hexamers No difference between mutant and reference sequence was found with this matrice.

PESS Octamers from Zhang & Chasin www.umd.be/HSF/4DACTION/input_SSF

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Human Splicing Finder - Version 3.1

No difference between mutant and reference sequence was found with this matrice.

IIEs from Zhang et al. Sequence Position cDNA Position 205

105

209 210

109 110

Silencer motif Silencer motif Variation reference sequence mutant sequence GCCTGT New Site GCCGGG TCGGGG

Site broken New Site

hnRNP motifs - Experimental No difference between mutant and reference sequence was found with this matrice.

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www.umd.be/HSF/4DACTION/input_SSF

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