DreEX0051154 @ danRer10
Exon Skipping
Gene
ENSDARG00000052139 | notch3
Description
notch 3 [Source:ZFIN;Acc:ZDB-GENE-000329-5]
Coordinates
chr3:53283328-53284139:-
Coord C1 exon
chr3:53283906-53284139
Coord A exon
chr3:53283664-53283816
Coord C2 exon
chr3:53283328-53283556
Length
153 bp
Sequences
Splice sites
3' ss Seq
AAATGCCTTCCAAACCACAGGCC
3' ss Score
4.8
5' ss Seq
CTAGTGAGT
5' ss Score
7.43
Exon sequences
Seq C1 exon
GTAACTTATGTCAGGTGAACATCAATGAGTGTGCCTCCAGCCCCTGTCTAAATCAGGGCACCTGTGTGGATGGAGTTGCTAGTTTCACCTGTCTCTGTGAACCACCTTATAGTGGACCCACTTGTGCAGAACTGCTCACACCTTGCTCTCCCAACCCCTGTGCCAACCATGCTTCCTGCGTGCACACACCTGACTACCTAGGCTACCAGTGTAACTGCCAACCAGGCTGGCAAG
Seq A exon
GCCATTTGTGCAACAATGACATCAATGAATGCACCTCTAACCCGTGTAAGAACCGTGGGACTTGCACAAATACCCTTGGAGGCTATGTGTGCTCCTGCCGTGCTGGCTACACTGGACCCAATTGTGAAACTGATATCAATGACTGCTCGCCTA
Seq C2 exon
ACCCCTGTCTGAATGGTGGATCCTGTACTGATGGAGTAAACTCATTCCGCTGCAGTTGTCTGCCAGGCTTTACGGGGGCACGCTGTGCGACTGAGCTGAATGAATGTCAGAGTGTACCCTGCAAGAATGGTGGTACCTGCACTGATTATGTCAACAGCTATACTTGTACCTGTAAACCAGGCTTCACAGGCCTTCTGTGTGAGACCAACGTACCAGACTGCACTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052139_MULTIEX1-4/19=3-5
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(3.3=1.3),PF0000822=EGF=WD(100=39.2),PF0000822=EGF=PU(90.9=38.0)
A:
PF0000822=EGF=PD(6.1=3.8),PF0000822=EGF=WD(100=59.6),PF0000822=EGF=PU(9.7=5.8)
C2:
PF0000822=EGF=PD(87.1=35.1),PF0000822=EGF=WD(100=40.3),PF0000822=EGF=PU(9.7=3.9)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAACTGCTCACACCTTGCT
R:
GGTACCACCATTCTTGCAGGG
Band lengths:
245-398
Functional annotations
There are 1 annotated functions for this event
PMID: 30674940
This study does not directly assess the function of the events. It reports that NOTCH3 has differential exon 16 depletion (-exon 16) between differentiation associated BAGS subtypes. Predicted vincristine resistant patients of the GCB subclass had significantly downregulated NOTCH3 -exon 16 transcript expression and tended to display adverse overall survival for R-CHOP treated patients. Thus, this exon display prognostic and predictive biomarker potential in GCB DLBCL.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]