BtaEX6037303 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000043971 | NOTCH3
Description
notch 3 [Source:HGNC Symbol;Acc:HGNC:7883]
Coordinates
chr7:8943621-8946435:+
Coord C1 exon
chr7:8943621-8943734
Coord A exon
chr7:8944686-8944841
Coord C2 exon
chr7:8946210-8946435
Length
156 bp
Sequences
Splice sites
3' ss Seq
ATTTCCCTCCCCACCCCCAGGCC
3' ss Score
10.6
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
Exon sequences
Seq C1 exon
GCCATCAGTGTGAGCTGCTGTCCCCCTGCACCCCGAATCCCTGTGAGCATGGGGGCTACTGTGAGTCTGCTCCTGGCCAGATGGCTGTCTGCTCCTGCACCCCTGGTTGGCAAG
Seq A exon
GCCCACGATGTCAGCAGGATGTGGATGAGTGTGCCAGCCCCTCACCCTGTGGTCCCCATGGTACCTGCACCAACCTGGCAGGGAGTTTCAGCTGTACCTGCCACGAGGGCTACAGTGGCCCTTCCTGTGATCAGGACATCGATGACTGTGACCCCA
Seq C2 exon
ACCCCTGCCTGAATGGTGGCTCATGTCAGGATGGGGTGGGCTCCTTTTCCTGCTCCTGCCTCCCTGGCTTTGCTGGTCCTCGCTGTGCCCGAGACGTGGACGAGTGTCTGAGCAGCCCCTGCGGCTCAGGCACCTGCACAGACCACGTGGCCTCCTTCACCTGCACCTGCCCACCGGGTTATAGCGGCTTCCACTGCGAGCAGGACCTCCCCGACTGCAGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000043971-'18-19,'18-16,19-19=AN
Average complexity
A_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(6.5=5.1),PF0000822=EGF=PU(90.6=74.4)
A:
PF0000822=EGF=PD(6.2=3.8),PF0764510=EGF_CA=WD(100=73.6),PF0000822=EGF=PU(9.7=5.7)
C2:
PF0000822=EGF=PD(87.1=35.5),PF0000822=EGF=WD(100=38.2),PF0000822=EGF=PU(9.7=3.9)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTACTGTGAGTCTGCTCCT
R:
CAGTGGAAGCCGCTATAACCC
Band lengths:
257-413
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]