RnoINT0102282 @ rn6
Intron Retention
Gene
ENSRNOG00000004346 | Notch3
Description
notch 3 [Source:RGD Symbol;Acc:620761]
Coordinates
chr7:14166216-14166672:-
Coord C1 exon
chr7:14166415-14166672
Coord A exon
chr7:14166335-14166414
Coord C2 exon
chr7:14166216-14166334
Length
80 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
TCCTGCATCTGTTTGTTCAGGGC
3' ss Score
7.58
Exon sequences
Seq C1 exon
GAGTTCTCTGTGAGATCAATGAGGATGACTGTGGCCCAGGCCCATCCTTGGACTCAGGCCTCCGGTGCCTACACAACGGCACCTGTGTGGACCTGGTGGGTGGCTTCCGCTGTAACTGTCCCCCAGGGTACACAGGTCTGCACTGTGAGGCGGACATCAATGAGTGCCGACCCGGCACCTGTCATGCAGCACATACCCGGGACTGCCTACAAGATCCAGGTGGGCACTTCCGCTGCATCTGTCTCCCTGGCTTCACAG
Seq A exon
GTGCGTATGATGGAGAGGCTGGCCAGGGCGCCGACGTGGTCCTACCGTTGCAGTTGACCCTCCTGCATCTGTTTGTTCAG
Seq C2 exon
GGCCTCGATGTCAGACTGCTCTGTTCCCCTGTGAGTCCCAACCGTGTCAGCATGGAGGCCAGTGCCGTCCCAGCCTAGGCCGTGGAGGTGGGCTGACCTTCACCTGTCACTGTGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004346:ENSRNOT00000037456:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(17.1=6.9),PF0000822=EGF=WD(100=43.7),PF126612=hEGF=PU(69.2=10.3)
A:
NA
C2:
PF126612=hEGF=PD(23.1=7.5),PF0000822=EGF=PU(80.6=72.5)
Main Inclusion 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:
ATACCCGGGACTGCCTACAAG
R:
CAGTGACAGGTGAAGGTCAGC
Band lengths:
178-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]