RnoINT0102290 @ rn6
Intron Retention
Gene
ENSRNOG00000004346 | Notch3
Description
notch 3 [Source:RGD Symbol;Acc:620761]
Coordinates
chr7:14181516-14182079:-
Coord C1 exon
chr7:14181937-14182079
Coord A exon
chr7:14181855-14181936
Coord C2 exon
chr7:14181516-14181854
Length
82 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAAA
5' ss Score
2.91
3' ss Seq
CCCTCTCCTGGTTCTTCCAGGCC
3' ss Score
10.65
Exon sequences
Seq C1 exon
GTGCCTGCCAGGCTGGGTGGGTGAGCGGTGCCAGCTGGAAGACCCTTGCCACTCTGGCCCCTGTGCCGGCCGAGGCGTTTGCCAGAGTTCAGTGGTGGCGGGCGTCGCCCGGTTCTCCTGTCGTTGTCTCCGTGGCTTCCGAG
Seq A exon
GTGAAAGGGTGGGCCTGGATGGGAACCCATGGTAGGCAAGGATGCGGTCAGTCCCAAGCTCACCCTCTCCTGGTTCTTCCAG
Seq C2 exon
GCCCAGACTGCTCCCTGCCAGACCCCTGCTTCAGCAGCCCCTGTGCTCACGGTGCCCCCTGCTCAGTTGGGTCGGATGGCCGATATGCCTGTGCCTGCCCACCTGGCTACCAGGGTCGCAACTGCCGAAGCGACATAGATGAGTGCCGAGCTGGTGCGTCTTGCCGTCACGGTGGTACCTGCATCAATACACCCGGATCCTACCACTGCCTGTGTCCACTTGGCTATACAGGGCTGCTGTGTGAAAACCCCATAGTGCCCTGCGCCCCTTCCCCATGCCGTAATGGTGGCACCTGTAGGCAGAGTAGTGATGTCACATATGACTGTGCTTGTCTTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004346:ENSRNOT00000037456:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(26.5=18.4)
A:
NA
C2:
PF0000822=EGF=WD(100=28.1),PF0764510=EGF_CA=WD(100=38.6),PF0000822=EGF=PU(81.2=22.8)
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:
TTCTCCTGTCGTTGTCTCCGT
R:
CTCGGCACTCATCTATGTCGC
Band lengths:
181-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]