RnoINT0102227 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3909760-3910102:-
Coord C1 exon
chr3:3909955-3910102
Coord A exon
chr3:3909858-3909954
Coord C2 exon
chr3:3909760-3909857
Length
97 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGC
5' ss Score
7.72
3' ss Seq
TCTCCTCGCTTCCTCTCCAGGCA
3' ss Score
11.05
Exon sequences
Seq C1 exon
ATCCTGCTCCGGAACAGAGCCACAGATCTGGATGCCCGAATGCATGATGGCACAACCCCTCTGATCCTGGCGGCACGCCTGGCCGTGGAAGGCATGCTAGAGGACCTCATCAACTCTCACGCTGATGTCAATGCTGTGGATGACCTAG
Seq A exon
GTAGGCCCAAGCTCCAGCCCAGCTCCTGAGGATGTCAGCCTAGCGCCTGATCCGCTCAGCCTTAAACTCCTCTCTCCTCTCCTCGCTTCCTCTCCAG
Seq C2 exon
GCAAGTCAGCTCTGCACTGGGCAGCCGCTGTGAACAATGTGGACGCTGCTGTTGTGCTCCTGAAGAACGGAGCCAACAAAGACATGCAGAACAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.212
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PD(10.6=26.0),PF0002325=Ank=WD(100=66.0)
A:
NA
C2:
PF127962=Ank_2=PU(31.1=84.8)
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:
CAGATCTGGATGCCCGAATGC
R:
AACAGCAGCGTCCACATTGTT
Band lengths:
179-276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]