RnoINT0102204 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3925358-3925781:-
Coord C1 exon
chr3:3925548-3925781
Coord A exon
chr3:3925469-3925547
Coord C2 exon
chr3:3925358-3925468
Length
79 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACT
5' ss Score
6.6
3' ss Seq
ACATGTCACGCTGCCCCTAGGAC
3' ss Score
9.07
Exon sequences
Seq C1 exon
GTTACACGGGGACCCACTGCGAGGTGGACATTGACGAGTGTGACCCTGACCCCTGTCACTATGGTTTGTGCAAGGATGGTGTGGCCACCTTTACCTGCCTCTGCCAGCCAGGCTACACAGGCCATCACTGTGAGACCAACATTAATGAGTGTCACAGCCAGCCGTGCCGCCATGGCGGCACCTGCCAGGACCGTGACAACTACTACCTCTGCTTATGCCTCAAGGGGACCACAG
Seq A exon
GTGACTGGCCAGAGCTGGCAGTGGGTGGAAAAGGGTGAGGCTAGGCTTGGAGGCTGACCACATGTCACGCTGCCCCTAG
Seq C2 exon
GACCCAACTGTGAGATCAATCTGGATGACTGTGCGAGCAACCCCTGTGACTCTGGCACGTGTCTGGACAAGATCGATGGCTACGAGTGTGCGTGCGAGCCAGGCTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:11
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(16.1=6.3),PF0000822=EGF=WD(100=38.0),PF0000822=EGF=PU(90.3=35.4)
A:
NA
C2:
PF0000822=EGF=PD(6.5=5.3),PF0000822=EGF=PU(93.1=71.1)
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:
TAATGAGTGTCACAGCCAGCC
R:
GCACACTCGTAGCCATCGATC
Band lengths:
183-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]