RnoINT0102209 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3921118-3921672:-
Coord C1 exon
chr3:3921553-3921672
Coord A exon
chr3:3921271-3921552
Coord C2 exon
chr3:3921118-3921270
Length
282 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
AATGAGTTTTGTCCTCACAGGTC
3' ss Score
8.44
Exon sequences
Seq C1 exon
GAGCCACATGTGAGGTGGTGTTGGCCCCATGTGCCACCAGCCCCTGCAAAAACAGTGGGGTATGCAAGGAGTCTGAGGACTATGAGAGCTTTTCCTGTGTCTGTCCCACAGGCTGGCAAG
Seq A exon
GTGAGGCTTGCCTGGTCCCACCAGACTGGGACAAGAATGGTGGGTGGGAAGTCAGGGGCCCCAGCTTGGCTGTGGGATGGTCTCCAGAGATGAGCCCATCCGTGCTGAACCACCAGCTCTGGGAAGCCCAGGAGCAGAAGAGGACCTTGGATGGCCTTTCCCATCCTGACTCCATAGCCTCTGTTCTCCAGAGGTCAGGGGAGAAGCCCTGGGGATAGCCGGACCAGCTAGCACAGAGGCTCAGAGGCTGGGGAGGTAACCAAATGAGTTTTGTCCTCACAG
Seq C2 exon
GTCAAACCTGCGAGATCGACATCAATGAGTGTGTGAAAAGCCCGTGTCGCCATGGTGCCTCTTGCCAGAACACCAATGGCAGCTACCGCTGCCTCTGCCAGGCTGGCTACACGGGTCGCAACTGCGAGAGTGACATCGATGACTGCCGACCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:16
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(6.5=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0764510=EGF_CA=WD(100=73.1),PF0000822=EGF=PU(9.7=5.8)
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:
CACATGTGAGGTGGTGTTGGC
R:
TGGGTCGGCAGTCATCGAT
Band lengths:
269-551
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]