RnoINT0102215 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3917778-3918511:-
Coord C1 exon
chr3:3918327-3918511
Coord A exon
chr3:3917911-3918326
Coord C2 exon
chr3:3917778-3917910
Length
416 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGG
5' ss Score
5.28
3' ss Seq
GACCTATGCCATTTCTACAGTGT
3' ss Score
6.11
Exon sequences
Seq C1 exon
GCATCGATGTCACTCTCCTATGCCAGCACGGAGGGCTCTGTGTGGATGAGGAAGACAAGCATTACTGCCACTGCCAGGCAGGATACACGGGCAGCTACTGTGAGGACGAGGTGGACGAGTGCTCACCTAATCCCTGCCAGAACGGAGCCACCTGCACTGACTATCTCGGTGGCTTTTCCTGCAAG
Seq A exon
GTGTGGGCCGTCCTGGGGTGGAGGAAGGTGTCGGTGTGAGTGTTGCTAAAGGAGGGCAAGGCTAGGACATAGTGTATCGTAGCAGACTGAGCCATGTTAGAGCCAAGTGTCCCGTATCTGCTCAGGATCCAGTCACATGACAGATGTGCTGGGGGAGGAAAAACATGCCAGGCAGTGCTTAGGGTATCTCTTCCCTCTGGTTTCATGGTATCTGACACCTGGTCCAAGTCCTCACCCCCGGGGAGCCAGGTGTTGTCCCCTCCCCACCTTGGACACTTACTTCAACTTACTGAGGTCCTACCTGGGGTCTGCTGGGTGGAGCTCCCACTTGAGGGCTGACAGGATATGGCTGCATGGCAAGTGGGGGACATGATACCACAATCCCAGCTAAGCTGTGACCTATGCCATTTCTACAG
Seq C2 exon
TGTGTGGCTGGGTACCATGGCTCTAACTGCTCTGAGGAGATCAACGAGTGCCTATCCCAACCCTGCCAGAATGGGGGTACCTGCATTGATCTGACCAACACCTACAAGTGCTCCTGCCCCAGGGGCACACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:21
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=WD(100=48.4),PF0000822=EGF=PU(67.7=33.9)
A:
NA
C2:
PF0000822=EGF=PD(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
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:
GCATCGATGTCACTCTCCTATGC
R:
GCAGGAGCACTTGTAGGTGTT
Band lengths:
302-718
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]