RnoINT0102216 @ rn6
Intron Retention
Gene
ENSRNOG00000019322 | Notch1
Description
notch 1 [Source:RGD Symbol;Acc:3187]
Coordinates
chr3:3917273-3917910:-
Coord C1 exon
chr3:3917778-3917910
Coord A exon
chr3:3917531-3917777
Coord C2 exon
chr3:3917273-3917530
Length
247 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
TGTCTGTTGTCACTCTGCAGGTG
3' ss Score
11.31
Exon sequences
Seq C1 exon
TGTGTGGCTGGGTACCATGGCTCTAACTGCTCTGAGGAGATCAACGAGTGCCTATCCCAACCCTGCCAGAATGGGGGTACCTGCATTGATCTGACCAACACCTACAAGTGCTCCTGCCCCAGGGGCACACAGG
Seq A exon
GTAAGGGTGGGGACCTGGGTGGGGACCTGGGTTTCATGGGCAGGATCCAGCCAGAGATCACTCAGTCTTGTCTTGTGAGGCCAAGGTGATTCAGAGCTGACCACGGGACAGGGATCTTAGTGGGAAGATGGGCCCCAAAAGCCCTGTGCTCCCTTCCCTTGGTCCCAGTTCCTGATTGGTTGCTGGACTGGGCCACACAGGACAGTACAGCCAGTATCTTCTGATGGTGTCTGTTGTCACTCTGCAG
Seq C2 exon
GTGTACACTGTGAGATCAACGTCGATGACTGCCATCCTCCCCTAGACCCTGCTTCCCGAAGCCCCAAATGCTTCAATAATGGCACCTGCGTGGACCAGGTGGGTGGCTATACCTGCACCTGCCCGCCAGGCTTCGTCGGGGAGCGGTGCGAGGGCGATGTCAATGAGTGTCTCTCCAACCCCTGTGACCCACGTGGCACCCAGAACTGCGTGCAGCGTGTTAATGACTTCCACTGCGAGTGCCGGGCTGGCCACACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019322:ENSRNOT00000026212:22
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(25.8=17.8),PF0000822=EGF=PU(90.3=62.2)
A:
NA
C2:
PF0000822=EGF=PD(6.5=2.3),PF0000822=EGF=WD(100=44.8)
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:
TGGCTCTAACTGCTCTGAGGA
R:
CAGGGGTTGGAGAGACACTCA
Band lengths:
300-547
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]