MmuINT0109753 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26462148-26462489:-
Coord C1 exon
chr2:26462342-26462489
Coord A exon
chr2:26462246-26462341
Coord C2 exon
chr2:26462148-26462245
Length
96 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGC
5' ss Score
7.72
3' ss Seq
TCTCTTTGCTTCCTTTCCAGGCA
3' ss Score
10.94
Exon sequences
Seq C1 exon
ATCCTGCTCCGGAACAGGGCCACAGATCTGGATGCCCGAATGCATGATGGCACAACTCCACTGATCCTGGCTGCGCGCCTGGCCGTGGAGGGCATGCTGGAGGACCTCATCAACTCACATGCTGACGTCAATGCCGTGGATGACCTAG
Seq A exon
GTAGGCCCGAGCTACAGCCCAGCTACCGAGGACATCAGCCAGTGCCTGGTCTGCTCAGCCCCAACCCACTCTCTCCTCTCTTTGCTTCCTTTCCAG
Seq C2 exon
GCAAGTCGGCTTTGCATTGGGCGGCCGCGGTGAACAATGTGGATGCTGCTGTTGTGCTCCTGAAGAACGGAGCCAACAAGGACATGCAGAACAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.212
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PD(14.3=26.0),PF127962=Ank_2=PU(31.2=58.0)
A:
NA
C2:
PF127962=Ank_2=FE(34.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAACTCCACTGATCCTGGC
R:
GTTGGCTCCGTTCTTCAGGAG
Band lengths:
175-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types