MmuINT0109796 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32153525-32153986:-
Coord C1 exon
chr17:32153753-32153986
Coord A exon
chr17:32153636-32153752
Coord C2 exon
chr17:32153525-32153635
Length
117 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
TACTTCTTCCCTCCCTGTAGGTG
3' ss Score
11.59
Exon sequences
Seq C1 exon
GCTTTGAGGGCACTTTGTGTGAGCGAAACGTGGATGACTGCTCTCCGGATCCCTGCCACCACGGGCGCTGTGTCGATGGCATTGCTAGCTTCTCGTGTGCTTGTGCCCCAGGCTATACGGGCATACGCTGTGAGAGCCAGGTGGATGAGTGCCGCAGCCAGCCCTGTCGATATGGGGGCAAATGTCTAGACTTGGTGGACAAGTACCTCTGCCGTTGTCCTCCCGGAACCACAG
Seq A exon
GTGGGGCCTGGGGCTGGGCTATAACAGTACGTGGGGGTGTGTGGGGGTCTGTGATGAATTTGTAACTGGTGCTTGACAATAGTAGGTACTCTTGCCATACTTCTTCCCTCCCTGTAG
Seq C2 exon
GTGTGAACTGTGAAGTCAACATTGATGACTGTGCCAGTAACCCCTGTACCTTTGGAGTTTGCCGTGATGGCATCAACCGTTATGACTGTGTCTGTCAGCCTGGATTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:11
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(90.0=71.1)
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:
GTGTCGATGGCATTGCTAGCT
R:
TAACGGTTGATGCCATCACGG
Band lengths:
247-364
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