MmuINT0109816 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32158419-32158982:-
Coord C1 exon
chr17:32158840-32158982
Coord A exon
chr17:32158758-32158839
Coord C2 exon
chr17:32158419-32158757
Length
82 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
CCCTCTCCTGGTTCTTCCAGGCC
3' ss Score
10.65
Exon sequences
Seq C1 exon
GTGCCTGCCAGGCTGGGTGGGTGAGCGGTGCCAGCTGGAAGACCCTTGCCACTCAGGCCCTTGTGCTGGCCGAGGCGTTTGCCAGAGTTCAGTGGTGGCGGGCACCGCCCGATTCTCCTGTCGTTGTCTCCGTGGCTTCCAAG
Seq A exon
GTGAAGGGGTGTGTCTGGACGGGAACCCTTGGTAGGCGAGAATGTAGTCAGACCCAAGCTCACCCTCTCCTGGTTCTTCCAG
Seq C2 exon
GCCCAGACTGCTCCCAGCCAGACCCCTGCGTCAGCAGGCCCTGTGTTCATGGTGCCCCCTGCTCAGTGGGGCCGGATGGCCGATTTGCCTGTGCCTGCCCACCTGGCTACCAGGGTCAAAGCTGCCAAAGTGACATAGATGAGTGCCGATCTGGTACAACTTGCCGTCATGGTGGTACCTGTCTCAATACACCTGGATCCTTCCGCTGCCAGTGTCCTCTTGGTTATACAGGGCTGCTGTGTGAGAACCCCGTAGTGCCCTGTGCCCCTTCCCCGTGTCGTAATGGTGGCACCTGTAGGCAGAGCAGTGATGTCACATATGACTGTGCTTGCCTTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(26.5=18.4),PF0000822=EGF=PU(91.4=65.3)
A:
NA
C2:
PF0000822=EGF=PD(5.7=1.8),PF0000822=EGF=WD(100=33.3),PF0764510=EGF_CA=WD(100=38.6),PF0000822=EGF=PU(81.2=22.8)
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:
CCCGATTCTCCTGTCGTTGTC
R:
TCACTTTGGCAGCTTTGACCC
Band lengths:
169-251
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