MmuINT0109741 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26470274-26471006:-
Coord C1 exon
chr2:26470822-26471006
Coord A exon
chr2:26470407-26470821
Coord C2 exon
chr2:26470274-26470406
Length
415 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGG
5' ss Score
5.28
3' ss Seq
GACCTGTGCCATTTCTACAGTGT
3' ss Score
7.22
Exon sequences
Seq C1 exon
GCATTGACGTCACTCTCCTGTGCCAGCATGGAGGGCTCTGTGTGGATGAGGGAGATAAACATTACTGCCACTGCCAGGCAGGCTACACGGGCAGCTACTGTGAGGACGAGGTGGACGAGTGCTCACCTAACCCCTGCCAGAATGGAGCTACCTGCACTGACTATCTCGGCGGCTTTTCCTGCAAG
Seq A exon
GTGTGGGCCGTCATGGGGTGGCGGGGAGGGTATCAGCGTGAGTGTTGCTGCAGGGGAGGGCTTTTGACTGGGAGCTAGTGCATCATGGCAGACTGAGCACATACCTGTGCAGGATCCGGTCACATTACAGATGTGCTGAAGGAGGAGAACTATGCCAAGCAGTGGCTTAGGGCACCCCTTTCCTATATGGTTTCATGGTACCTAATACCTGCTCCAAGACCTCATCCCTGGGGGACCAGGTGTTGCCCCACACACACACACCTTGGACACTTATTTTAACTTACTGGGGTCTACTGGGTGGAGCCCTCGCTGCAGGGTGGGACAGTGTAGTCTAACTGGGTATATGGCCTGCATGGCAAGTGGAGGACATGATACCACAACCCCAGCTAAGCTGTGACCTGTGCCATTTCTACAG
Seq C2 exon
TGTGTGGCTGGCTACCATGGGTCTAACTGCTCCGAGGAGATCAACGAGTGCCTGTCCCAGCCCTGCCAGAATGGGGGTACCTGCATTGATCTGACCAACTCCTACAAGTGTTCCTGCCCCCGGGGGACACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:21
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGACGTCACTCTCCTGTGC
R:
GGGCAGGAACACTTGTAGGAG
Band lengths:
302-717
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