MmuINT0109751 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26463710-26464971:-
Coord C1 exon
chr2:26464806-26464971
Coord A exon
chr2:26464006-26464805
Coord C2 exon
chr2:26463710-26464005
Length
800 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TGTTTCTGTCCTCTCTGCAGATG
3' ss Score
13
Exon sequences
Seq C1 exon
TTTGAGGAGCCAGTAGTTCTCCCTGACCTGAGTGATCAGACTGACCACAGGCAGTGGACCCAGCAGCACCTGGACGCTGCTGACCTGCGCATGTCTGCCATGGCCCCAACACCGCCTCAGGGGGAGGTGGATGCTGACTGCATGGATGTCAATGTTCGAGGACCAG
Seq A exon
GTAAGGCCACTGGAGACACATGCACACATTCCCTAGCATAGACTTAAGAGGCCAGTAGGACTTGAGGAGGGCTGGGTCACTGAAGGGCTCTGCCAGAGCAGCATCCTGCCCTGAGCTGATCGTCTGGCTCCTCCTGCCCACACAGTATACTTTTTCATGAAATGCTGCTTTGCAATAGTCAAAGTGTTAATTTTTTTTTTTTTTTTTGGTCTCAGTTTTTAGTATGCTGGGATTATAGGTGTGTCCCCATGCCCAGCTAAAGTGTTGACTTTTAAAATTATATGCATATAGGTGTATATAAAGATATCTTTTATTTTATGTGCATGGTTCTGCCTACATATATGTCTGTGTAGTGTTTAGATACCCAGTGCCTGTGGGGAGCCTGAAGAGGCCATTGGATCCCCTGAAGCTGCAGTTACAGATGGTAGTGAGCAGCTATATGGGTACTAGGGATTGAACTCAGGTCCTCTGGAAGAGAAGCCAGTGCTCTTAACCACTGAGCCATCTCTGCAGCCCTTATTTTATGTTTTAAAGCATTTCTTCATTTGAGTGTAAGGGGCACACATGTGCCATAGTACACACGTGGAGGTCAGAGGACTACTTGTATGAGTGTGGGTTCTCTCCTTCTACCATGTTGGTCCCAGAGTGCCTTCCAGGGAGGCAGCACTGCATCCCTGGGGACTTCATCCGGGGTCCCTTAAACTGCAGGACTGCCTGCCAGGGCTATGGTTGAATGTTGACCCTCCCTGAGGCTGACACCATCCTTCCCACACCTACCCTTGTTTCTGTCCTCTCTGCAG
Seq C2 exon
ATGGCTTCACACCCCTCATGATTGCCTCCTGCAGTGGAGGGGGCCTTGAGACAGGCAACAGTGAAGAAGAAGAAGATGCACCTGCTGTCATCTCTGACTTCATCTACCAGGGCGCCAGCTTGCACAACCAGACAGACCGCACCGGGGAGACCGCCTTGCACTTGGCTGCCCGATACTCTCGTTCAGATGCTGCAAAGCGCTTGCTGGAGGCCAGTGCAGATGCCAACATCCAGGACAACATGGGCCGTACTCCGTTACATGCAGCAGTTTCTGCAGATGCTCAGGGTGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.786 A=NA C2=0.424
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF127962=Ank_2=PU(83.5=76.8)
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:
GCCAGTAGTTCTCCCTGACCT
R:
GCTTTGCAGCATCTGAACGAG
Band lengths:
356-1156
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