MmuINT0109745 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26467629-26468803:-
Coord C1 exon
chr2:26468232-26468803
Coord A exon
chr2:26468031-26468231
Coord C2 exon
chr2:26467629-26468030
Length
201 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TGCATCCTATACCTCCTCAGCCC
3' ss Score
5.77
Exon sequences
Seq C1 exon
GGCTTCGAGGGTGCCACATGTGAGAATGATGCCCGCACTTGTGGCAGCTTACGCTGCCTCAACGGTGGTACATGCATCTCGGGCCCACGTAGTCCCACCTGCCTATGCCTGGGATCCTTCACCGGCCCTGAGTGCCAGTTCCCAGCCAGCAGCCCCTGTGTGGGTAGCAACCCCTGCTACAATCAGGGCACCTGTGAGCCCACATCCGAGAACCCTTTCTACCGCTGTCTATGCCCTGCCAAATTCAACGGGCTACTGTGCCACATCCTGGACTACAGCTTCACAGGTGGCGCTGGGCGCGACATTCCCCCACCGCAGATTGAGGAGGCCTGTGAGCTGCCTGAGTGCCAGGTGGATGCAGGCAATAAGGTCTGCAACCTGCAGTGTAATAATCACGCATGTGGCTGGGATGGTGGCGACTGCTCCCTCAACTTCAATGACCCCTGGAAGAACTGCACGCAGTCTCTACAGTGCTGGAAGTATTTTAGCGACGGCCACTGTGACAGCCAGTGCAACTCGGCCGGCTGCCTCTTTGATGGCTTCGACTGCCAGCTCACCGAGGGACAGTGCAA
Seq A exon
GTAAGTAAGGCTGAGTTTCTTTAGAGTCCCAGGGCTCAGGATGCTACGGGAGGACCTAACCAAACACCAGGCTCCTGAAGCCAATGTCTATCCCTGCCCATTGCGAGTCGCCAAGCACATTTCCCAGATCTGGCCTATTCAAGGTATGGGTTTGAGGTCCACAGGCTGGGATGGGACTGAGTGCATCCTATACCTCCTCAG
Seq C2 exon
CCCCCTGTATGACCAGTACTGCAAGGACCACTTCAGTGATGGCCACTGCGACCAGGGCTGTAACAGTGCCGAATGTGAGTGGGATGGCCTAGACTGTGCTGAGCATGTACCCGAGCGGCTGGCAGCCGGCACCCTGGTGCTGGTGGTGCTGCTTCCACCCGACCAGCTACGGAACAACTCCTTCCACTTTCTGCGGGAGCTCAGCCACGTGCTGCACACCAACGTGGTCTTCAAGCGTGATGCGCAAGGCCAGCAGATGATCTTCCCGTACTATGGCCACGAGGAAGAGCTGCGCAAGCACCCAATCAAGCGCTCTACAGTGGGTTGGGCCACCTCTTCACTGCTTCCTGGTACCAGTGGTGGGCGCCAGCGCAGGGAGCTGGACCCCATGGACATCCGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:25
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=0.030
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(14.7=2.6),PF0000822=EGF=WD(100=15.7),PF0000822=EGF=WD(100=16.8),PF0006612=Notch=WD(100=19.4),PF0006612=Notch=WD(100=19.9),PF0006612=Notch=PU(12.8=2.6)
A:
NA
C2:
PF0006612=Notch=PD(84.6=24.4),PF068168=NOD=WD(100=42.2),PF076847=NODP=PU(4.8=2.2)
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:
CACGCAGTCTCTACAGTGCTG
R:
GAGTTGTTCCGTAGCTGGTCG
Band lengths:
297-498
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