MmuINT0109731 @ mm9
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
Notch gene homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26332467-26333510:-
Coord C1 exon
chr2:26333400-26333510
Coord A exon
chr2:26332660-26333399
Coord C2 exon
chr2:26332467-26332659
Length
740 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GAGCCCCTTCCCACCCACAGGAA
3' ss Score
8.82
Exon sequences
Seq C1 exon
GGCCCAACTGTGAGATCAACCTGGATGACTGCGCCAGCAACCCCTGTGACTCTGGCACCTGTCTGGACAAGATTGATGGCTACGAATGTGCCTGTGAACCAGGCTACACAG
Seq A exon
GTGAGTGGCTGAAGGCAGAGGTCAGGGTCATCCCTAGAGTCTGGGAGGGACTGTGGGGCTAGCCAGGGTCCAAGGGCTGGATGTCACAAGCTGGGTGTCAACTACCCAGATCTTGATCTGCCAACCAGTAGAGGTATCTATCATAAAGACTGGGTGGCCTCCATATGCCTCCTTTCCCCTGTCAGTGTCAGCCCTGGCCATGCCAGACTTAAAGCCCCAGTAGCCTGAAGTGGGGTGGCCAGAGCTCCGAGGCCAGGCTTTTGGATATGTGTTTAGATCTGATAAAATCCTTAGTTTCTCTGAGCACCGAGGACATTGTCCACCAGAGGATAGAAGAGGATGGGTGGTCTCAGGCTGAGGTAAAGCTGGGCTGCAGAGTGACTCAGTTGGTAAGGTGTTGACCTAGCATGTGTAAACCCTGGGTTCAGTCCTCCTGCCATGTTAACCAGATGCAGTGGCATGCATACGTTGTAACCCTAGCACTCTGACATTGGAAGCGAGAGGATCAGAAGTTTAGGTCATTCTCAGCTACATGTGAGTTTGTGGCCAGACTGGATCACATGAGGCTCAGAAGCTACTGGCACTACGGTCATGTAACTCATCGCTACATAAGGCACTTTACTATCGCTCAAAGTTTCATAGATTAGCACAAGGGGAAACTTAGACCCAGCTAGGTCTAGCTCTAGGAGGGGTAGGCTCTGGGTGGCAGGCTTGGAATCTGAGCCCCTTCCCACCCACAG
Seq C2 exon
GAAGCATGTGTAACGTCAACATTGACGAATGTGCGGGCAGCCCCTGCCACAACGGGGGCACTTGTGAGGATGGCATCGCGGGCTTCACTTGCCGCTGCCCCGAGGGCTACCATGACCCCACGTGCCTGTCCGAGGTCAACGAGTGCAACAGTAACCCCTGCATCCACGGAGCTTGCCGGGATGGCCTCAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923-Notch1:NM_008714:12
Average complexity
IR-S
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(6.5=5.3),PF0000822=EGF=PU(93.1=71.1)
A:
NA
C2:
PF0000822=EGF=PD(3.4=1.5),PF0000822=EGF=WD(100=58.5),PF0000822=EGF=PU(53.3=24.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCCAACTGTGAGATCAACC
R:
CCATTGAGGCCATCCCGG
Band lengths:
304-1044
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: