MmuINT0109732 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26476348-26477139:-
Coord C1 exon
chr2:26476947-26477139
Coord A exon
chr2:26476494-26476946
Coord C2 exon
chr2:26476348-26476493
Length
453 bp
Sequences
Splice sites
5' ss Seq
TGGGTATGG
5' ss Score
6.23
3' ss Seq
CAGCTCAGGCCTCTCCGTAGGTA
3' ss Score
3.04
Exon sequences
Seq C1 exon
GAAGCATGTGTAACGTCAACATTGACGAATGTGCGGGCAGCCCCTGCCACAACGGGGGCACTTGTGAGGATGGCATCGCGGGCTTCACTTGCCGCTGCCCCGAGGGCTACCATGACCCCACGTGCCTGTCCGAGGTCAACGAGTGCAACAGTAACCCCTGCATCCACGGAGCTTGCCGGGATGGCCTCAATGG
Seq A exon
GTATGGCAGACTGACCTGGGAGGGACTAGCTGTAGCCTTGGGCAGACACAGGCTGGGTGAATGGGTGCTCCTGTGAGACCAGTGATCTGAGGTCAGCCCCTAGTGTCTTCCCAGCATCCCTGGGCTGTATCCTCATTGGCTAGCATCAGCTCAGGATATAGACTCTAAGCACACTGTGGCTGCTGAAACAGTTGTCTGATACTGTGGTGACAGCAGCCCTTTGTCAGTGTGTGGGGGACGAGGAGATTACTAAGGTCTCCGTTAAAACTATTAAAGTTTTATACAGAGGGTCAGCATTGTCAAGGTGGCATTGTTCCAGTCTGGAACCCTTGCACGGTCTTGGGCCAGGTGGGTACCTCCAGCCCAGTGGATGATGTGGCCTTGTCCTCAGACTGGAACTGTAGTTTAGCAGGAGAGCTCTGAGCCCAGGCTACAGCTCAGGCCTCTCCGTAG
Seq C2 exon
GTACAAGTGTGACTGTGCCCCTGGGTGGAGTGGAACAAACTGTGACATCAACAACAACGAGTGTGAGTCCAACCCTTGTGTCAACGGTGGCACCTGCAAGGACATGACCAGTGGCTACGTATGCACCTGCCGAGAAGGCTTCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:13
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=0.388
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(3.4=1.5),PF0000822=EGF=WD(100=58.5),PF0000822=EGF=PU(53.3=24.6)
A:
NA
C2:
PF0000822=EGF=PD(43.3=26.0),PF0000822=EGF=PU(90.3=56.0)
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:
AGCATGTGTAACGTCAACATTGA
R:
TTCTCGGCAGGTGCATACGTA
Band lengths:
327-780
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