MmuINT0109750 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26484268-26485449:-
Coord C1 exon
chr2:26485187-26485449
Coord A exon
chr2:26484607-26485186
Coord C2 exon
chr2:26484268-26484606
Length
580 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CCCTCTTCTCTGCCTCCCAGGAA
3' ss Score
10.89
Exon sequences
Seq C1 exon
CTGCAGCGGAGCCTTTGTGGGCCAACGATGCCAGGACTCCAATCCTTGCCTCAGCACACCGTGTAAGAATGCTGGAACGTGCCACGTTGTGGACCATGGTGGCACTGTGGATTATGCCTGCAGCTGTCCCCTGGGTTTCTCTGGGCCCCTCTGCCTGACACCTCTGGACAACGCCTGCCTGGCCAACCCCTGCCGCAATGGGGGCACCTGTGACCTGCTCACTCTCACAGAGTACAAGTGCCGCTGCCCACCAGGGTGGTCAG
Seq A exon
GTAAGGGCTATAGGAGGTTGTGAACTTCACGGTTGGGACCCTTAGGCCTGGGCCCAAGGACCCTATCTTTGTTGACTTGACATACTCTGGTACACTAAACTTTATCCTCTCCTGGATCAGAGTTAAGCTGGGATCTACTATCCAGAAAAATCTTGGGGATTCCTTGGGAACTCTGGTCCTTTTCAACCCCAAACTATCTGATTTTTGGCTGCCCTGTTCCAGGACCCCAACCTCTCACTGTTTCTGTGCGTAAAGAATGAGTCCTCATGTAGCCCGGGTCTTACCATCTCCTTGTCAGGGTGCCTCAGGTTTCCATTGCTTCTCTATGTGGGGTCCAGGAGACAGCTAGGTACAAATTTTAGACTGCCATTCCTACTTTCTGTCCTTGAGCAGTCACTTAGTCTCTTATGACTTACAGTCCTCTGTATGCAGAAAGATGGCCACATTCTGCAACAGATACTGAGCATCATGAAGATAACACTTTAGATCTATCCCTGGTTGGTACCTACATGATGTCCAAATCTGCCCTGGGTTCACAGGGAGGCCCTGGCAACAGCTGACCCTCTTCTCTGCCTCCCAG
Seq C2 exon
GAAAATCATGTCAGCAGGCTGACCCCTGTGCCTCCAACCCCTGTGCCAATGGTGGCCAGTGCCTGCCCTTTGAGTCTTCATACATCTGTCGCTGCCCGCCTGGCTTCCATGGCCCCACCTGCAGGCAAGATGTTAATGAGTGCAGCCAGAACCCTGGGCTGTGCCGCCATGGAGGCACCTGCCACAATGAGATCGGCTCCTATCGCTGTGCCTGCCGTGCCACCCATACTGGTCCCCACTGTGAACTGCCCTATGTGCCCTGCAGCCCCTCACCCTGCCAGAATGGAGGCACCTGCCGTCCTACAGGGGACACCACCCACGAGTGTGCCTGCTTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:3
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=39.3),PF0000822=EGF=PU(90.6=32.6)
A:
NA
C2:
PF0000822=EGF=PD(6.2=1.8),PF0000822=EGF=WD(100=27.2),PF0764510=EGF_CA=WD(100=34.2),PF0000822=EGF=PU(81.2=22.8)
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:
TGTGGATTATGCCTGCAGCTG
R:
CCGATCTCATTGTGGCAGGTG
Band lengths:
354-934
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