MmuINT0109752 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26462342-26464005:-
Coord C1 exon
chr2:26463710-26464005
Coord A exon
chr2:26462490-26463709
Coord C2 exon
chr2:26462342-26462489
Length
1220 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGC
5' ss Score
10.12
3' ss Seq
AACCCATCCCTGCCTTCCAGATC
3' ss Score
9.2
Exon sequences
Seq C1 exon
ATGGCTTCACACCCCTCATGATTGCCTCCTGCAGTGGAGGGGGCCTTGAGACAGGCAACAGTGAAGAAGAAGAAGATGCACCTGCTGTCATCTCTGACTTCATCTACCAGGGCGCCAGCTTGCACAACCAGACAGACCGCACCGGGGAGACCGCCTTGCACTTGGCTGCCCGATACTCTCGTTCAGATGCTGCAAAGCGCTTGCTGGAGGCCAGTGCAGATGCCAACATCCAGGACAACATGGGCCGTACTCCGTTACATGCAGCAGTTTCTGCAGATGCTCAGGGTGTCTTCCAG
Seq A exon
GTACGCAGCACTGCATCCTTGGAGCCAGTGACCTCATCAGGTCTGACTGGCATGGACCCTGCAATCTCTAATTCCAAGTGTGACTGGGCAGGGAAACTTGGCACCTCCACACTGCATTTTGAAGGAAGTCCAGGTACAAAGGGCATCAAGTCCCACCTGTGTTCTCTGAGCAGGCTGGCTGAAGGTGGTCTTGCGGAACCTACAGGGTGAGGCAGGGCCTCCTTACTCTCAGTAAAACCCTCCCAATCTCAAGGCTATGGCCTTGACTTGAGGTCTCCACCTCCGTGCTAAAACCTTTGCAGACTAACCCTACCCCATTCAGCTGTGGCTGCAGGCATAGCCCATGGCGGCAGAAAGAGAGCTTTAGAGGCTGCTGGTCCTGGCCTGCAAAGCTATCTCCTGGCTTTGCCTAGAAGCCTGGAGCCAGCCTGGGTGGATTTAAGGATTTAGCTGCCTGGGTCTGCAGGGACCAACCCTAGTAGTTGCTCCTGCATGTTGCCAGCCAGTGACCCCTGCTACCAGACCTGTCCTCTAGGCGGCCCTGGAGCAAACTCCAATGGGGAATAGACCAGGCATCAAAAAGCTTGTCATTTAATCATTTCTTAACTTGAACCACACTTTGTCGGTCTGTAGAAGAAATTAAACAAGACAGGGCAATGTACACCTTTTATCCCAGCACTCTAGAATCTGAGAGGATTGTGAGCATGAGGCTAGCCTGGTCTTCATAGAAAGACCCTATTTCAAAATAGCAAAGAGAGGTTGAGACCAGCCACAGGTTATGTTGACTGCCTGGTGTACAGCTCTCCACATGGCCTGCCTTGCTTGCATAGACAGATGTGTGTACGTTTTGTAGGAATCCAGGCAGTGCTGTGAATCCTTACCCAGGTCACCAACCCACTCCCTCCTCTCACCTTAACAGTTCCAAGTACGGCTATGGGCCATGAGCGGGATTCCTAGCCTGGTTACTCTCCCCTCTCTCCCCCATGCTATGCAGTTTGATTTCCTCAACCTGGAGGTAGTTCTGGCAACCATAACCAAAAGATGAGGTCCCAGTAGATCCCCCACTGTCACTAGGGACTGGGTAAGAGCCCCAGCTCTTGCACATGGAATGTAGCTCCTGCCTTCCTCAGGGGCTCAGCTGAGCCCAGTCCAGGCATTGGTTTCTGGAGATACAGGCTTGCATTTAGATCACCCTGCCTGAACCCATCCCTGCCTTCCAG
Seq C2 exon
ATCCTGCTCCGGAACAGGGCCACAGATCTGGATGCCCGAATGCATGATGGCACAACTCCACTGATCCTGGCTGCGCGCCTGGCCGTGGAGGGCATGCTGGAGGACCTCATCAACTCACATGCTGACGTCAATGCCGTGGATGACCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.424 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(83.5=76.8)
A:
NA
C2:
PF127962=Ank_2=PD(14.3=26.0),PF127962=Ank_2=PU(31.2=58.0)
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:
CACACCCCTCATGATTGCCTC
R:
CAGGATCAGTGGAGTTGTGCC
Band lengths:
358-1578
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