MmuINT0109765 @ mm10
Intron Retention
Gene
ENSMUSG00000027878 | Notch2
Description
notch 2 [Source:MGI Symbol;Acc:MGI:97364]
Coordinates
chr3:98111550-98113155:+
Coord C1 exon
chr3:98111550-98111742
Coord A exon
chr3:98111743-98113009
Coord C2 exon
chr3:98113010-98113155
Length
1267 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
ACACCTCTCTCTTCTTGCAGCTA
3' ss Score
12.03
Exon sequences
Seq C1 exon
GCCAGAGGTGCAATATTGACATTGATGAGTGTGCCTCCAACCCCTGTCGCAAGGGTGCGACGTGCATCAATGATGTGAATGGTTTCCGGTGTATATGCCCCGAGGGACCGCATCATCCTAGCTGCTACTCACAGGTGAACGAGTGCCTGAGCAATCCCTGCATCCACGGAAACTGTACTGGAGGTCTCAGTGG
Seq A exon
GTGAGTAGCTACCCTGTGCTAGCTAGTAGTTACTGATTGGCCCAGTTGGCCTTTAAAACCAACTGAAGGAAACACTAACACAATAGCTTCAGTTTGTCGGTTGGGAACTTGACCTGATATTTAGGTAAAGGTTTTGAAGGTCTGTGTCAAAGTCTTTCAAATCACCGCTCTGTCTCTAGAAGCTGGCCTGTCTCCTAGGACTGAGAGCTTACTTGAGAAATAAACACTGTCTCCTTTACATGAGTAATCAATGAGGACCCCACAGGAGGGTCCAGGAATTCATACATGTAGCAGTTGTGTTTTACACTACAGGATTGAGATCTGACGAGTGTTCTAGAGCCACGGGCACCTTAACACCGTCTATTCCTGTTCTGTCATGGAGCCTGGGATAATGCATTTGCAGCCTGCATGCCCTCAGAGTTGTGCAGCATGTGATGGTTTTAGAACAAGAGTGTCTTAGACACTATGAGGGGCATGGCCATGCCTCAAGCCTAAAAGAATGGAGAGTGTGTTAGATAACTTCCTTTTCTTACTGGCTTAAGCTAGATTTCTGATCCAGAACATGATGATCTTTAAAGCACCCTTTCACGGCTCTCCCCTCCTCCACTCTCTCTCCATCCTTCCCCCACTTCCCAGCTCCCCTTCTCTGCCTGATCTGATATTATACTTACGTACTAATGATGTTGAAGTCAGATATTATATGTGTTGCAGATATCTTCAGCTTTTTGGCTTTTTTTGGTCTGAAGAAAGTGTGACTGACCTGTTAAGACTCCAGTCAATCCTCAGCAGGCTTAAGTGGCTTATTTTCTGATGTCTACTTTGTACTAGCGATTCTGAGCTTTGTTCATGTTCATGTTTCCTTCAGATTGCCCCAGTATATTTGACAAGCCATAGCTTGTGCTTGCAATTCATCAGCTTCCTCATGATCCAGGGAAGCACTGTGTAGGTCTCCCATCTGAACATACTAGATGGATTCATGACTCTTACCATGTGGTGATGATTCCAGTATAGATCCATAGGAATATAGAAATGAGCTAATTCCTGTAATCTTTGTACTAGGGAGGCTTAAGCAGGAGGATTACCATGAGTTTGCAGCAAGCCAAGACCACATAGTGGTTCTAGGCCAGCCTGGGCAACAGAGTGAGACTCTGTCCTCAAAATACCAGACAAAAGGAAAGGTGAAACTGGCTTTCACCTATCTCTTATGTGTCTCTTATGACTCAGTTGTACCTTTGGACCACATAGTCACACCTCTCTCTTCTTGCAG
Seq C2 exon
CTATAAGTGCCTCTGCGATGCAGGCTGGGTTGGTGTCAACTGTGAGGTGGACAAAAATGAGTGTCTTTCTAACCCATGCCAGAATGGAGGAACGTGCAATAACCTGGTGAATGGCTACAGGTGTACCTGCAAGAAGGGGTTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027878:ENSMUST00000079812:13
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=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=PD(6.7=3.1),PF0764510=EGF_CA=WD(100=55.4),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:
GCCAGAGGTGCAATATTGACA
R:
AACCCCTTCTTGCAGGTACAC
Band lengths:
334-1601
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