MmuINT0109768 @ mm10
Intron Retention
Gene
ENSMUSG00000027878 | Notch2
Description
notch 2 [Source:MGI Symbol;Acc:MGI:97364]
Coordinates
chr3:98116701-98117345:+
Coord C1 exon
chr3:98116701-98116820
Coord A exon
chr3:98116821-98117192
Coord C2 exon
chr3:98117193-98117345
Length
372 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
TCATTCTCCTGTCTTCATAGGTA
3' ss Score
10.82
Exon sequences
Seq C1 exon
GCAAGAACTGTCAAACAGTGTTGGCTCCCTGTTCCCCAAACCCGTGTGAGAATGCTGCTGTTTGTAAAGAGGCACCCAATTTTGAGAGCTTCAGCTGCTTGTGTGCTCCTGGCTGGCAAG
Seq A exon
GTAATGATGCTGGATGCATCCTGCACTTTAAACAAAGCCATCGGCCCTCAGATGACATGGGAGACCATGCTGACACCTGTAATCTCTGTAGGGAGCGACTAGCTGGAAGGGCTCATAACACCTTCTCAGATTCCATCTTTATAGTCCTCAAGTAGCTGAGACCCTCCAACCCAAGTGTTTCAAGCTGTGAGTAGCAGTTGGGAGGAGTTTCCGAAGGACCTCCTGCATCGGACCAATCAGGTGGCCTCCTGCACCAAAACACCCTAAGCTCACAGTGGACTGAAACTCACACCCACCTAAGCTTACACCCTGCCTTGATTTCTATGGGAATTTTCTTCCAAGGACTGGCTGTTCATTCTCCTGTCTTCATAG
Seq C2 exon
GTAAACGATGTACAGTTGACGTTGATGAGTGTATCTCCAAGCCGTGTATGAACAATGGTGTCTGCCACAACACTCAGGGCAGCTACGTGTGTGAGTGTCCTCCCGGCTTCAGTGGGATGGACTGTGAAGAGGACATCAATGATTGCCTTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027878:ENSMUST00000079812:16
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(6.5=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0764510=EGF_CA=WD(100=73.1),PF0000822=EGF=PU(9.7=5.8)
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:
TGTCAAACAGTGTTGGCTCCC
R:
GGCAAGGCAATCATTGATGTCC
Band lengths:
264-636
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