MmuINT0109836 @ mm10
Intron Retention
Gene
ENSMUSG00000015468 | Notch4
Description
notch 4 [Source:MGI Symbol;Acc:MGI:107471]
Coordinates
chr17:34580920-34581491:+
Coord C1 exon
chr17:34580920-34581172
Coord A exon
chr17:34581173-34581378
Coord C2 exon
chr17:34581379-34581491
Length
206 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTATCTCACCCCCACCACAGGCC
3' ss Score
8.18
Exon sequences
Seq C1 exon
TGTGCCCCAGGCTATGAGGGACAGAACTGCTCAAAAGTACTTGACGCTTGTCAGTCCCAGCCCTGCCACAACCACGGAACCTGTACCTCCAGGCCTGGAGGCTTCCACTGTGCCTGCCCTCCAGGCTTCGTGGGACTGCGCTGTGAGGGAGATGTGGATGAGTGTCTGGACCGGCCCTGTCACCCCTCGGGCACTGCAGCTTGCCACTCTTTAGCCAACGCCTTCTACTGCCAGTGTCTGCCTGGGCACACAG
Seq A exon
GTAAGGCCTGGCATCTCTGGGGCATATCTAAGACCAGGACAATCTTGACGGTCCCTTCCCAAAAGACAGCCTCTCTCCTCACCCTCTGCCTTCACACCTCTCCCCTTAGAAGTCCCCTACATCTTCTTGCCCACATATCATGTGCTGAACCGTCAGGAGGCAGCCACTGAAGCCAGGTGTGACCTCCTATCTCACCCCCACCACAG
Seq C2 exon
GCCAGCGGTGTGAGGTGGAGATGGACCTCTGTCAGAGCCAACCCTGCTCCAATGGAGGATCCTGTGAGATCACAACAGGGCCACCCCCTGGCTTCACCTGTCACTGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015468:ENSMUST00000015612:19
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(25.8=9.4),PF0000822=EGF=WD(100=36.5)
A:
NA
C2:
PF0000822=EGF=PU(79.4=71.1)
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:
CCCAGGCTATGAGGGACAGAA
R:
AGGGTTGGCTCTGACAGAGG
Band lengths:
293-499
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