MmuINT0109809 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32143244-32144286:-
Coord C1 exon
chr17:32144168-32144286
Coord A exon
chr17:32143810-32144167
Coord C2 exon
chr17:32143244-32143809
Length
358 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
TCTCCTCACTTCACCATTAGCCA
3' ss Score
4.47
Exon sequences
Seq C1 exon
GGCCTCGCTGTCAGATTGCTCTGTCCCCCTGTGAGTCCCAGCCATGTCAGCATGGAGGCCAGTGCCGTCACAGCCTAGGCCGTGGAGGTGGGCTGACCTTCACCTGTCACTGTGTCCCG
Seq A exon
GTAGGTGTGATTGGTAGGGGTTGGAACCCTTGGGGAAAGAAAAGGCCTGTGGCTTTAGGGAAGCATAGGTCTATACGGGAAAAGTAGAAGGAAAGGAGGTTCTGAAATTATGAAATTATGAAATTATGGTTTGGAGTGTAACTTAGTGAAATTGTGACTTGGCTTTGTTGCCTCCTGGGGAGGTATGGCTTATCTTCAAAATGAGGTCAGTAGAGGAAAGGTTGCTGGAATTGGAGGGGTGGGGGTGGGGTGTCAGCATTTCTCAAGTCTTGACCTCCATTCTTTTCTCTCTTTTCCACTCTCCTGTTTCTTCTCACTACCAATTTTTTCTCTTTCTGTCTCCTCACTTCACCATTAG
Seq C2 exon
CCATTCTGGGGTCTGCGTTGTGAGCGGGTGGCACGCTCTTGCCGAGAGCTGCAGTGCCCAGTGGGTATCCCATGCCAGCAGACAGCCCGTGGACCACGCTGCGCTTGTCCTCCGGGGCTGTCCGGGCCCTCCTGCCGGGTTTCTAGGGCGTCACCCTCAGGAGCTACTAACGCCAGCTGCGCCTCTGCCCCTTGTCTGCATGGGGGCTCATGCCTACCTGTACAGAGTGTCCCTTTCTTCCGCTGTGTGTGCGCTCCGGGCTGGGGCGGCCCGCGTTGTGAGACCCCTTCCGCAGCCCCTGAGGTCCCCGAGGAGCCACGGTGCCCGCGAGCGGCTTGCCAGGCCAAGCGAGGGGACCAGAACTGCGATCGTGAGTGCAACACCCCAGGCTGTGGCTGGGATGGCGGTGACTGCTCACTGAACGTGGACGACCCCTGGAGGCAGTGTGAGGCACTGCAGTGCTGGCGTCTCTTCAACAACAGCCGGTGTGACCCGGCCTGCAGCTCTCCAGCCTGCCTCTATGACAACTTTGACTGCTACTCTGGTGGCCGCGACCGCACCTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:23
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:
PF0764510=EGF_CA=PD(14.3=15.0),PF0000822=EGF=PU(80.6=72.5)
A:
NA
C2:
PF0000822=EGF=PD(13.9=2.6),PF0000822=EGF=WD(100=17.5),PF0006612=Notch=WD(100=19.6),PF0006612=Notch=WD(100=19.6),PF0006612=Notch=PU(12.8=2.6)
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:
GATTGCTCTGTCCCCCTGTGA
R:
GCGGAAGAAAGGGACACTCTG
Band lengths:
349-707
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