MmuINT0109817 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32132202-32133692:-
Coord C1 exon
chr17:32133388-32133692
Coord A exon
chr17:32132350-32133387
Coord C2 exon
chr17:32132202-32132349
Length
1038 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATGGCTTTTGTCGTCGTTAGATT
3' ss Score
6.93
Exon sequences
Seq C1 exon
ATGGCTTCACCCCACTTATGCTGGCCTCCTTCTGTGGGGGAGCCCTGGAGCCGATGCCAGCTGAGGAGGATGAGGCGGATGACACATCAGCCAGCATTATCTCAGATCTGATCTGTCAAGGGGCCCAGCTCGGGGCACGGACTGACCGCACTGGCGAGACCGCCCTGCATTTGGCTGCCCGCTATGCTAGAGCGGATGCAGCCAAGCGTCTCCTGGATGCTGGGGCGGACACCAACGCCCAGGATCATTCGGGCCGCACCCCCCTGCACACCGCAGTGACAGCTGATGCCCAGGGTGTCTTCCAG
Seq A exon
GTGAGACAGGCCTGTCTCTTCAGACTGCAGAGCTGCTGGGAGGGGATCAGACACACCTAGATTGGAGCCCCGGTCTGTCTTGCAAGGCTTTTGTCATTTGGAAATAGGAATAGGTAGTATCTCACCTAGATTTCCCGCCGGCCCCCCCCCCCCCCCCCCAGGACAGGGTTTCTGTATAGTCCTGGCTGTGCTAGAACTCACTCCAATAAACCAGGCTGGCCTCGAACTCAGAAAGATCCACTTGCCTCTGCCTCTGGAGTGCTAGGATTAAAGGCATGCACCACTAACACTGGATAGAATTTTTTTCTTTTTTAATTTTATTAATATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGAACTTGTTGCAGATGGTTGTAAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCTGGATAGAATTTTTTAAAAAGTATCATTAAAATTACATTTATTTGGTGTGTGTGTGTATGTTATGCTGATTGGTTTGTGTTTGTTTGTGTGGCATATGTGTACCTGGGTATGTACATTGCCCAGCTTGCTGAAGCTAGAGGAGGCTGTTGATTGTTCTGCTCTATCGTGCTCCACCCAATCTTTTGAGACAGAGCCCATCAGCGAGCCTGGAGTTGAGCTGGTGTCCAGAAAGCTCTCTTGATCCTCTTGTCTTCTTCCCCACAGCCCTGGGGCACACATGACCAAGACTGGCTTTTTAGGTGGACTTTGGGCTCTGACGTCAGGTGCTTGTCCCCTGAGCCATCTCCCTGTCCTTCCATATCATACTGTTACTTAAATCCATTTTGAATGAGCATATTTTTTGATTTATAATGTGCTTAGCAGGAATAGCACCTCATTTTAAGTCAGGAGATATCTGTAGCTCCTGGGTTCCAAAGCTGTGGCATTTGGGGTTCAGGGTGTGGTATACTCCTCCCTTGGCATAATGTCCTGCCATGGCTTTTGTCGTCGTTAG
Seq C2 exon
ATTCTCATCAGGAACCGCTCCACTGACCTGGATGCCCGAATGGCAGATGGCTCTACTGCACTGATCCTGGCAGCCCGCCTGGCAGTGGAGGGCATGGTGGAAGAGCTCATCGCCAGCCATGCCGATGTCAATGCAGTGGATGAGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.373 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF127962=Ank_2=PU(83.7=75.5)
A:
NA
C2:
PF127962=Ank_2=PD(14.1=26.0),PF127962=Ank_2=PU(30.9=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:
GGATGAGGCGGATGACACATC
R:
GATGAGCTCTTCCACCATGCC
Band lengths:
349-1387
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