MmuINT0109811 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32139645-32141549:-
Coord C1 exon
chr17:32141217-32141549
Coord A exon
chr17:32139800-32141216
Coord C2 exon
chr17:32139645-32139799
Length
1417 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CCTCTGCTCTGTTCCCACAGCTC
3' ss Score
11.54
Exon sequences
Seq C1 exon
CCCTGTTTATGAGAAGTACTGCGCCGACCACTTTGCAGATGGCCGTTGTGACCAGGGCTGCAACACTGAGGAATGCGGCTGGGATGGGCTGGACTGTGCCAGCGAGGTCCCGGCCCTTTTGGCCCGAGGGGTTCTGGTCCTCACAGTTCTTCTGCCTCCTGAAGAGTTGCTGCGCTCCAGTGCCGACTTTCTGCAGCGACTCAGCGCTATTCTGCGCACCTCACTGCGCTTCCGCTTGGACGCACGTGGCCAGGCCATGGTCTTCCCCTATCACCGGCCAAGCCCTGGCTCTGAATCCCGGGTCCGTCGTGAGCTGGGTCCTGAGGTGATCGG
Seq A exon
GTGAGTGACTGTGGCTCAGGGCTGGGTACAGCGGTTAGGGCACCCGTGGTCCAGACCGTCTGTTTCACGCTTCTTAGTTGAGAGCTCTCTTGGCAAGGCGTCTTCCACAGGTTTTTCCGTGTCTGTCGGGTTGACATCTTTGCTATGGGGGGGGGGGGGGTTCATCCTCTGTACACTACAGGGAGCCTCGCTGCAGCGCTGAGATTTTACTCTTCAAATGCAGGTGACAGCACCTTCTTGTGTGCATGATGTGTGTGTGTAGGTCCCCAAGTGCCATGACGACGCATGCCTGTAGAGGTTAGAGGACAACAGTGTGAAGTCAGTTCTCTCTTCTCATCAGGATGTCAGGCTTGCATGATGAGCATGTTGCCTGTGAGCCATTTCGCTGGCTTGTTTGTTGTTTTCTTCTCGTTGTTTGCTTTGTTTGTGTTTTATAGGCACTAACCTGAAATTCAATCTGTAGCCCAGGTTGGCTTTGAACTCATGGTTCTCCTACTCAGCCCTTCCAAGTACTAGGATTGCAGGCATACAATATCGCCCCCGACACTCACTCTCTTTCCTCCCCACTCTCTTCATTCCCCTTTCCCCTCATCTCACAAAAGTTGTAGAACTTGCTCACTGGTGACCTGGTAGGGGGAACCTGAAGTGGGAGAGGCATTTTTTTGAGGGTGGACCAGGGCCTGAAGATTGGGCCCTGACAAGGAAAGGAGAGCTGAACTTTAGAGATGCTGTGGTTTGTGGGTTCTGATTGGATGCAGGCAGAAGTCAAGTAGATGGGTGAGGTGACACATGGCCCCTTTCTTGGCTAAAGTGGCTTAGTGATGAGGACATAGGGCTAAGCAGGGGCCACCTTGGAACTTGCTATTCTTAGGGGGTCTTGAGGTATGGGGAGGAACCCCAGGAGATGACTGAGGGCTGAAGATGCATACAAGACAACTGGGTATTGGAGGCCATTGGAGGGAAAGAAGGGAGAATCAAGGAAGCAGGAGAGAAGGAAATGAAGAAGGAATCTAAGGACTCTCAGAGACCTAAGAATTGGGGGACAGTAGAGGACGTGGCTCAGTGGTAGAGAACCTACCTTGTATATTCAAGGCCCCAAGTTCATCTCCAATACCACAAAGAAGGATAAAGGAGAAAAAGCAAGCTTTTAGAGAAACTGACATGGTACACTGTCCCAGCAAAGGGCGACACCAACAGACTCTACCAGGGCGAATGAAGACATTATTGAATTCACAGCTTTGAGACACTGTGACCAATAAGATCTGTTGGGAGAGACAGTGGAGTTGGATGCCAGCTGAGAGCTGGGTGGGTGGTAGAGACATGGAGAGTGGAGACGGATGTGGCTCTCTGAGGTCGGGTGTCTAGGATGCTGTAGACAAGTGTTGAGCCTTTGGGTCCCTCTGCTCTGTTCCCACAG
Seq C2 exon
CTCTGTGGTGATGCTGGAGATTGACAACCGGCTCTGTCTGCAGTCAGCTGAGAATGACCACTGCTTCCCTGATGCCCAGAGTGCTGCTGACTACCTGGGAGCCTTGTCAGCAGTGGAGCGACTTGATTTCCCATACCCACTTCGGGATGTGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006612=Notch=PD(84.6=29.5),PF068168=NOD=WD(100=50.9),PF076847=NODP=PU(4.6=2.7)
A:
NA
C2:
PF076847=NODP=FE(80.0=100)
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:
CTTTGCAGATGGCCGTTGTGA
R:
CAGACAGAGCCGGTTGTCAAT
Band lengths:
343-1760
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