MmuINT0109797 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32151516-32153635:-
Coord C1 exon
chr17:32153525-32153635
Coord A exon
chr17:32151709-32153524
Coord C2 exon
chr17:32151516-32151708
Length
1816 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
GTTGCCTGTATGCTCCCCAGGGC
3' ss Score
7.95
Exon sequences
Seq C1 exon
GTGTGAACTGTGAAGTCAACATTGATGACTGTGCCAGTAACCCCTGTACCTTTGGAGTTTGCCGTGATGGCATCAACCGTTATGACTGTGTCTGTCAGCCTGGATTCACAG
Seq A exon
GTGGGTAGGTGGCTGCCATGTAGTGGGGGGGGGGGGGCTTGTAAGATAGGGATTAAGACACAAGTCTCTTGGGTGTCCCCACTTTATTTTTTTAAAAAAGGAAATATTACATTTCATTTATTTTGTGTATGTCTGGAGGTCAGAGGGCATCTGGGGGGAGTCAGTTCTCTCCGTAAAGGTCTCAGGGACCCCACTCATGTCATCAGGCTTGGGGACACGTGTGCTTTCCCCCCAGTTAAGTCCCTTTCTTCCCTTTATCAAGATTATCTCCAATACTCAGAAGGCCAAGGTTGGAGGATTAGTGCATGTTTGAAGCTAGTCTGAGCATCATAGTGAGCACTAGGCCAGCCAGGGCTGCATAGCAAGATCATGTCTCAAAATAAAACAATATATAGAGAGGGCTGGAGAGATAGATGGCTCAGCAGTTTCAAGCACTTGCTCTTGCAGACGACTCGGGTTTAGTTCCTAGCATTAACACGCTGGCTCACAAGTGCATAGTTTTGTTTTTGTTTTTGTTTTTTAAATAATAAAGTAAAATAAGATAAAACAAAGCAAAAAAAAAAAAAAAAAAAACACATCAGAAATGGACAAAACAAAACAAAATCAGGAGGGAAAAGAGCCCAGGAGAAGACACAAGAATCGGAAACTCATTCATTCACACACTCAGGAGTCCCACAAAAACACCAAACTGGAAACTATAATGTATAGGCAGAGGGTCTGGGGAGGGCCTGGCAGGCTCCGTGCATACTGCCCCAGTCTTGGTGAGATTGTCTGAGCTTTGATAATGTTGATTTAGAGGGCCTTATTTTCTTGATTTTCTCCATCCCCTCTGGCTCCCAGTCTCCTTCTGCCTCTTCTTCATCGGAAAAGGGATTTGAAGGAGACACCCCCTAGGTTTCTTAGTCTCTCACTCTCTGTGTACAGTCTAGGAGTGGGTCTTTGTATTTGTTCCCATCAGCTGCAGGAGGAAGCGTCTGTAATGATGGCTGAACAAGGCACTGGTCTGTGAGGTATTAGGAGTCATTTTAGCCTTACCTTTTTTCCCCTTAAGGCTGGTTCTACCCTTGCCCTCTGGGCTATCTAGCCGCAGGTTCTTGGTCACTGAAGCAATATTGGGTATGGGTTCTGTCTTGTGGAGTGGGCCTTAAGTCACACAGATATTGGTTGGTTACTCCTGCAAGCTCTGTGCCACCACAGCACTAGCAGATCTAGAGGCAGGACACCACTGTAGATCAAAGGGTTTGTGGTTGGGTTGGTGTTTATGTTTCTCTAGCATGCAGAAAACCTTTCTGTACCAAAGACCCTAGAATATAGAAGGCTCTATGTAGGCATAAGTTTGACTTCTCCATGTTCAGTGAGTCTCACAACTGCTTATAACTCCAGAGTAAACTTATAATTCCAGGAATCTGACATTCTCTGCTGGCTTTCATGGGCACCAGGAATGCACCATGATGCACTAACATACATCCAAGCACTCATATAAAATAAATAAATAAATAAATAAATAAATAATCTTTTAAAAAGCAGAGAGAGAAAGAGGAGAGAGATGGAGAGAGGGAGGGAGGGAGGGAGATAGGTGCACACCTGTGCACACACACACACACACACACACACACACACACACACACAAAGTTGGGGGCGGGGGGGGGAAACCACCTTGGACTATCCTGAGCTTGTTTCCTCAGTGGCATGGGGCTGTCGTTCTGTCAGCAGAGTGAGGTCAGGATCAGCTGTGTGATAGAGAACAGGACGTCCCTTTCCTTCAGTTGGCACCACTGTCTTCGTTCTGGAATGAAGTTGCCTGTATGCTCCCCAG
Seq C2 exon
GGCCCCTCTGCAACGTGGAGATCAATGAGTGTGCATCCAGCCCATGTGGAGAGGGTGGCTCCTGTGTGGATGGGGAAAATGGCTTCCACTGCCTCTGTCCACCTGGCTCCCTGCCTCCACTTTGCCTACCTGCGAACCATCCCTGTGCCCACAAGCCCTGTAGTCATGGAGTCTGCCATGATGCACCAGGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:12
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=5.3),PF0000822=EGF=PU(90.0=71.1)
A:
NA
C2:
PF0000822=EGF=PD(6.7=3.1),PF0000822=EGF=WD(100=41.5),PF0000822=EGF=PU(53.3=24.6)
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:
GTGTGAACTGTGAAGTCAACATTGA
R:
GCCTGGTGCATCATGGCAG
Band lengths:
302-2118
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