MmuINT1024448 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32137816-32139353:-
Coord C1 exon
chr17:32139131-32139353
Coord A exon
chr17:32137901-32139130
Coord C2 exon
chr17:32137816-32137900
Length
1230 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGA
5' ss Score
6.42
3' ss Seq
TTCTTCTTGTTTTCCCCAAGGAA
3' ss Score
8.8
Exon sequences
Seq C1 exon
GAGAGCCGCTGGAGGCCCCAGAGCAGAGCGTGCCACTGCTGCCACTGCTGGTGGCAGGGGCTGTCTTTCTACTCATCATCTTCATCCTGGGTGTCATGGTTGCCAGGCGAAAGCGAGAACACAGCACCCTCTGGTTCCCTGAGGGTTTTGCATTACACAAGGACATAGCTGCTGGCCACAAGGGCCGGAGGGAGCCTGTGGGACAAGATGCACTGGGAATGAA
Seq A exon
GTAAGAACCTCACATGCTCTACATCCCCAACTGTGGGTCCCTTGTAAGCTCTAGACCATACTCACCTCGGTCATATTCCAACCTCTGACCCCAGCCTAACCTTAACTACAGACTCCATCTGGGCCTTCAGTGTTAATCCTCTTGACCTATGACCCCATGATCCCTGAGGATTGCCCCAACCCCTATCCCTTGACGTGATTTTCTATTTCTATACATTTCCTGACTCATATCTTTCCCTGACGCCATCCTGAACTAACCTCACAAAATTCATTCTTATGACTGCTAACCTCAAGACTTTTGTCATTTCAACCTGTCCCTGACCACGACTGTATCCTTGATGACTCCTGAATCATCTCTGGCTTCAACCCACCTGTACCTTTGACCTCACCTCAGACCCCTGTTTCTACCCAATCCTGTGTTAATTCCCTTGTGATCCTCAATCCCAAGCCTTCAACTTGACTTATTCCTCAACACCAATAGCCATATTCTGACCTTAACCCTTCCCTATGACACCATAACTCCTGACTCCTCATCCTGATGTTTCAAGCCTGGCTATCCCGTTTGTCACAAGAGAGTAACTCCTCTTCCATGAGCTTTGATAACTCCTTTATCAAAGTTATGAGAGGAAACTTCCTTTGCCCCTGCAGTTTGTCTCATCTATCCTCATGCATCCATGTTCCATTGTGTGTGCCACTCTTGACTCTGAGTTCACCTTATGAGTCTGGCCACCTCAGATGTGAGGTGTGGAGCAGGTATAAAGACCGTTGTTTGGATCCCTAGAACCTGTATAAATGCCATAAAATCCTTAAGTGCTCAGTGGGCCCGGCAGCCTGACTTGGAAGATGGAGTCCTGGTCCCTAGAGCAAGCTGACTAGTGAGTCTAGTCATATCCGTGAGCTCTTGGTTTGATTGAGGGACCCTTCCTCGATGACCAAGACTGAGGAGAGATTCCTCTTTATCAACCTCAGACCTGTGCACCCAAAACACACACCTGCACTCACAGATGGAAAGAGAAAACATTTTGATTGCCACCTGACATGCTTCCTGCAACTTCATCTCTATCCTCCTATCCATCATTGGAATCTTTGTCAACGACCCAGGACCCCTCCTCAGTTCCTGACCCCTTACCTACCTCTATGACCTCTGCCTGAACCAAACCCTAAACCCTCTTCCCAGGCCAGAGTTCTCTAGTGTACTTTCTCACGTCTTTTTCTTCTTGTTTTCCCCAAG
Seq C2 exon
GAACATGGCCAAGGGTGAGAGTCTGATGGGGGAGGTGGTCACAGACTTGAATGACTCAGAATGTCCAGAGGCCAAGAGACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.552
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(13.8=12.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGCCCCAGAGCAGAG
R:
TCAGTCTCTTGGCCTCTGGAC
Band lengths:
296-1526
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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