MmuINT0109747 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26465350-26466615:-
Coord C1 exon
chr2:26466467-26466615
Coord A exon
chr2:26465567-26466466
Coord C2 exon
chr2:26465350-26465566
Length
900 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CCTGCCGCCCCTGCCCGCAGGTG
3' ss Score
12.99
Exon sequences
Seq C1 exon
CTCCATTGTCTACCTGGAGATCGACAACCGGCAATGTGTGCAGTCATCCTCGCAGTGCTTCCAGAGTGCCACCGATGTGGCTGCCTTCCTAGGTGCTCTTGCGTCACTTGGCAGCCTCAATATTCCTTACAAGATTGAGGCCGTGAAGA
Seq A exon
GTGAGTAATCAGGGGCTGGAGGGATGGCTCGGTGGTTAAGAGCACTGGCTGCTCTTGCAGAGGACAAGGGTTCAAATCCCAGCACCCACGCAGCATCTTATAACTATGTGTTACTCTAATTCCAGGGCATCCAACACTTTCTGACCTCTGCAGGCACCAGGCATGCACAGGGTCCTGACGTACATGCAGGCAAAACACCCATACACATTACATATTTTTTAAATGAGTTCCCTACCCCGACCAGCCCTGCCTCTTCAGGGATGGGTTCATTGGGTGGCGGGTCACAGGCAGGCGGTCTCTCACTCCTTGTGCCAGCTGCCATTCCCAGCTCAGGAAGTGCTTTTCTGGAATTTTTTTCCAAGGCCTTCCCTCCCTGTGGCTAGTGGGAGCCGTAAGTAAAAGCTGTCCCCTAAGATGTATACATATACCAGAAAGTATGGAGGAGTCTTTCTTCTCTCCTCATTCTTTACCCCTGATTTTTCTTTGTTGGATATTATTTCAAAATCATTACTAGAGTTTTTTTGTGTGTGTTATTTTTTTTAAGAGAGAGAGAGAATTGATCGGTGTCATGTGAAGTGTTGAAGTTTGTATCTTGAAAATCCCCCTAAATCCTTTGTCTTAACAGCTCAATGCGAGCGCAGTGATTTGAAGTTCGCTAATCCTCCTTCTCGAAAGGGGAGAAGTGAGCACTGTCTCCAGACAGATCAGCTGGTGCAGGAGAGAATTTAGCGATAGTTTGCAATTCTGATTAATCACGTAGAAAATGACCTTATTTTGGGGGGTGGGATGGAGGAGAGTGGGTGAGGAGGCACCGGCCGTGGAGCCAGTCCTCCGCCCCCCGCCAGCCCACAGCATCACCACGCCTGACGAGGGGTGCTTGCCTGCCGCCCCTGCCCGCAG
Seq C2 exon
GTGAGCCGGTGGAGCCTCCGCTGCCCTCGCAGCTGCACCTCATGTACGTGGCAGCGGCCGCCTTCGTGCTCCTGTTCTTTGTGGGCTGTGGGGTGCTGCTGTCCCGCAAGCGCCGGCGGCAGCATGGCCAGCTCTGGTTCCCTGAGGGTTTCAAAGTGTCAGAGGCCAGCAAGAAGAAGCGGAGAGAGCCCCTCGGCGAGGACTCAGTCGGCCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:27
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=0.233
Domain overlap (PFAM):
C1:
PF076847=NODP=FE(79.4=100)
A:
NA
C2:
PF076847=NODP=PD(14.3=12.3)
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:
GAGATCGACAACCGGCAATGT
R:
TTGAGGCCGACTGAGTCCTC
Band lengths:
350-1250
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