MmuINT0109760 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26478607-26479560:-
Coord C1 exon
chr2:26479447-26479560
Coord A exon
chr2:26478721-26479446
Coord C2 exon
chr2:26478607-26478720
Length
726 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTCGTCTTCCCTGGCCACAGGCT
3' ss Score
7.97
Exon sequences
Seq C1 exon
GTTATGAAGGTGTATACTGTGAAATCAACACGGATGAGTGCGCCAGCAGCCCCTGTCTGCACAATGGCCACTGCATGGACAAGATCAATGAGTTCCAATGTCAGTGCCCCAAAG
Seq A exon
GTGAGGCCACCTACTTACCACAGGACCCGTATCCTCATGATCTCTTCCCAGACTCCTTTGAGGGAGGACTTGAGTTGACTAGGGCGTTTTCAGGCTTTCCTCAAAAGGTAAAGGCCCACGTGAGCAGTGGACGCTGTAGGGGACCTGGCACCGGAAACCCTTTACTAAAGGAGGGAAGGATGGGCAGGAGCTGCAGCGCTCCTAAGATAGGAGAGTCCACCTGCTTGGCTCTGTCCTCTTCCTGATGGTCATGGGAGTAAGGACATAGTGTGGGGATCTGACCTCTATGCCTGGGAAGGACTTGGAGGAACTGAAGAGGGGACCAAAGTCCTGGGAATCTGTCTCTTGCCTACTCCAGGGCTGGACCAGGCCTTGGGCCTTCTGAGATGTAAATAAGCCATCCTAGACTTGGTCCAGCTAGGGGAGTCCCATTCACAGCCTAGTGCAGCTGTAACCATAGCAACCAGAGTCTATTTAGGAAAAAGGCCCCTCTGTTGGGCCAAGGAGGCAGCCACTGAGCAGTGCTAAACAAGGAGCTGATTAGAGGGGCAGGGTGCAAGGGGCAGGATATAAGGGCTGGTTGAAGCCTGGAGGTTAGTGGCCCCTGTTATCAAAGTACCCTCTAGGGAGCCCATGTGAGCAGACATTCAACTCTAAGGTTTGTGGGTAGCAACCAAGGGGTTAGGATACTGTCAGATATAACCATCTCGTCTTCCCTGGCCACAG
Seq C2 exon
GCTTCAACGGGCACCTGTGCCAGTATGATGTGGATGAGTGTGCCAGCACACCATGCAAGAACGGTGCCAAGTGCCTGGATGGGCCCAACACCTATACCTGCGTGTGTACAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:9
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:
PF0764510=EGF_CA=PD(25.0=25.6),PF0000822=EGF=PU(80.6=64.1)
A:
NA
C2:
PF0000822=EGF=PD(16.1=12.8),PF0000822=EGF=PU(80.6=64.1)
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:
TGAAGGTGTATACTGTGAAATCAACA
R:
TCTGTACACACGCAGGTATAGGT
Band lengths:
222-948
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