MmuINT0109735 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26473681-26474240:-
Coord C1 exon
chr2:26474121-26474240
Coord A exon
chr2:26473834-26474120
Coord C2 exon
chr2:26473681-26473833
Length
287 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ATGAGTTTTTGTCTTCACAGGTC
3' ss Score
9.4
Exon sequences
Seq C1 exon
GAGCCACGTGTGAGGTGGTGTTGGCCCCATGTGCTACCAGCCCCTGCAAAAACAGCGGGGTATGCAAGGAGTCTGAAGACTATGAGAGTTTTTCCTGTGTCTGTCCCACAGGCTGGCAAG
Seq A exon
GTGAGGCTTGCCTGGTCCCACCAGGCTGGGACAAGGATGGTGGATGGGAAGTCAGGGGCCCTGGCCAGCCTGTGGGGCAGTCTCGAGAAAGGAGCCCATCAATGCTGAGCTACCTGCTCTGGGAAGCTCTGGGAAGCTCTGGGAGCAGGAGATGGTCCTTCCCATTCCAACTCCATATCCTTCTGTTGCCCAGAGGTCAGGGGAGAAGCACTGGAGATAAACAGACCAGCTAGGACAGAGGCTCAGAGGGTGGGGGCAGGTAACCAAATGAGTTTTTGTCTTCACAG
Seq C2 exon
GTCAAACCTGCGAGGTTGACATCAATGAGTGTGTGAAAAGCCCATGTCGCCATGGGGCCTCCTGCCAGAACACCAATGGCAGCTACCGCTGCCTCTGCCAGGCCGGCTATACAGGTCGCAACTGTGAGAGTGACATCGATGACTGCCGCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:16
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=4.9),PF0000822=EGF=PU(90.9=73.2)
A:
NA
C2:
PF0000822=EGF=PD(6.1=3.8),PF0764510=EGF_CA=WD(100=73.1),PF0000822=EGF=PU(9.7=5.8)
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:
CACGTGTGAGGTGGTGTTGG
R:
GGGGCGGCAGTCATCGAT
Band lengths:
268-555
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