MmuINT0109738 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26471152-26472272:-
Coord C1 exon
chr2:26472071-26472272
Coord A exon
chr2:26471306-26472070
Coord C2 exon
chr2:26471152-26471305
Length
765 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACCAGCGCCTGTCTCCTCAGAAC
3' ss Score
8.21
Exon sequences
Seq C1 exon
CTCCTGCTTCAATGGTGGTACCTGTGTGGATGGTATCAACTCCTTCACCTGTCTGTGTCCACCTGGCTTCACGGGCAGCTACTGTCAGTATGATGTCAATGAGTGTGATTCACGGCCCTGTCTGCACGGTGGTACCTGCCAAGACAGCTATGGTACTTATAAGTGTACCTGCCCACAGGGCTACACTGGTCTCAACTGCCAG
Seq A exon
GTGAGCTGAGGTTACAGGGTATGACCCAGAAGGCCTAGGGCTCTCCAGTGCCCATTGCCCAGCCCTGGGCCACACTACCTTCAGAGGGCCAGGGACACAGAAGCAGAGAGGCTCCCTGGTGTCATCATTGGTTGATGAGCCAGAATGAACCCACATCCTCTGGGAAAATGCCAAGTTGGGTGCTTCTGAGGGAGACAGGTGGGCATGGGTGCCAGCCAGGCTCTTCTGTGGAGTGCATTATGTGGCCATCTGTCTGAAGCAGCCTGGGGCAGTGCTCACTTCTGGTGGAGGATGTCCAAGGGGAGGTAGCCAGTGGGTTGTGGAGAGCCTTGAAAGAGAGCAAGGAAGACGTGGAGCCCAGGCCTATGTTGTTCGGAGGGCGGGCAGTGTTTGTGAGTCCTGTGCCTGGGATTTCTTAGGTGATATTCTTTCTGAGATGGTGGGGGTGGGGGTGGGGAAGTCAGAGCATAAAATGCCTTATTCCAGTGGCGCTCAGCCTGTGGGTCATGACCCCAATAGGGGTCATATATCAGATATCCTGCATATTTTTGCTACATGACAGTAGCAAAATTACAGTTATGAAGAAGCAATGAAATAATTTTATGGTTGGAGGTCACCACAACACGAGGAACTATATTAAAAGACTGCAGCATTAGGAAGGCTGAGAACTGCTGTGCTTCTCAGAGCCAGCCAGGACCAGGGCAGGAGGGTGCCCTAGCAGTCAGAGTTGGTCAGGGAGAAGCTAACCAGCGCCTGTCTCCTCAG
Seq C2 exon
AACCTTGTGCGCTGGTGCGACTCGGCTCCCTGCAAGAATGGTGGCAGGTGCTGGCAGACCAACACGCAGTACCACTGTGAGTGCCGCAGCGGCTGGACTGGCGTCAACTGCGACGTGCTCAGTGTGTCCTGTGAGGTGGCTGCACAGAAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:19
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(87.1=39.7),PF0000822=EGF=WD(100=45.6)
A:
NA
C2:
PF0000822=EGF=WD(100=59.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGCTTCAATGGTGGTACC
R:
CTTCTGTGCAGCCACCTCAC
Band lengths:
351-1116
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