MmuINT0109728 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26501881-26503822:-
Coord C1 exon
chr2:26503498-26503822
Coord A exon
chr2:26501960-26503497
Coord C2 exon
chr2:26501881-26501959
Length
1538 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
CTCTTCTGACCTTCCCCCAGGCT
3' ss Score
9.75
Exon sequences
Seq C1 exon
TAGTGCCTCTGCCGCGGGAGGGAGCGCAGGGGCGTGGGGCGCAGGGCGCGGGCGCTGGGCGCGGGTGCGAGCGCAGTGAAGGAACGAGCCCGGGTGCCTTGTAGGGCCCAGCGCCGCTGAGAGCCCAGCGCCGCCCACCCGCCAGGAAAGAGGGCATCAGAGGGTGGACGCCTGCGGGACCGCCGGTGGTGTGCGTCAACGTCCGATCCCCGCCGGCCACCCCAAGAGGCCGCCGCCCGGGCTGCGGGCAGCTGGCGAGCAGGCATGCCACGGCTCCTGACGCCCTTGCTCTGCCTAACGCTGCTGCCCGCGCTCGCCGCAAGAG
Seq A exon
GTAGGCTCCCGCGAGCCCGCAACTTCGGGCGCCTTTCAGAAACTTCTGTTGCGCCCTGCGCACGCTTTGGGTAGATAGGAGTAAGGGACCAGCTGCCAGAGTTGAGAGCCAGAGCGGGTGGACGGGACCGTGGGACCTGGTGTCCTGGCGTGTGAGGAGGACCCTTCTCTTTCCAGGGGTACCCACTTTTCTCATAGCGCCCAAAGACGCTGGAAGTGTGGTATGGGGCCCCGGAGGCCCAACCCTGGCTCGCACTTGGGTAGACGCTCCTGGGGCTCGCCGCGGGGGCGGACATGCTGCTTGCGCCTCTACTTTTCGATTTGAATCGAATCGGTTTTGGTTTCCTGTTGCTTCTTGGGACCATTTATTTTCATTCTTCTTTGCCTCCGGCCCGTGCTAGGGCGGATGTTGGGGTGCAGTGTGAGGTCAGGGGCGCTATACTCTCGTTGCTTACTTAGAGCGGGGCAGAGACGATGTGCCCTGGACTCCTAGTATGGGGTTTTGGGATCGCTGTCCCCTAGCCGGAATCAAACTTTCGAAGAGGGGCGATGTGCAGGCGGCTTGCTGCCTAGGGTGGGCGTGGGACTGACTCATTTCGGAAGTTTGAAAATCCTGTGCTGATTGGAACGGGAGCCGGAGAGGGGAGCCCTTATTTCCCTTCCGGCTTCACAGAACGGGGTACTCCTGTTGTAGTAACCAACTGCACTCTTCTCCCAGTAATCGAAGGAGAGAACTGCCTGCCCTTTCCTTAAAAGTGGGGTTTTATGTGACGCTCGAGCTCAGCCCTACATCGAGGCTTAATTTTTAGAGCTCTTTAAGATGGCGTGGGAGGGGCTTGATTAATAATAGCCCCTTCCCGAGAACGGGGTGGAATTCCTTCTAAGTGGGGTTTCTAAGACCCCCTCCCTGGGTGCGGCGGGGGCTGCCCCTGGAGATGCCTGCGAACAGGTATTGGGTGTCGGAGTAGGCGGGGCAGGTCTCCGGGTGCGGCCCCGCTGCCCCAGGAGGCGGCCCTGGCGCGACAATGGGCCGCTCTGATTCCCGGGCCGGCGCTTTGTTGGAGGGCGGGGTGGCGGGCTCCGCAGCTGTCGCTTTTTCCCACGATCCGGGGAGCTGAGTGTGGCCACCCCCTCCCTCCTGCGGTCCCCTCGTATCTTGTGTTTGAACTGAGGCAAGGGTGGAGGCTTGTCGGGGGGCTTTGCTGGGCACCTTAATCCCCTCCCACTTTGGCTGTGTGGTTAGAAGTTTGGGAGAATTTGCTAAGTCTTTCTGTTGCCGTCCACTTCGCCTCACTATGAGTGGGGCGGTACACCTGCCACCTAGCCAGCCTATCCTTTCCCCACTAGTTTTTGACTACAATACTGTGAGCAGAACATTGATTCGTAAGCCGCCCCCCCCACCGCGTCCCGCACCCCCTCAGGACTGCCAATAACTCTAGTGCATAGGCACCATGGCTTTAATCTCCGTCCACCATCAGGACTATAAGGAGTTAGGTGCCCAGAACCAAGCCTGACCTCTCTCTTCTGACCTTCCCCCAG
Seq C2 exon
GCTTGAGATGCTCCCAGCCAAGTGGGACCTGCCTGAATGGAGGGAGGTGCGAAGTGGCCAACGGCACTGAAGCCTGTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCGCAGTGAAGGAACGAG
R:
GTTGGCCACTTCGCACCTC
Band lengths:
319-1857
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