MmuINT0109754 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26457903-26462245:-
Coord C1 exon
chr2:26462148-26462245
Coord A exon
chr2:26460977-26462147
Coord C2 exon
chr2:26457903-26460976
Length
1171 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CTCCTGTCCGTGTCCTACAGGAG
3' ss Score
10.06
Exon sequences
Seq C1 exon
GCAAGTCGGCTTTGCATTGGGCGGCCGCGGTGAACAATGTGGATGCTGCTGTTGTGCTCCTGAAGAACGGAGCCAACAAGGACATGCAGAACAACAAG
Seq A exon
GTAAGCAGACGGGCTGCTTAACCGCAGGCGCATGATGGGGACTCCGGGGCACCCATACGTTGACCACTTAGAGGTTTAAGAGTGTCTGGGACAACAGCAGCCTAAAATAACCCGTGCTCTTGCTGGAGAGGAGCTGAGGCGTAAGCAGCTGTCCCATGTCACGGTTACTTGAGCCTTGCCTTCTGTCCCCTTCTGTCCCTGGTGGCTGTGGTGACCCTAGGGGTTCAGGATTGGCCAAGGGGCAGGGATGGGGTGGCCCTGTCTCTTAAGGCCTGCAAGGCTTCTGGCTTGGTCCACCACTACCATGCTCCCTCCTTTGGGATAAGAAAACTGCTGAGCTGGGCTGCGTGTCTCCACCTCGCCTCCCAGTGTCTCTGTTTGTGCAGGGCTAGTTGCTTCATCAGGACTCTGCTTAGTTGCTCACAGGGCAGAGTTTGTGCCTCCCTTACCAGCTCCACTGCAGGCTGGGAAATGGAGCAGGAGTCAGGTACCTGGAGTTGCTGTTGGGCACAGGTTCTCCACAGTCCAGGGTGGGCCAGTGGTTATAGAGAATCCAAGCCTGATAGACATTCTGTTGTGGTGTATGATTATGTCTGCTGGACAGAGCAGACCTGGAAGGAGCTGAGATGCCCTAGCCACTGGTGACCCTTTGGCATGGTAGTACCTTCCCCATGGCCATTCACTTGCCTTAAAGGTCCCTGAGTCCCAGGATTGCAGTACTTGTGCCTGCATTTTGGGGAGGAAAGCAAAGGGCACACAGTTACATTCTGTTTTCGGCAGTCTGACTCCACACAGGGGAAGAAGCCCTATGTATTTATCCCACAGATCTCTGGGGTGTGAGGTGTTAAATCTAGGTTCTCTAAAAAAAGAACTCGGGACCAGCCATGTGTGCGTGCTAGCACCGAGAAGCTGAGGCAGGACGATACTGAGTTCCAAGTACGGCTGTGGGCCCTGAGTGAGATTCCTAGCAACATAGGAAGGCCCCACTATAAATACTCTCTGAGCCTGGTGGTCTAGGATGCTTGGGTCTAGATAGATCTCTCCAGATAAGAGAAGAGAAAGAGGCAGCACCTGCTTCCCTAGCCCCTCCCCCCAGGCCATCCATCATCAATGACTCAGCAAATTCTACACCTGCCCGCTCCCTCATGTACCTCCTGTCCGTGTCCTACAG
Seq C2 exon
GAGGAGACTCCCCTGTTCCTGGCCGCCCGTGAGGGCAGCTATGAGACTGCCAAAGTGTTGCTGGACCACTTTGCCAACCGGGACATCACGGATCACATGGACCGATTGCCGCGGGACATCGCACAGGAGCGTATGCACCACGATATCGTGCGGCTTTTGGATGAGTACAACCTGGTGCGCAGCCCACAGCTGCATGGCACTGCCCTGGGTGGCACACCCACTCTGTCTCCCACACTCTGCTCGCCCAATGGCTACCTGGGCAATCTCAAGTCTGCCACACAGGGCAAGAAGGCCCGCAAGCCCAGCACCAAAGGGCTGGCTTGTGGTAGCAAGGAAGCTAAGGACCTCAAGGCACGGAGGAAGAAGTCCCAGGATGGCAAGGGCTGCCTGTTGGACAGCTCGAGCATGCTGTCGCCTGTGGACTCCCTCGAGTCACCCCATGGCTACTTGTCAGATGTGGCCTCGCCACCCCTCCTCCCCTCCCCATTCCAGCAGTCTCCATCCATGCCTCTCAGCCACCTGCCTGGTATGCCTGACACTCACCTGGGCATCAGCCACTTGAATGTGGCAGCCAAGCCTGAGATGGCAGCACTGGCTGGAGGTAGCCGGTTGGCCTTTGAGCCACCCCCGCCACGCCTCTCCCACCTGCCTGTAGCCTCCAGTGCCAGCACAGTGCTGAGTACCAATGGCACGGGGGCTATGAATTTCACCGTGGGTGCACCGGCAAGCTTGAATGGCCAGTGTGAGTGGCTTCCCCGGCTCCAGAATGGCATGGTGCCCAGCCAGTACAACCCACTACGGCCGGGTGTGACGCCGGGCACACTGAGCACACAGGCAGCTGGCCTCCAGCATAGCATGATGGGGCCACTACACAGCAGCCTCTCCACCAATACCTTGTCCCCGATTATTTACCAGGGCCTGCCCAACACACGGCTGGCAACACAGCCTCACCTGGTGCAGACCCAGCAGGTGCAGCCACAGAACTTACAGCTCCAGCCTCAGAACCTGCAGCCACCATCACAGCCACACCTCAGTGTGAGCTCGGCAGCCAATGGGCACCTGGGCCGGAGCTTCTTGAGTGGGGAGCCCAGTCAGGCAGATGTACAACCGCTGGGCCCCAGCAGTCTGCCTGTGCACACCATTCTGCCCCAGGAAAGCCAGGCCCTGCCCACATCACTGCCATCCTCCATGGTCCCACCCATGACCACTACCCAGTTCCTGACCCCTCCTTCCCAGCACAGTTACTCCTCCTCCCCTGTGGACAACACCCCCAGCCACCAGCTGCAGGTGCCAGAGCACCCCTTCCTCACCCCATCCCCTGAGTCCCCTGACCAGTGGTCCAGCTCCTCCCCGCATTCCAACATCTCTGATTGGTCCGAGGGCATCTCCAGCCCGCCCACCACCATGCCGTCCCAGATCACCCACATTCCAGAGGCATTTAAATAAACAGAGATGTGGGATGCAGGACCCCAGCTTCCGTTCCCAAGCCCTGTTGGGAGTCCTTTCCAGTGCTTCAGGATGCTGGGGCGACCAAAGGAGCCTTTTAAAAAATGTTTTTATACAAAATAAGAGGACAAGAATTTCCATTTTTTTTTTTAGTATTTATTTATGTACTTTTATTTTCCACAGAAACACTGCCTTTTTATTTATATGTATTGTTTTCTATGGCACTAGGGAAAAACATATCTGTTCCAAGAAAATAAACTAGTTCTCAGAGCCTTGATTTTCCTGGTCAGGGTGAAGTTCCCTGTGTGTCTGTAAAATATGAACAAGGATTCATGATTTGTAAATGCTGTTTATTTATTGATTGCTTCTTTCCAAAATCGAAAAGAAAGAAAAAAGAACGTGACAGGAGAAGGGAAGCTGGAAACTGCCATGGCCAGAATTGCCCCTCCCCCACACTCACTGCCCCTCCCCCCAGCGTCACCTGGGATTTGCAGATGTGTTTAGAAACACGCCCAGACCTTGAACCTTGGGTTCATGGATTAGTTTTGTATCTAAAACAGGAAACAAGTCAGATGATGTGGTTTGTACACTTTCTGTAACCACCAGTGTGGACTTGAAGAAGTGTCCTCAGCATGTGCAGAGTCTACTACCCAGTACCAGTCGTGAGTCTGCAGGCTCCAGTGTTCTGTAGTAGTGTTTATGGGCCTTGGGAGTACTTCTCCCCTGCCCTGCCCCACTGTCCCCTTCCTGACAACTTGAGCCAGTAAGCCATGCAGGGTGTGGTGCCTCCTAGAGAAAACACTGCCTGGACTGTTCTGTGCATCCCTCCAAACAGCATCATCCAAATCCAACTGAGGACAGACGGACTGTCCCGGCCTGGGCCTGGGCTCCTAACACCTGACTGCCAAAGGGCTCCAATGTGCATTGTGGACTCGCCAGAGTAGCCTGCATTGAGACTCCAAGAAAACAGAAGCTATGTGGCCTCTGATCCCCAAACTGGCCTGGGTGGGGACATGCCTTGAGTGTGCTGGAATGTGGGTGGAGCCTGCTTCTGGGCCACCCCTCCTGGTTCAGGGCTGTGCTCACAGCAGATTCTTGCAGTATCAAGTATACGCCTGTGGCAGAATAAGTATCTGTAAATACATGTTTAAAGATGGATTTTGTTTAAAAAATCTAAAGGAACAAGTGTGTCGTGTGTCAAGCTGATGAGGACTGTCAGACTGTGGCTTAGCTCAGTGTGACCCAGACCTTGTGACCTGTAGCTGCCGAACCAGTAGCTCCTAAGAGCACAACCCAGGATGGCCCATCTGCTGCCCACCAAGTCCCTTTCCAGCCACTGTGTGCTGGGGGCTTTCGGGGGCAGTTGCCCACCTCCTCAGGGCAGCTCTTTCTGGCCTTTTGGGGGGCAGTGTCTGTGCCATGCCTAATAGATATGACCAGACGCATCCTAAGATGTTGATTCTTACTGTGTTGTATAAAATAAAGTGTAGTTTACAAAAAAAAGAAACGTAAAAAAAAAAAACTACATGCAAAACTGTAGGTAATGAAAATGATGTATTTTTTTCATCTTTTTTTGTTAACTAATTTGCAATAAAAATGATACTGATGGTTGTCCACATTTTGCTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.212 A=NA C2=0.784
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(34.4=100)
A:
NA
C2:
PF127962=Ank_2=PD(32.3=6.2),PF119363=DUF3454=WD(100=13.5)
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:
GAGCCAACAAGGACATGCAGA
R:
CTACCACAAGCCAGCCCTTTG
Band lengths:
358-1529
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