MmuINT0109734 @ mm10
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
notch 1 [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26474121-26476187:-
Coord C1 exon
chr2:26476074-26476187
Coord A exon
chr2:26474241-26476073
Coord C2 exon
chr2:26474121-26474240
Length
1833 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
CTACAAATCTTTCTTTCTAGGAG
3' ss Score
9.01
Exon sequences
Seq C1 exon
GCCCTAATTGCCAGACCAACATCAACGAATGTGCCTCCAACCCCTGCCTGAACCAGGGGACCTGCATTGATGATGTCGCTGGATACAAGTGCAACTGTCCTCTGCCATATACAG
Seq A exon
GTACGAACAGCCAGGGACTGGAATTGGCTCTGGTGGTAGCTAGTGGAGCTAAGAGTATATGGGCTTACCAGGCACTGAAGAAGGTTCTGTTCCTCGCTGAGGGTCTTAGGTCCTCAGACTGGAACTGTAGTTAAGCAGGAAGGCTCTGAGCCCAGGCTACAGCCCAGGCCTCCTGGGCCTGGGGATAGTCACCAGATGGGCAAACACAGAGGATGCCTAGGAGGAAGCTCCAGGCCGTGTGTCCGGGTGTTTATCTGGTATGTCTGGAGTGAGGTGAGCACTGGACTCCTCCAGAGAAAGTCTGGGAGGCTGACTGGTAGGTACTGCATGGATCAGGGTCCACTTTGCCTGTGCCTCTGGGGGCCCTGGCTGCCCTCCTCTGCTGGCTGGGCCTGGGATTCCTTTGATGGCAGCTTCTTTGTGTGAGGAGACAAGGAGCCCTCTGTTAGATGAACAGAGGCAGCTCCTGCCATGGGCACTGCCTGAGGAATGGCGAGAAATAGACCCCCTGCAGGAGAGATGTGCATTGAACATGAAAGCCGTGACCACATGGCCCCCAACCCTGCAGCTCCAAATACTGCCACAGAGTACTGGTGGCTTCATGCTGCTGCTGCTAGGTTCTGGACATAGCAAGTGGGTCTGTGAAGGTGGAGGCCCTTCCAGTGTTCCTATGATGCCTGGCAGGATGCTGTTTTCTTTGACAAAGTTAAAGGGCCTGGATTTTGTCTCCTGTGTTGGTCAGTGAGGAAACTGTCAGCAGCCAGGCACACCCCATGTTCCTTTTGGTCTTGCTGCTATCGGGGCTAGCGGGAGGAGTCAAGCCGCGCTGACCAGCTTCCTGCTTCCCTTTGCACAATTGTCGGAAACTCTGTCAAAGTTCCTGTCTGCCCAGGTCACCGTGGAAACCGATAGAGAGAGAGGCCCTGGAGAGTCTCACCAGTGGGCTGGGGACATGGTGGGAGACAAGGAAGATAAGGTTTCCTTGCTTAGCTCCTGGAGCCAACCATGGCCATAAACAGGAAAGCTAACTGGGATTGCAAGGAGAGTCACCTGGGTTACTCGTGGCTCCCCCAAGCGGTTATCAGATTTCACTGCCCTAGTGTGAGGCTGCACCCCATGTTCCCCAAGTAGGATATGCTTGGGGTAGCCACAGTAGCTCTGTCTCAGGAGTGAGCCTGCTGTGACCTAAAGCTTCAGAATCAGCTCAAGGATTTTCCTGGAATGGGGAGCAGGCCAGGTTCCTCCAGGCTCAACCACCTGTTATAGTAGGGTCTTGTTTTGAGGTTTTCTGGTTGGGCAAGGCCCAGGCTTCATCGTGGAGCATTTGGGAGATGAGAGATGGCTTCCGGGACTACATAGATGGCTCATGGAGAAAGAGTGCTTGTGGAAACATGAAGCCTGTTTCATGAAAACAGGGTACCTCTAAATGCCCATAACCCCAACATTTGGGAGCAGAGACATCTTGAGAGCTCTCTGGCTGGCCAGCCTAGCTAAGATGGCAAAGCGTCTGATTCAGTGAGACTCTGTCTCAAAGGAATAAGATGCGGGGTTGGTAGAGGACACCTGATATCCGTCTCTCCTTCTGCATACACTCTTACACACCTGCATGCAATATACTATGCTCGTTAAAAAAAAAAAAAAAAAGTGACTTAAGAGAGAAACTTGATTCTGCTTTATCTCTAACCTCCTGTCAGTAATCGTCATTCCTCCCGGGATCAGAGTCTGGCTGGCCAATCATACAGCATCTCCTATACCTACCCCCCGCCCCCCTTTATGGAAGACCCTATGGGCCAGGCTCACTGGGTTCTATCTTCTACAAATCTTTCTTTCTAG
Seq C2 exon
GAGCCACGTGTGAGGTGGTGTTGGCCCCATGTGCTACCAGCCCCTGCAAAAACAGCGGGGTATGCAAGGAGTCTGAAGACTATGAGAGTTTTTCCTGTGTCTGTCCCACAGGCTGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923:ENSMUST00000028288:15
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=5.1),PF0000822=EGF=PU(90.3=71.8)
A:
NA
C2:
PF0000822=EGF=PD(6.5=4.9),PF0000822=EGF=PU(90.9=73.2)
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:
GCCCTAATTGCCAGACCAACA
R:
TGTGGGACAGACACAGGAAAA
Band lengths:
224-2057
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