MmuINT0109783 @ mm9
Intron Retention
Gene
ENSMUSG00000027878 | Notch2
Description
Notch gene homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:97364]
Coordinates
chr3:97874783-97876845:+
Coord C1 exon
chr3:97874783-97875042
Coord A exon
chr3:97875043-97876509
Coord C2 exon
chr3:97876510-97876845
Length
1467 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TTCTGTTACCCTTCCTTTAGGGA
3' ss Score
10.11
Exon sequences
Seq C1 exon
ATGTCCAGAGGGCTTCTTGGGAGAATATTGCCAACATCGAGACCCCTGTGAGAAAAACCGCTGTCAGAATGGTGGTACTTGTGTGCCGCAGGGCATGTTGGGGAAAGCTACCTGCCGATGTGCTCCAGGATTCACAGGAGAGGACTGCCAATACTCCACCTCTCACCCCTGCTTTGTGTCCCGCCCTTGTCAGAATGGGGGTACCTGTCACATGCTCAGCCGGGACACCTACGAGTGCACCTGCCAAGTCGGCTTCACAG
Seq A exon
GTAATGGGTTCAGCCAGAGCACGTGCTTTCCGGTCTCCGTGGTGACCTGTACTGTGCACGTCTAGTCCTCAGTGCCTTACCCTGTGTTAGCTACTTCTCACTGCTGTCATAGAACACTTCGATCACAGCAGCTCAGAGCACCACAGCTCCAAGAAGAGTTTGTTTTCTGTTAGTTCTAGAGGAAGGATACATAGTATCTAGGGAAGGTATGGGGGTGGGGTGGGAGGTGGGGGCTGCACCCTGTCAGAAAGTTGGCTGGTCAGGTTTCAACCCCAGATAGGAAGCAGCTCAGCTCACAGCCTGCCCTTGTCTCTGGGCTTCCTGCAGTAGGGGCTCCCCAGGCAGCAGTGCCAGCTGTTAGATACCAGCCTGGGAGGGATGTTTCTCATTCAAACTCCCACACCCGGGTCCCCCAACTCCAGTGCACGTTTAGCGTTATAATACAAGTTGGAATATGGGGAAAAGGCTCAGGGACACTTAAAAAAATCTGTTAATAGATAAATGTTAGCTATTTTAAACAAGTAAAAGGTTAAAAATATGGTTAAGAGGACATAAAATATGTGAGATCTTTTATATAGTATAGAAAGAAAATAATTCAAGAACATTCTAAAACATCTTTTATATTGAGGCACTGAGAATCTTCTAATTTGTCAGATGAGCAGTCAGTGCGTCCTCTACCTTTGGAGAGTTTGAAGGGATAGAGGGGGAGAAAGGAAAAAGGTCAGACACCTTGAAGTTTCTGCTTAGACACTGGCTTTTCTGGCTTCTCCAACTCTTCTTCTCCCTACAACTTACTGACAAAAGGAGAATTGTTTGTCATTTTGGTCCCTGCTGGAGACACTAAACCAATGGTTCTATAAATCTATAAGCCAAAATGAACAGGGTGTTCAAAAAATTAGACTTCCTCTCTTGTGCTTGAAGAAGCATGGTCTTGTTTCTCTAAGAAGTGCTCAACTCGGCAACCATCAGCAGACATGACTGAGAGCTGTGGGGTCTCAGCTTTGTTGCTGTGGTGGCTGGCATGGGTGGAAGGACACAGCATTGGGTGGGCATTGAGGGCAGTTTGAAGAGGTGGCAGCTGTTGGGCAGAGTGGTCAACAGCCAGTAAACAAGAGGCGTTCCCAGCTGAGAAGCAGCTTAACAGCGGACCTGGAGCTAGGAGAGCGATGGATCCTGACCCTGGGCTGCAGGACTAATGGACTCCTGCCGGCCTGGCTTCATGTAGCCAACACTCAGTCCCCTCAGGTGCCCTGTCCCCTGAGTCTTTGAGTCTCACCTTAAGGCCTCAGCCTCTGAAAAACACCATTTGTCTGAAGATCTTCAGGTGACACTGCTATGCGCTGTAGAATCCAAAGTCTAGGGGTCTCCATGTAAGGTCTTGTTGTTCGCTGGCTGGGAGACAGAGCTGCTGAGTGTGGGGCTGGCTCCCTTTGCGAGTGGTACTAAGTTCTGTTACCCTTCCTTTAG
Seq C2 exon
GGAAGCAGTGTCAGTGGACAGATGCCTGTCTATCTCATCCCTGCGAAAATGGAAGCACCTGTACATCTGTGGCCAGCCAGTTCTCCTGCAAATGCCCTGCAGGCCTCACAGGGCAGAAGTGTGAAGCTGATATCAATGAGTGTGACATTCCAGGACGCTGCCAACATGGTGGCACCTGCCTCAACCTTCCTGGTTCCTACAGATGCCAATGTCCTCAGGGCTTCACAGGCCAGCACTGTGACAGCCCTTATGTGCCCTGTGCACCCTCGCCCTGCGTCAACGGAGGCACCTGTCGTCAGACTGGCGACTTCACTTTCGAATGCAACTGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027878-Notch2:NM_010928:3
Average complexity
IR-S
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:
PF079748=EGF_2=PD(28.6=11.4),PF0000822=EGF=WD(100=37.5),PF0000822=EGF=PU(90.9=34.1)
A:
NA
C2:
PF0000822=EGF=PD(6.1=1.8),PF0000822=EGF=WD(100=27.4),PF0764510=EGF_CA=WD(100=36.3),PF0000822=EGF=PU(81.2=23.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCACAGGAGAGGACTGCCAA
R:
GTGAAGCCCTGAGGACATTGG
Band lengths:
356-1823
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: