MmuINT0109781 @ mm10
Intron Retention
Gene
ENSMUSG00000027878 | Notch2
Description
notch 2 [Source:MGI Symbol;Acc:MGI:97364]
Coordinates
chr3:98138642-98139682:+
Coord C1 exon
chr3:98138642-98138852
Coord A exon
chr3:98138853-98139585
Coord C2 exon
chr3:98139586-98139682
Length
733 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGA
5' ss Score
6.42
3' ss Seq
TCTCCCCTGAATATCATCAGAAA
3' ss Score
4.6
Exon sequences
Seq C1 exon
GTGAACTGGAGAGTCCAAGAAACGCCCAGCTTCTCTATCTGCTCGCGGTCGCTGTTGTCATCATCCTGTTCTTCATCCTGCTGGGGGTCATCATGGCCAAGCGGAAGCGCAAGCATGGCTTCCTCTGGCTGCCGGAAGGGTTCACCCTCCGCCGAGACTCTAGCAATCACAAGCGCCGTGAACCTGTGGGACAGGATGCCGTGGGGCTGAA
Seq A exon
GTAAGAGGGCTTTACAATAAGACACAGTTCACAGGGAGAAGCAGAGATGAGCAGATGGGCATATTACTGAATCATAATCTCAAATTCTAAATTCACCTTTAGTCACCTTGACCACAGCTCCTAATGGCTTGTCTAGGTCTTTGAGTATGGCCGCCTCTTTCTGTGCACACCTGACGAAGTGCCGCTCAATGTTTGAGTGGGAGAACACTCAAAAGACATGGTCTTTTAGTGAGAAGAGAAAGAATGAGTGCTCAGAAGTGTCACATCTCACATTGCCCATCAGAGTTGGTGTGGTGGCCCTGTAGGTGAAAGTGCCCCCGCCACGTCTGCTGACCTGAGTGTGATCCCCAGTGCCCATAAGCTAGAAGGACGGAAGTGACTTCCTCATGTTGTGCTGTGAGTGTGTAATATAATTAGAGGGCTGGAGGGATACTTCAGTAGTCAAGAAAGGAACTGACCTGGGTTCAGTGCCCAGCACCCATGCTGGGCAGCTTACAGCCCCTGTGATTCCAGCTGCCACGGGATCTGTAGACACCTGAACTCACATGCTCAGATACACACAGACATAGACACTTAATTTTGAAAAATGTTAATATAATTTTGAAAAAGTGCTGTGCATCCTATCCCGTTGGACAGAGTGAGAGGATGTGTGGGAGTGCTGGTGAAGTGCAGAAAGCTACTGCGTTTGCCCAGCTGTAACCTCTCCTCTTGTTTCTCCCCTGAATATCATCAG
Seq C2 exon
AAATCTCTCCGTGCAAGTGTCAGAGGCTAACCTGATTGGTTCTGGGACAAGTGAACATTGGGTTGATGATGAAGGACCCCAGCCAAAGAAAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027878:ENSMUST00000079812:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.155 A=NA C2=0.515
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(14.8=12.7)
A:
NA
C2:
NO
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:
GAGAGTCCAAGAAACGCCCAG
R:
CTTTCTTTGGCTGGGGTCCTT
Band lengths:
295-1028
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