MmuINT0109838 @ mm9
Intron Retention
Gene
ENSMUSG00000015468 | Notch4
Description
Notch gene homolog 4 (Drosophila) [Source:MGI Symbol;Acc:MGI:107471]
Coordinates
chr17:34718324-34719867:+
Coord C1 exon
chr17:34718324-34718436
Coord A exon
chr17:34718437-34719343
Coord C2 exon
chr17:34719344-34719867
Length
907 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCT
5' ss Score
7.56
3' ss Seq
TTCTCTTCTCTCTGCCACAGGGT
3' ss Score
11.43
Exon sequences
Seq C1 exon
GCCAGCGGTGTGAGGTGGAGATGGACCTCTGTCAGAGCCAACCCTGCTCCAATGGAGGATCCTGTGAGATCACAACAGGGCCACCCCCTGGCTTCACCTGTCACTGCCCCAAG
Seq A exon
GTATCTGATGCAACAGTCCTTTCTCTCTTCTCCTTACACTGATAAGAACACCAGACCCAGAACCCTAGGGCCTTGAGTGGGGCTGGAGTCAGGATTACTGGAGAAGGCCCAATGGTGAGTGGCTCTCAGAAACAGTCATGGGAAAGGCAGAATCAGACACTAGCATGGTGCAATTCTGTAGTCCCTGCCTTTGGGCATCGAGGCAGGAGGATAAAGAGTTGGACGTCATCCTTGGCCACACAATGAATTTGAGCTGGTAAGATGGCTCAGTGGTCTCTTCCAAAGCTCCCAAGTTCAAGTCCCAGCAGCCACAGGGTGACTCACAATGAATCTGACACCAGACTTTCATCTCAAAAAGCAAAATGAAACAACAAAATCCACCTTTTCAAAAATGGCTTTCGACAAGATTTCTAAACACTGTGTGGGTGACAGGTGTGGGTGAGGAGCTCCAGGCAAGAAACTGGCTGAGCCTTGGTTTGTGACAACAGGTTGTACCTTCTTTTCTCACCCTAATGTTCTTGAGCCAAACTCAAGAATCACAATAATAAACACTTTCCCCACTTCCACCTTCCTCCTGTTTACCCTGGGAAAGAAGAGAGCATGTGGACTGTCTCCAGGGATTAAAATGCCACAGTAATCAGTCAACTGCACCAAGCAATGATCTGCCTTCTTGGACTTGCACCCTGAAACACAGCATAGCCACACGTCACCCAGTCCCACCAAGGGCAATAAGCCAGTGTGCGCAGTTAGCAGGGGACCCAGCGACAACATCCATTACAAGGGACGTGATGCTGTCTGAGGTCCCTGTCCTATAGGATTGTCTAGAACCCTCTGTGCCATGTTGTCCTAGCTTGCTTCAGGAAAGAATAACGCAAGGTCCTTTTGCATTCTCTTCTCTCTGCCACAG
Seq C2 exon
GGTTTTGAAGGCCCCACCTGCAGCCACAAAGCCCTTTCCTGCGGCATCCATCACTGCCACAATGGAGGCCTATGTCTGCCCTCCCCTAAGCCAGGGTCACCACCACTCTGTGCCTGCCTCAGTGGTTTTGGGGGCCCTGACTGTCTGACACCTCCAGCTCCACCGGGCTGCGGTCCCCCCTCACCCTGCCTGCACAATGGTACCTGCACTGAGACCCCTGGGTTGGGCAACCCGGGCTTTCAATGCACCTGCCCTCCTGACTCTCCAGGGCCCCGGTGTCAAAGGCCAGGGGCAAGTGGGTGTGAGGGCCGAGGTGGTGATGGGACCTGCGATGCTGGCTGCAGTGGCCCAGGAGGAGACTGGGATGGAGGGGACTGTTCCCTGGGGGTCCCAGACCCCTGGAAGGGCTGTCCCCCGCATTCCCAGTGCTGGCTTCTGTTCCGGGACGGACGGTGTCACCCGCAGTGTGACTCTGAGGAGTGTCTCTTTGATGGCTACGACTGTGAAATCCCTCTAACCTGCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015468-Notch4:NM_010929:20
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:
PF0000822=EGF=PU(79.4=71.1)
A:
NA
C2:
PF0000822=EGF=PD(14.7=2.9),PF0000822=EGF=WD(100=20.6),PF0006612=Notch=WD(100=22.9),PF0006612=Notch=WD(100=21.7),PF0006612=Notch=PU(12.8=2.9)
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:
AGATGGACCTCTGTCAGAGCC
R:
GGAGGGCAGGTGCATTGAAAG
Band lengths:
352-1259
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: