MmuINT0109828 @ mm10
Intron Retention
Gene
ENSMUSG00000015468 | Notch4
Description
notch 4 [Source:MGI Symbol;Acc:MGI:107471]
Coordinates
chr17:34572678-34573908:+
Coord C1 exon
chr17:34572678-34572800
Coord A exon
chr17:34572801-34573748
Coord C2 exon
chr17:34573749-34573908
Length
948 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
CCCCAAACCCTTCCACACAGGTC
3' ss Score
6.5
Exon sequences
Seq C1 exon
GCTTTGAAGGGCCACACTGTGAGAAAGAAGTGGACGAATGTCTGAGTGACCCCTGCCCCGTGGGAGCCAGCTGCCTTGATCTCCCCGGAGCATTCTTCTGCCTCTGCCGTCCTGGTTTCACAG
Seq A exon
GTCAGGAGACAAGAGAAAGAACTGGGAGGGTGTGTGAGCCCACTGCAGGTGGGGAGGAGGCCCCTGGCGGGTGTTAGGTGGTCAGGATGACTAAAACAGAATGAGAACGGCCTTCTGTGCACTGGCCAGGGAGAGCTAGGAGCGTGGCTTGGAAGCAAAGACCTCACTGAATATGCAGGAGTCCCTGGGGTGCCCAGCACTAGAAAAAAACCAGGACAGGATGAATAAATAAGCAAGCAGGTAAAAGCAAGCAATCGTAAACTGACAACCTGCGCTCGGAACTCAGAATCCAGGGGACATGGATGGCAAGAACGGACTCTGCAAAGTCTGACCTCTACTTGTGTGCCTATGGCCCATGCATGTCAGCATACACACACACCACACACACTACACACACACACCCTCACACCACACACATACCACACAGTCATACACACACCACACATAACACACACATACTCACACAAACACACAAACCACACACCTACTCATACACACACATCAAATGCACACACACCCATACACATCACACATACCACACATTTCACACATACACATACCACACACACTCACATACCACACATACACAGCTCACACACCACACACACATACATACACACCTCACACACACCACATACATCATATGTACACACACACCATACCACACACACATCATATGCACACACACCACACGAACACTCACATACTCATACACACACATACACACACAGACACACACACACACAAACAGGACACGATCATACACACACACACTCGGAGCACAGCGAGGTACAGCACAAAGACAAGGACATAGGAAGAGAGAGTGAAAGTGAAGAAAGGACTTGTGCACAGTGAGGAAGCCACACCTGGAGGTGGCCTTTGACCCCCTCAGGACACAAAGGGACTTTCTTTCCTCGTAGACTCATCTCCCCAAACCCTTCCACACAG
Seq C2 exon
GTCAACTTTGTGAGGTTCCCTTGTGCACCCCCAACATGTGCCAACCTGGACAGCAATGCCAAGGTCAGGAACACAGAGCCCCCTGCCTCTGCCCTGACGGAAGTCCTGGCTGTGTTCCTGCCGAGGACAACTGCCCCTGTCACCATGGCCATTGCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015468:ENSMUST00000015612:11
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(16.1=11.9),PF0000822=EGF=PU(90.3=66.7)
A:
NA
C2:
PF0000822=EGF=PD(6.5=3.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGAAGGGCCACACTGTGAG
R:
TGACAGGGGCAGTTGTCCTC
Band lengths:
263-1211
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