MmuINT0109819 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32120820-32124379:-
Coord C1 exon
chr17:32124282-32124379
Coord A exon
chr17:32122861-32124281
Coord C2 exon
chr17:32120820-32122860
Length
1421 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTGCCCCTCCCCCGCCTCAGGAA
3' ss Score
8.66
Exon sequences
Seq C1 exon
GGAAATCTGCCTTACACTGGGCTGCAGCTGTGAACAACGTGGAGGCTACCTTGGCTCTGCTGAAAAATGGAGCCAACAAGGACATGCAGGACAGCAAG
Seq A exon
GTGAGCCACTGGGGGCCTACAGTGCTACAGCCCCTGAATGTGACAAAGCAGAGTCAGGGAGGAATAAGCCTGTTAGGGGCATCCATCTTGCTTGCAGTCAGCTCTCAGGAGTGGGATTCTGGCCTGAAGGCTGTGAGAGCAAACTGTTGAAGTCGCTGTGTGACATCGAACGCAGTTGTCCCCATTGTGACAGGGGAAGCAGCAGCATGAGCTGCTGAGCTTGAACAAGCCTACTTTTCTTCCTTCCTTCTTTCTTTCTTTTTGAGACTAACTTCCTACCTCAGGTTGGCCTTGAACTCACAATTCTCATATTTCTACTAACTAAATGCTGGTATATGCTCTCATGCCTGGCTTTTTCTTTTTTCAATGATATATTTTATTTTTAAATAGTGTGTGCGTGTAAGTATGTGGACATGAGTTGCAGATATCCTTGAAGCAAGAAGAGGGTGTTGAATCCCCCTAGAGCTGAATCTATAGGCAGTTGTGAACTGCCCGTGTGGATACCAGGGATGGCACTGAAGTCACCAGGCTGAGTGACAAGTGTGGTTACCCACTGTGCCGTCTTGCCGTCTTGCCAGTCTTTACATTGTTTCCTTCTCTTTTGGAGATCATGTCTTACTGGTTAATTTAGCAAAAGCTGACCTCAAACTCTTGGTGAGTCTTCTGCCTTAGCCTCTCAAGTGCTGGGGTCATAGGCTCAGGTTCTCTCTCTGTCTGTCTCCATCTCTGTCTTTCCCTCCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTAAGACAAGGACTCACTTTGTAGACCAGGCTAGCCTAGAACTCAGAGACCCTTTTGCCTTTGTGTCCTGGATGGTAGGACTGAAGGTGTACAGGACCACCAGAACCCCAACAACTCACTTTTTAATCTTTTGTTTTTTTGGTTTTTCAAGATAGGGTTTCTCTGTATAGTCCTGGCTGTCCTGGACCTCACTTTGTAGACCAGGACAAAGAAACTGGTAGAACTCAGAAATCTGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCTTTTTAATCTTTTATAACTCTTTTTAAAACTTTTATAACATCACCATGCAGTTTATTTTGATGACTGGAAGTTTTGATGCCCCTTTAAATTTTGTGCCTAAGGTAAGTCCTGGCCAGATGTGCCTGCTACAGAGAGAGCTTGTTTCTTCAACAGAGCTGGAATCCAAACTCAGGTCCATCTATTTCCAGGGTATCAACTCTTAGTTCTCAGGCTGCCCTAGAGATTAGAAAGCTAGGTGTTGGCCAGAGTGACTGACCTCCGTGGGTTCTGCCCCTCCCCCGCCTCAG
Seq C2 exon
GAAGAGACGCCGCTGTTCTTGGCCGCTCGGGAGGGCAGCTATGAGGCTGCCAAGCTGCTGCTGGATCATCTCGCCAACCGGGAGATCACAGATCACTTGGACAGGCTGCCCCGGGACGTGGCCCAGGAGCGGCTGCACCAGGACATTGTGCGGTTGCTGGACCAGCCCAGTGGACCTCGAAGTCCCTCTGGTCCCCATGGCTTAGGGCCATTGCTCTGCCCACCAGGGGCCTTCCTTCCTGGCCTCAAAGCGGTGCAGTCTGGGACCAAGAAGAGCAGGAGGCCACCTGGCAAGACCGGGCTGGGGCCACAGGGAACTCGTGGTCGGGGCAAGAAGCTGACACTAGCCTGTCCAGGACCTCTGGCAGACAGCTCTGTCACACTGTCACCGGTGGACTCTCTGGACTCACCACGGCCTTTCAGTGGGCCCCCTGCTTCCCCTGGAGGCTTCCCCTTGGAGGGCCCCTATGCCACCACGGCCACCGCGGTGTCCTTGGCACAGCTAGGCGCAAGTAGGGCGGGTCCTCTGGGGCGCCAGCCTCCTGGGGGCTGTGTGCTCAGCTTTGGTCTGCTCAATCCTGTAGCTGTTCCCCTCGACTGGGCCAGGCTGCCTCCACCTGCCCCTCCAGGGCCCTCATTCCTGCTGCCCCTGGCTCCGGGACCCCAGTTGCTCAACCCAGGAGCCCCAGTTTCTCCCCAAGAGCGGCCCCCACCCTACCTGGCTGCTCCAGGACATGGAGAGGAATATCCTGCAGCAGGAACCCGCAGTAGCCCCACCAAGGCCCGCTTCCTGCGGGTTCCCAGCGAGCATCCTTATTTGACCCCGTCTCCTGAGTCCCCAGAGCACTGGGCCAGCCCATCCCCCCCATCCCTCTCAGACTGGTCTGACTCAACACCTAGCCCAGCAACTGCTACCAATGCCACAGCCTCTGGAGCCCTGCCTGCTCAGCCACACCCCATATCTGTTCCCTCCCTCCCTCAGTCCCAGACTCAGCTGGGACCCCAACCAGAAGTTACCCCCAAGAGGCAGGTGATGGCCTAAGTTCTTGGATTTGAGGGGTGCTGAAGTGACACTCCTCTATGACTTCTTTCTTCCTCCTTTTTAATCTTACTCTCATCCCTTTCTCTCTGTCCCAGCCTTCCTGCACCTCTCTGTCTTGTAGTGTGACCAAGTTGGTCACCAGCCCAGACCCCCAGTCTTCCTTTATTTATAATGGGTAGGGGCTGACCTTCCACCACCTTGGCCCCCTAAGGGATCTGGGACCTCCTTTTGATCCCTCTCCCTGCCTCAACTTCCTCCCCCCCCTCTTTCTGCTTCTCATTGTCTCACACTCTGACAAGAGTGAGTTATTATTTTTTTCTTTTTTACATTTTGTATAGAGACAAATTCATTTAAACAAACTTATTATTATTATTATTTTTTACAAAATATATATATGGAGTTGCTCCCTTCCCCCCGCTGCAAATTCCTCCAGCGCCCCCGTGGGGCTGAGTCTGTGGGCCCGTTTGGCCAATCCGGACTCTGTGTACTGAGTACACAGATATGACTAGGGCTCCACGTACTGAGTATGTGGCCCTCGTATGTACCAAGTAGCCAGCCTTGGGCACACCCTCCCCTGGGGTCAGGGGACATTTGGGAGCCTCCTTCCCCTCCCCATTCCCCTTCCTCACTTCACTGCATTCCAGATAAGACGTGTAGACTCACTGGGAAAGGGGTCTTGTCTGCTCAAAGCCTCAACTCCAGGCTCACCTCCCAGAGCCTGGCTCACCTTTTAGGGCCTGGGGTGGGGGGGCACGTCAGGGGAGATGTATTTTGTATGCATTCCACTTCTAATTGTAAATACAGGGCAGAAGGTGGGAGTGGCTCTCCCTCTTCCTGTTGTTCTCTTGGCTCAGCCTGCCTAATAGAAATGTTTTTAGGCTGTTTTTGTAATATGGCACCTGGTCACAGTCCTTTGTAGCTGAATTCCCAGGTCCTGCACTGTACAACCCTCACCTTCTCAGTTCCCTTACCACCTAATAAAGGAATAGTTAATACCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.821
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(34.0=100)
A:
NA
C2:
PF127962=Ank_2=PD(33.0=8.9),PF119363=DUF3454=WD(100=19.3)
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:
GTGAACAACGTGGAGGCTACC
R:
TCTTCTTGGTCCCAGACTGCA
Band lengths:
343-1764
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