MmuINT0139090 @ mm10
Intron Retention
Gene
ENSMUSG00000038095 | Sbno1
Description
strawberry notch homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:2384298]
Coordinates
chr5:124381683-124382005:-
Coord C1 exon
chr5:124381859-124382005
Coord A exon
chr5:124381778-124381858
Coord C2 exon
chr5:124381683-124381777
Length
81 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
ACTGCTGTCTGTGCCTTAAGATC
3' ss Score
6.89
Exon sequences
Seq C1 exon
ACTATAACAATATAGGAAAGTTCTTAAACAGAATCCTGGGCATGGAGGTGCATCAGCAGAATGCGCTGTTTCAGTATTTTGCAGACACACTTACTGCAGTTGTTCAGAATGCCAAGAAGAACGGAAGATACGACATGGGAATCCTAG
Seq A exon
GTGAGTGGGGACACCTAACTGTACTCTGAGCTTCTGGTCCGGAGGATCTCTTCACTTACACACTGCTGTCTGTGCCTTAAG
Seq C2 exon
ATCTGGGTTCTGGAGATGAGAAGGTGAGGAAGAGTGATGTCAAGAAGTTTCTAACTCCAGGGTATTCAACCTCCGGCCATGTAGAGTTATACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038095:ENSMUST00000199808:26
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:
PF138711=Helicase_C_4=FE(17.7=100)
A:
NA
C2:
PF138711=Helicase_C_4=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCGCTGTTTCAGTATTTTGCA
R:
CGTGTATAACTCTACATGGCCGG
Band lengths:
181-262
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