MmuINT0139112 @ mm10
Intron Retention
Gene
ENSMUSG00000035673 | Sbno2
Description
strawberry notch homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:2448490]
Coordinates
chr10:80062162-80062759:-
Coord C1 exon
chr10:80062568-80062759
Coord A exon
chr10:80062332-80062567
Coord C2 exon
chr10:80062162-80062331
Length
236 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
ACCTTCTGCCCCATCCCCAGGTT
3' ss Score
9.71
Exon sequences
Seq C1 exon
GGCGGCCTCGGGGTCGTGGCCCCAAGGCTTCCAGACTGTCACTGGAGGCAGCAGGAGTTATCCGTATTAGTGATGGCAGCAGCACAGAGTCAGATGCTGGCCTGGATAGCGACTTCAATTCATCCCCAGAATCCCTGGTAGACGATGATGTGGTCATTGTAGACGCCCCCACACACCCCACAGATGACCGAG
Seq A exon
GTGAGCCTCCATCATCCAGCCAGACTCAAGGCAGCAGACATAACCACATGAGGCCTATTCCACCAAACACCCTTGTTACAGATGGGGAAACTGAGACTCACAGCCAAGGTCAGGGCTATGCTATCAAATAAAACAGAGTGACTGCTGTTGTACCCATGGGTCTCCATTCCTCTCCTGTGAGTCTTCTCATCCTGGTCCTGCAAAGCCACCTCACTGACCTTCTGCCCCATCCCCAG
Seq C2 exon
GTTCCCTGTACCCACTTCAGAGAGACCTGCAGGGCCCTGGTGTCGTGGAACGGGTAGAACGGCTGAAACAGGGTCTGCTTGCCAAGGTGCGAGCGCTGGGCCGGGAGCTGCCAGTCAACACGTTGGACCAGCTCATCCACCAACTTGGGGGTCCTGAGTGTGTGGCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035673:ENSMUST00000219260:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.588 A=NA C2=0.202
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138711=Helicase_C_4=PU(6.1=29.8)
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:
CCAAGGCTTCCAGACTGTCAC
R:
GATGAGCTGGTCCAACGTGTT
Band lengths:
308-544
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