MmuINT0139112 @ mm9
Intron Retention
Gene
ENSMUSG00000035673 | Sbno2
Description
strawberry notch homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:2448490]
Coordinates
chr10:79524907-79525504:-
Coord C1 exon
chr10:79525313-79525504
Coord A exon
chr10:79525077-79525312
Coord C2 exon
chr10:79524907-79525076
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-Sbno2:NM_183426:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.732 A=NA C2=0.211
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138711=Helicase_C_4=PU(6.1=29.8)
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:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: