MmuINT0139085 @ mm10
Intron Retention
Gene
ENSMUSG00000038095 | Sbno1
Description
strawberry notch homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:2384298]
Coordinates
chr5:124387477-124388660:-
Coord C1 exon
chr5:124388525-124388660
Coord A exon
chr5:124387590-124388524
Coord C2 exon
chr5:124387477-124387589
Length
935 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TATACACATTATTGTTACAGGAA
3' ss Score
7.06
Exon sequences
Seq C1 exon
AATATTGCTATTATCTCAGAAGCTGCCAGCTCAGGTATTTCATTACAAGCAGATCGGAGAGCTAAAAACCAAAGGCGAAGAGTTCACATGACTTTAGAATTACCTTGGAGTGCTGATAGGGCGATTCAGCAGTTTG
Seq A exon
GTAAGTGTCTCTACTGCATCCCACTGTGAGGAAAGGTGAGAGTCCTCTGTCTGTATGAGATACCAGAAGCTTAGGGAACTCTCAGATTCTATCCTGGAAGTGTGTTCTCTGTATGCTGTGATGTGCAATGCATGAGGAACTCCTTTTTACCAGTTTTCAAATGATATTGAGATCTCTGGTAGGATTGCAAAGGGGTCCTGGCCTTCCAGAACAGGGTTTCTCGGAAGTATCTTCATTGTGTGTTTGTATACTATGTGAGTCTTTCACAGTAGCCCACTATTTCCACAGTCGTTTCAGCTCTCAGTAGCTACATGTGGTGTACATTACTCTTCATGTGCATGGTTCTGTGACCTGGTGATCTACACATGACATCTAAAGTGGCTATGTAGTAACACTGGCTAACCAAATGATGGCAGCGTTTGAACAGTTATGGCAGATTCTGATCCTTGGGTGGTAATGCCAATGACTAGCGTTTCAATTGCTGTTATGGGGAGCTGGGAAGGGTTGTATTATTTTTAATTTTCGTTTTGAGGGTTCATTCTTTCTCTCTGTTTCCCTCCCTCCCTCCCTCCCTCCCCCCCCCCCTCTCTCTCTCTCTCTCTTTCTCTCTTTCTCTCTCTTTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTTTCTCTCTTTCTCTCTTTCTCTCTTTCTGTGTGCATGCTAGCTTGGCCAGGTTGATGTGTGCATGCTTGCACTCTCAGCACTTGATTTGTAGACACAGAATTACCAGGTGTTTAAGGCCTGACTTTAGCTGCATAGTGTGTTTGAGGCCATTTTGGATCTTGTCTCTTTACCTATTAAGTATTCAAGCTATGAATTAGGGCCTCAGACCCTCCCATTTCTACCTACGTGATCATTGAACTATACACATTATTGTTACAG
Seq C2 exon
GAAGAACACACAGGTCAAACCAAGTGACTGCTCCAGAGTATGTTTTTTTGATTTCGGAACTGGCTGGAGAACAGAGATTTGCATCTATTGTTGCTAAAAGACTTGAGAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038095:ENSMUST00000199808:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(16.2=100)
A:
NA
C2:
PF138711=Helicase_C_4=FE(13.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGCTATTATCTCAGAAGCTGCCA
R:
CAAACTCTCAAGTCTTTTAGCAACA
Band lengths:
246-1181
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