MmuINT0149660 @ mm10
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:93283202-93283687:+
Coord C1 exon
chr1:93283202-93283385
Coord A exon
chr1:93283386-93283574
Coord C2 exon
chr1:93283575-93283687
Length
189 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
CTCCTGTCCACTTCTGACAGGGA
3' ss Score
7.39
Exon sequences
Seq C1 exon
GACCCCGCCCTATAGAAGACTTTGAGGTCACCAACATTTCAGCCAATGCCATCTCAGTGCAGTGGGCTCTTCACAGGATCCAGCACGCCACTGTCAGCAGGGTCCGGGTGTCCATCCTCTACCCCGAGGCCTCTGCGGTCCAGTCCACTGAGGTGGACAGGAGTGTGGACCGCCTCACATTTGG
Seq A exon
GTAAGAGAAGATGCTGCAGGAATACAGGTCCCAGAGTGTTCTTTGTGTACCTGCCTGCCATCCATCATCTGAGGGGGGTGGGGCCTGATCTGACCCTCACAGAGTTGGCCAGGACCACTATCAGCAAAATAGGACTCCTGGTCATTTAGAGCTCCTAGATGCTCCTCTCCTCCTGTCCACTTCTGACAG
Seq C2 exon
GGACCTGCTGCCAGGGAGAAGATACACTGTGCGGCTAACCACCCTTAGTGGGCCTGGAGGAGCTGAATATCCTACCGAGAGCCTGGCTTCAGCTCCACTGAACGTGTGGACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793:ENSMUST00000062202:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.234
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(71.4=96.8)
A:
NA
C2:
PF0004116=fn3=PD(27.4=59.0)
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:
GACCCCGCCCTATAGAAGACT
R:
ATATTCAGCTCCTCCAGGCCC
Band lengths:
254-443
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