MmuINT0149662 @ mm10
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:93284385-93285940:+
Coord C1 exon
chr1:93284385-93284666
Coord A exon
chr1:93284667-93285795
Coord C2 exon
chr1:93285796-93285940
Length
1129 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TCCCCCTTCTTTTTTGGCAGCCC
3' ss Score
8.94
Exon sequences
Seq C1 exon
GGCCTTTGCCACCAGCAAACCTGACTGCCTCTCGAGTCACAGCTACCTCTGCCCATATGGTCTGGGACACCCCCGCTCCAGGTATCTCACTGGAGGCTTATGTCATCAATGTGACCACAAGTCAAAGTACCAAGAGCCGCTACATCCCCAATGGGAAGCTGGTGTCCTATACAGTGCGTGATCTGATGCCAGGTCGGCGGTACCAGCTCTCAGTTACAGCTGTGCAGAGCACAGAGCAGGGCCAGCTGCACAGTGAGCCTGCACACCTCTACATCATCACCT
Seq A exon
GTGAGTTCCGGGACAGGAGGAGGCTGGGGAGTTGTTGAAACCTAAGCTGCTGTTTGCTGCTCTCGGGGTGCAGTGTCCTTGCCCAAAAGAGGCAGCATAGACAACTTGCATGGGCCACTCCTGGGAACAGAGACCTAGGCATAAGGGTAAGGAAGGACAAGTGATAGCATGAGTCTCATCTTATTGTTTTACCAGTCTAATCCCAGCAGGCTTAGCAGCAAATACAGGACCTCATCATGAAAGAGCTACCAAGCAGGCAGCAATGCAGGGGCCCAGGCCTGACCCAAAAGGAGCCACAGGGCATGAGCACCGGAGAGAAGGGCAAGAGACTACAAGTGGCTGGGGAGGACAGGAAGGAACACCTGGACAGAGGACAAAAGCAAAAGGCTGGGGTGTAGACATTCAGGTGGCCACATTAACGACCTCAGTCTATTCCTATGGGTGACAGGGTACTCTACTGGAACCCGAAAGTGCCCTGCATACCCTTTATTCTCAAATCTTACATGAGGTGCCGTGCGAAGAGTTTCGGGAGTGCAGGGAGCAAAACTCAGTGAGAAGACAAGCGGAAGGTGCACAAGAACAGACAAGACAGCAGGTTCTCAGAGTAGGGCTGATGCTCTCCAAGAGAGTGAGGCTCCACTCCAGCCTTCCTGGTCCCCTTCTCCTTTCTCATCCCAGCCCATGAGGCTGCTTTGTGGACATGACAGTGAAGGCAGAGTCTATATGCTATGCTAATCTCAGACCCAACCCTGCCATTCTACCAGCTGGGCTCCAGGCATACCTGCCCTATGAGCCTATCAGTCAGGAGGAGGCAGGTAGAGAAGGAAGGAAGTCACCTAGCTTGAGATGCTGAAGGGCTGTGATCCACAGTCTAGCCTCACTTGGTAAATCGGGACTCTGCTGGAAGTGTGGGGAGCTGATCTTCCAGGCCAGTGTTGTCTGTTACAGCATAAGTGCATGGCCTCTGCTTAGAAAGGTGTAATAGGTGACACAGGCTTCTTAGGCAATGTGCACCCCCTCTGCCCCTGCCTAAGCAGGGCTGGGTGTGAGTTGCCCCTTCTGCAGTGGGGTCAGATACCGGAACACTAGGCAATCTAGTTGGTGGCTACTCCCCCTTCTTTTTTGGCAG
Seq C2 exon
CCCCCAGGGATGGCACCGACAGACGCTGGCACCATGGAGGACACCACTCACGGATGCTCAGAAACAGACCAGCCCCTGTGCGCCTGCCTGAGCTGCGCCTGCTCAATGACCACAGTGCCCCTGAAACACCAACTCAGTCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793:ENSMUST00000062202:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.280 A=NA C2=0.990
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=86.3)
A:
NA
C2:
NO
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:
CGCTCCAGGTATCTCACTGGA
R:
CTGAGTTGGTGTTTCAGGGGC
Band lengths:
346-1475
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