MmuINT0149671 @ mm10
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:93261649-93262217:+
Coord C1 exon
chr1:93261649-93261774
Coord A exon
chr1:93261775-93262103
Coord C2 exon
chr1:93262104-93262217
Length
329 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CAGCCTGCTCCATGTTTCAGATG
3' ss Score
8.08
Exon sequences
Seq C1 exon
CCTCTGTGTGCCTGGTCCTGCGTCCATGCCTCAATGGTGGCAAGTGCATTGATGACTGCGTCACGGGCAATCCCTCTTACACCTGTTCCTGTCTCGCTGGCTTCACAGGCCGGAGATGCCACCTGG
Seq A exon
GTGAGTCACTGGGACCCAGGTGGGGGCAAGGTGCCCACTGATTATCCCATACCACACCATTTCCTACCGGCTGGTCATACACCAGGTTCAGGGGAGACACTGCAGGTCCAGTAGTGGCTTTGAGGTCAAAGATCTCTGTCCGCATGATGTCGAAACAGATGGCGGCCACATGCTTTGGTTATGTGGCAGTGAGTGTCGCTGCTGCTGCTCCTAGACACTCTAAGGCCTGTCTGGGACTGGGGCCTAGTCTGTCCTTTACCCCTACCCAAAGCCCTGGCAATTCCTTCACAGTTTCCTCTACTGAGGCCCCAGCCTGCTCCATGTTTCAG
Seq C2 exon
ATGTGAACGAGTGTGCTTCCCACCCCTGTCAGAATGGTGGGACCTGCACCCATGGTGTCAACAGCTTCAGCTGCCAGTGCCCAGCCGGCTTCAAGGGACCCACCTGTGAATCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793:ENSMUST00000062202:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=83.7)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Main Inclusion Isoform:
NA
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:
CCTCTGTGTGCCTGGTCCT
R:
GATTCACAGGTGGGTCCCTTG
Band lengths:
238-567
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