MmuINT0149666 @ mm9
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:95185885-95186662:+
Coord C1 exon
chr1:95185885-95186001
Coord A exon
chr1:95186002-95186574
Coord C2 exon
chr1:95186575-95186662
Length
573 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
CTTTCTCTTTTGCATCATAGCCT
3' ss Score
7.5
Exon sequences
Seq C1 exon
GTACCCCTGGCAGCTGTTCAGAAGATGCTTGTCAGAATGGAGGCACCTGTGTCCCAGGTGCCGATGCCCACAGCTGTGACTGCAGGCCTGGGTTCAAAGGCAGACACTGTGAGCTTG
Seq A exon
GTAAGTCAGAGCCTGCTACTAAGGGGGTATTGGCCTCAGGGCAACTGTCGTGCTAGCCTGGAACTTGGCGCTGAGATGCCCAAAGCACTGGTTGAGAAGCACTGCAGAATAAAGCCTAGGAAGTCAGGAACTGGGGTGGTGATTCCAAAGCAACATCTCAGAGCCAGACCGATGAGAGGGACAACAGATTCAGTGGCAGGATCATAGGCTCCTCAGAACACATTTGGACTGAGTACCCAAAGTGTTGGAAGCTCCAGGAAGACACAAAAGAATCCTGAGGCCACATGAAACTTAAAGAAAACCAGCCTGCAGATGCTGAACACCCTACCCTGAAGCAAGGCCCCAGAAAGGAACTGGCACAGATCCACAGGCTCACACACAGATCCACAGGCTCACACACAGATCCACAGGCTCACACACAGATCCACAGGCTCACACACAGATCCACAGGCTCACACACAGATCCACAGGCTCACACAGGCTTGCAGGGGCTTCCTGGAGGAGGGGTCTCACTTGAGAGGTGGAAAGAGCCTCTGCCTAAGAGCTGCCCTTTCTTTCTCTTTTGCATCATAG
Seq C2 exon
CCTGTGAAAAAGTGCCCCGCCCCTGCACACGGCTGTTCTCTGAGACCAAGTCATTTCCTGTCTGGGAAGGCGACATCTGCCACCATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793-Sned1:NM_172463:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=77.5)
A:
NA
C2:
NO
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:
TGGCAGCTGTTCAGAAGATGC
R:
ACATGGTGGCAGATGTCGC
Band lengths:
198-771
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: