MmuINT0149669 @ mm9
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:95192297-95193025:+
Coord C1 exon
chr1:95192297-95192378
Coord A exon
chr1:95192379-95192843
Coord C2 exon
chr1:95192844-95193025
Length
465 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAT
5' ss Score
4.89
3' ss Seq
GGTTTTCTTAATTCTTTCAGGAA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GTATAAGAAAGTCTACAAAGTTCACCAGGACGTGTGCTTTAAGGAGCGCTGCCAGAGCACAAGCCTCAGGAAACCCAAACAG
Seq A exon
GTGCATCTCTGGGCCAGGCCAGGTTGTGCATGCAGTTCTGTGGGTGGGTAGTGACAGGGCTGGGTCAAGCTAGGTTGTTTGCCCAAAATTGCAGCCCATGTGTGGCTATACTCTACTCAGAATCTAGTGCCCACATGTGCACACAAGAGTGCACAGATAGGCCCAGCTGTGCCTGGAGGTGGTCACTGCCGTTCTGCACAGGGAATGTGGTGCTGACAGGAAAACATGAAATGTGACCAACAGGTCAGTGCCTAACCTGAAGTCCCCCCACAATGCCTGGTTGCTTTCTGCTCATCCCATAGCATCCTTCAGCTGGTGTGTGCAGCTGGACTGAAAGGCCAGGCTCCCTGTCAGCCTGTGAGGGCTTCGCTGGGTTACATATGAGGAACCGATGAGGCTGACAGAGGTAGGGTTTCAGGTACACAAGAGTCTTTCTCACCAAACTGGTTTTCTTAATTCTTTCAG
Seq C2 exon
GAAACAAAGTAACAGTCAAACACTGAAGAGATCTTAAGGAAATCATTCTCCTTCATACCAAGATCTGTTGAGAACTGGAGACACCATCACACCCAGCAACCTGGACACCAAGGTCCTTTATCAGACACTGATGGTGACAACTCAGCACTGTGCTGTTACAGACCCAACCAGGAAGGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793-Sned1:NM_172463:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAAAGTCTACAAAGTTCACCAGGA
R:
CCTTCCTGGTTGGGTCTGTAAC
Band lengths:
254-719
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: