MmuINT0149675 @ mm10
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:93271142-93271703:+
Coord C1 exon
chr1:93271142-93271267
Coord A exon
chr1:93271268-93271598
Coord C2 exon
chr1:93271599-93271703
Length
331 bp
Sequences
Splice sites
5' ss Seq
AGAGTATGT
5' ss Score
5.66
3' ss Seq
AATCCCCTCACCCCACACAGGGA
3' ss Score
6.79
Exon sequences
Seq C1 exon
GAAGCTACCTGGTGCCTTCACCCTGCCTCTCCAACCCCTGCCAGAACGGGGGCACCTGTGTGGATGCTGATGAGGGATACGTGTGTGAATGCCCTGAAGGCTTCATGGGCTTGGACTGCAGAGAGA
Seq A exon
GTATGTTGGGGCTGCTGGGGCTGTGCCCAGGGTTGGAGCAGAGTTGGGGAGGGTTCTCTCGGGTTGTATGTGCAGGAAACTCCAAGAGGGAAAAAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTCAGTAGTTTTTTGGGAGGGTGGCCAGGGTGGCCAGGGTTGACCAGGGTTAGGAAAAGGGGGCCACATTCTTTCACCCATGGATGCTTTTACTCTATTCTCACACAAGAATCCCCTCACCCCACACAG
Seq C2 exon
GGATCCTCAATGACTGTGACTGCCGGAACGGAGGCAGATGCCTGGGTGCCAACACCACCCTCTGCCAGTGTCCTCCAGGCTTCTTTGGGCTCCTCTGTGAATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793:ENSMUST00000062202:9
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=72.1)
A:
NA
C2:
PF126612=hEGF=WD(100=36.1)
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:
GAAGCTACCTGGTGCCTTCAC
R:
CAAATTCACAGAGGAGCCCAA
Band lengths:
231-562
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