MmuINT0152934 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48472394-48472813:+
Coord C1 exon
chr6:48472394-48472564
Coord A exon
chr6:48472565-48472648
Coord C2 exon
chr6:48472649-48472813
Length
84 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TGGTGTGCTGTCCCCTGCAGTAG
3' ss Score
7.83
Exon sequences
Seq C1 exon
CAAGTGCTGAGCCCTTCACTGTGCCTACTACTGCCCTCCCTGGGTTACCAGCCTCAAAGGCCCTCTGCTCCCCAAGTCAGCTGAGATGTGGCAGTGGGGAGTGTCTACCTTTTGAGCATCGCTGTGACCTTCAGGTGAACTGCCAGGATGGCTCTGATGAAGACAACTGTG
Seq A exon
GTACGTGCTGGCCTAAGGCACCATCTTGAGGGTCCTATTCCTGCTTGAGCCGCCTTCTAAGCCCTGGTGTGCTGTCCCCTGCAG
Seq C2 exon
TAGACTGTGTGTTGGCACCTTGGTCTGGCTGGAGTGACTGCAGCCGCAGCTGTGGCCTGGGCCTCATCTTCCAGCACCGAGAGCTGCTAAGACTTCCCCTGCCTGGAGGCAGCTGTCTGTTGGACCAGTTCCGTAGCCAGTCCTGCTTTGTGCAAGCCTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=WD(100=63.8)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.5)
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:
TTGAGCATCGCTGTGACCTTC
R:
TCCAGGCAGGGGAAGTCTTAG
Band lengths:
167-251
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