MmuINT0152973 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48490403-48490676:+
Coord C1 exon
chr6:48490403-48490555
Coord A exon
chr6:48490556-48490629
Coord C2 exon
chr6:48490630-48490676
Length
74 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGC
5' ss Score
8.15
3' ss Seq
GAATCCAGGCTCTTTTCTAGCTC
3' ss Score
0.71
Exon sequences
Seq C1 exon
GTCCTCCACGTCAGGCTCGTGGGCCCTGGAGTGTCAGAAGGAGCAGTCACAGAGCCAGCCTTGCCCTGAGGTCCCCTGCCCACCCCTGTGCCTACATGAAGCCCACCTCCATGAGCTGGGGGACAACTGGCTGCATGGAGAATGCCAGCAGTG
Seq A exon
GTAAGCACGGTCCAGGAAAGGGTGACCCACTGTCCTACTGGACAGCAAGACCCTGAATCCAGGCTCTTTTCTAG
Seq C2 exon
CTCCTGCACCCCGGAGGGAGCGATCTGCAAAGACACTGATTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:83
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:
PF0009014=TSP_1=PD(53.1=50.0),PF0009313=VWC=PU(31.8=40.4)
A:
NA
C2:
PF0009313=VWC=FE(24.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGGAGTGTCAGAAGGAGC
R:
AGTGTCTTTGCAGATCGCTCC
Band lengths:
167-241
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