MmuINT0152901 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48456974-48457364:+
Coord C1 exon
chr6:48456974-48457163
Coord A exon
chr6:48457164-48457269
Coord C2 exon
chr6:48457270-48457364
Length
106 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
TGCTTTTACCCTTCACGCAGGAC
3' ss Score
8.49
Exon sequences
Seq C1 exon
CATCTGCCAGGAGAGGGGCCTCTGGAACTGCACAGCCCACCACTGCCCCCGACAGTGGGCTCTCTGCCCTCGGGAGCTCATCTATGTCCCTGGTGCCTGCCTTCTCACCTGTGACAGCCCCCGTGCCAACCATTCCTGTTGGGCTGGAAGCACTGATGGCTGTGTCTGTCCCCCTGGCACTGTATTGCTG
Seq A exon
GTGAGGCTGGAAAAGGGACCCATGGGGCAACAAAGTGCCTCTCCCTACACAAGGAGCCTGCCCTGCTCCCTAGATGCCCAAAACAGTGCTTTTACCCTTCACGCAG
Seq C2 exon
GACAAGCACTGTGTGTCTCCTGATCTTTGTCCCTGTCGCCACAACGGGCAATGGTACCCACCCAATGCCACCATCCAGGAAGACTGCAACATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:18
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:
PF053758=Pacifastin_I=PD(61.8=32.8),PF0182612=TIL=PU(78.8=64.1)
A:
NA
C2:
PF0182612=TIL=PD(17.3=28.1)
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:
CTGGAACTGCACAGCCCAC
R:
AGTCTTCCTGGATGGTGGCAT
Band lengths:
254-360
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