MmuINT0152952 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48480620-48481129:+
Coord C1 exon
chr6:48480620-48480826
Coord A exon
chr6:48480827-48480958
Coord C2 exon
chr6:48480959-48481129
Length
132 bp
Sequences
Splice sites
5' ss Seq
ATCGTAAGT
5' ss Score
10.44
3' ss Seq
CTCCTCTGCTGCTCCCTCAGAAG
3' ss Score
6.88
Exon sequences
Seq C1 exon
GCCAGCCTGCATGGTCATCCTGGACTCCATGGAGTGTGTGTTCAGCCTCCTGCAACCCTGCCCGACGCCACCGGCACCGCTTTTGTGCCAGGCCCCCCCATAGGGCACCCTTCAGTTTGGTTCTGCTGACCACAGTGGCTGCCCCCACAACCCTCTGCCCAGGCCCTGAGGCTGAGGAAGAGCCGTGCCTCCTGCCAGGATGTAATC
Seq A exon
GTAAGTGGCCCTTTAAGCTGATGCTTGCCCTGAAGCCCTGGATGGGACCATCTCTGGGGTACCTCATCCTTGTACCAGCAGCCTCCAGCAACCTCAAACCTTTTCACATTTCCTCCTCTGCTGCTCCCTCAG
Seq C2 exon
AAGCAGGGGGCTGGAGTCCTTGGAGCCCCTGGTCTGGCTGTAGTCGGAGCTGTGGAGGAGGCCTGCGGAGCCGGACCCGAGCCTGTGACCAGCCGTCACCCCAGGGCCTGGGGGATTTTTGTGAGGGACCTCAGGCCCAGGGGGAGGCCTGCCAGGCTCAGCCATGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:64
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=90.0)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCATCCTGGACTCCATGGA
R:
CTCCTCCACAGCTCCGACTAC
Band lengths:
255-387
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