MmuINT0152975 @ mm9
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48440817-48441575:+
Coord C1 exon
chr6:48440817-48441161
Coord A exon
chr6:48441162-48441407
Coord C2 exon
chr6:48441408-48441575
Length
246 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CCATCCCTGCCCATCTCTAGACG
3' ss Score
6.79
Exon sequences
Seq C1 exon
TGCCCAGAGGCTGGACATTGTGGTCCTCCTGGTCCTACTGTTCTGTCTCTTGCGGAGGGGGAAGCCAGGTCCGCACTCGATCCTGCACGGTGTCAGCCCCTCCGCATGGGAGCCTATCTTGCGAGGGCCCAGACACCCAGACCCGGCACTGTGGGCAGCAGTTGTGCCTGCAGAAGCTAGAAAGGTGCTCCTGGGGACCATGGGGACCCTGTTCCCGCAGCTGTGGCACAGGTCTGGCCTCCCGCTCTGGATCCTGTCCCTGTCTACTGACCAAAGAGGACTCCAAGTGTAATGACACATTCTTAGGCCTGGACACCCAGGCCTGCTACTCAGGGCCCTGTCAGG
Seq A exon
GTGAGTTGTTCCCCTGCTTTTCTTCCTTGGAAAATTCAGGGAATAAAGGTTTGCCCAGGCCAGATTCTCTCTCTGAAATGTCCCTATTTCTACTTCACAACAACTTACATCATTCCCTTCAGAGCCCTTTGTGGAGTACTCTTAGCCTGCCTTGACTTCCTCTTTCCCTTTTCCAGCTAAGGGAGGGAGGGTGTGGGCACAGGGGAGGATGTGGGACCCCCAGCCTCCATCCCTGCCCATCTCTAG
Seq C2 exon
ACGACTGCACGTGGGGCGACTGGAGCAGCTGGACACGCTGCTCCTGTAAGGTCCTGGTGCAGCAGCGTTACCGACATCAGGTGCCAGCACCTGGCCAGGCTGGAGAGGGCACCCCTTGCACCCGTCTGGATGGCCACTTCAGGCCTTGTACCATTGGCAACTGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797-Sspo:NM_173428:85
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.018
Domain overlap (PFAM):
C1:
PF0009313=VWC=PD(42.4=24.1),PF0009014=TSP_1=WD(100=44.0),PF0009014=TSP_1=WD(100=44.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGGGAGCCTATCTTGCGAG
R:
ACCAGGACCTTACAGGAGCAG
Band lengths:
299-545
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: