MmuINT0152945 @ mm9
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48427574-48427940:+
Coord C1 exon
chr6:48427574-48427620
Coord A exon
chr6:48427621-48427769
Coord C2 exon
chr6:48427770-48427940
Length
149 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
CTGCCCCTTCACCCTGGCAGTGG
3' ss Score
6.82
Exon sequences
Seq C1 exon
CACCTGCATCTCTGGAGAAATGGTGTGCACCTCAAAGCGCTGTCCAG
Seq A exon
GTACTCCCTTCATGTGGTGGTCAGTGCTGAGACTATGCAATTTTAGACCCTTCAGAGATAACCTCTTAGGGTGTTGGTAATGTCCCAGGAAAGTCAGGGTCCAGGACAGCTTGCCCTGGTCTCAGACATCTGCCCCTTCACCCTGGCAG
Seq C2 exon
TGGCCTGTGGCTGGAGCCCCTGGACTCCATGGAGCCCTTGCAGCCAAAGCTGTAATGTGGGCATTCGACGGCGCTTTAGAGCAGGCACTGAACCACCTGCTGCCTTTGGGGGTGCTGAGTGCCAAGGTCCCAATCTAGATGCTGAATTCTGCAGTTTGAGGCCATGCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797-Sspo:NM_173428:58
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=0.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=FE(26.2=100),PF053758=Pacifastin_I=FE(53.3=100)
A:
NA
C2:
PF0009313=VWC=PD(39.3=41.4),PF053758=Pacifastin_I=PD(3.3=1.7),PF0009014=TSP_1=WD(100=87.9)
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:
CCTGCATCTCTGGAGAAATGGT
R:
GCATGGCCTCAAACTGCAGAA
Band lengths:
212-361
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: