MmuINT0152933 @ mm9
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48420877-48422563:+
Coord C1 exon
chr6:48420877-48421020
Coord A exon
chr6:48421021-48422392
Coord C2 exon
chr6:48422393-48422563
Length
1372 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
CTCAAATGACCAATTGGCAGCAA
3' ss Score
-1.55
Exon sequences
Seq C1 exon
GCCAAACTGTCAGCCCCAGGCCCTTCCCACCCATGCCGTGTGGCCCTGGGCAGGTGCCCTGTGATGTGTTGGGCTGTGTGGAGCAGGAACAGCTGTGTGATGGGAGGGAAGACTGTCTTGATGGATCCGATGAGCAGCACTGTG
Seq A exon
GTGAGCTGGAGAGATTACATCACACACTGGGCATGCCAAGAGGGTTTCAGGTCTGGGAAGCTCATATGGGAAGGATATAAGAGGGGCTGGAGCAGCAGGGAATGGGGAGACATTGTTAAAAATGACTAGGAGCACCAGAGTCTTTGAAGATGATGAAGAGAACGGGCTAGGCATCGGGTCCCAGCCTGTTTTGTTAAACCTATTTGACTGCTAAGGATACTCAACTGTCCATCAGTCTACCTTCCCAATTATCTGTTGATACATCCACCCATCCATCCCCCCACACTCACCCATCTACCCACCCACTTATCCATTGCTCCATCCACCTCTTTATGTGTCTGTCATCCACCTTCTCTTTTTAAAAATATTTTTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCGCGCGCGCATGCGCGCGCGCGCTCCTGCATGCATGAGCATATACCACATGCGTGTACTCATGGAGACCAGATAAGGATATTGAATCCCTTGAAATTAGAATTAAAATGGTTGTGAACCACCATGTGGGTGCTGGGAATCAAACATGGGTCCCCTGGAAGAGAAAGCAATGCTCTTAACCACTGAGGTATCTCTAACCCCACCAATATACTCTCAAACCTACCCATCCATACACACCCATACATCTGATCATTTATTCAATATGTCCATCCCTTTCTCCAAACGTATATCCATTAATCTATTGACCCATCTATCTACCCATCTTCCCACGTATCCATTTGCTATCTATCATATTATCTGTTGTCTGTCTGTCTGTCTGTCTGCCTATACATTCATTTATTTACTCTTGCACCTGCCTACCCACCTATTTACTTACCATCTACTTAGCTATCTCATTCACACACTCATCTCTCTGTCCATCCATCTATCCATGTACCCACATATTTATCCATCTATCCACATAGTCTACTCATCTGTCCATCCACCTATCCACCCATTCACCTACCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAAGGTAAATCATTTTCATCAGTTTGGTTTTACAACCCAAAGAAAAGGTGTTAACCAGTTATAGTAACTGGCACCCTGGGGAGAACCCATTCGGAGAGAGGATAACCAAGGGGTAGGGCTGTTCTGCATGCACTGACTTCTCTCTGGAAAGTGGAGAAACTGTGAGAACTGTGTAGAGCAAAGAGCTTGTGTGGGCTCATCCTGGGTAGAAGATGCCAGAAGCACTGGGAGGAGTGGAAAGGCCAGAGCCCCTGCTCAGCAAACTGTCCTGATCAAGTTCAAGGGACTCAGTTTCTTACCCAGCCAGAAATCATTTATGGGACTCCCTTCTCTCTCCTCAAATGACCAATTGGCAG
Seq C2 exon
CAAGTGCTGAGCCCTTCACTGTGCCTACTACTGCCCTCCCTGGGTTACCAGCCTCAAAGGCCCTCTGCTCCCCAAGTCAGCTGAGATGTGGCAGTGGGGAGTGTCTACCTTTTGAGCATCGCTGTGACCTTCAGGTGAACTGCCAGGATGGCTCTGATGAAGACAACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797-Sspo:NM_173428:47
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=WD(100=75.5)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=63.8)
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:
GCCAAACTGTCAGCCCCAG
R:
CACAGTTGTCTTCATCAGAGCCA
Band lengths:
315-1687
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: