MmuINT0152904 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48457572-48458240:+
Coord C1 exon
chr6:48457572-48457828
Coord A exon
chr6:48457829-48458105
Coord C2 exon
chr6:48458106-48458240
Length
277 bp
Sequences
Splice sites
5' ss Seq
GAGGTGACT
5' ss Score
5.88
3' ss Seq
CACCTTCCCTTCTTCTTCAGGCC
3' ss Score
10.94
Exon sequences
Seq C1 exon
TGTGTGCCAGGGCCAGCGCTGGCACTGTACAGGTCAGCGGTGCAGTGGATGGTGCCAGGCGTCCGGCGCACCCCACTATGTGACGTTCGATGGGCTGGTCTTTACCTTTCCTGGGGCCTGCGAGTACCTGCTGGTGAGAGAGGCTGGTGGCCGCTTCAGTGTCTCCGTCCAGAACTTGCCTTGTGGGGCCAGTGGCCTCACATGTACCAAGGCGTTGGTTGTGCGTCTGGACAGCACTGTTGTGCACATGCTGAGAG
Seq A exon
GTGACTGTGACCTAGCAAGAATGGCTGGATACAGGCAGAGGGTGTGGGGTAAAGCAGCGTAGCATCATAGCTCTTCCCAGCTCCTCCCTGGGTTTTGTTGTCCTATGGTGGGGTGGGGTGGAGCCAAAACTCTGGAAGGCTGTGAGATCGAGGCCCAGAGAAGACTAATGACCCACCCAAGGTCACCTAGGAAATGATGCAAAAGAAAGTTTGGAAGAGTGGCTGGGTGGATCTCTCGGGGACCAAACTAAGTTTAACACCTTCCCTTCTTCTTCAG
Seq C2 exon
GCCAGGCCGTAACAGTGAATGGAGTGAGCATAAGGCTCCCCAAAGTCTATACAGGCCCCGGCCTGAGCCTGCACCATGCTGGCCTCTTCCTGCTGCTGACAACACGCCTGGGTCTCACTCTGCTCTGGGATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:20
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:
PF0009420=VWD=PU(45.3=78.2)
A:
NA
C2:
PF0009420=VWD=FE(30.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGATGGGCTGGTCTTTACCT
R:
ATCCCAGAGCAGAGTGAGACC
Band lengths:
302-579
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