MmuINT0152932 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48470427-48471021:+
Coord C1 exon
chr6:48470427-48470591
Coord A exon
chr6:48470592-48470877
Coord C2 exon
chr6:48470878-48471021
Length
286 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
TGATGGTGTCCTGTCTGCAGGCC
3' ss Score
9.17
Exon sequences
Seq C1 exon
CAGGTCTCATCCCTGCTTCTGAGGGTACTCTGCCTGTTTCAGGGCAGCCCATGCAGACACTGTCTGCTACCTCCACCTTCCCTCCTGGTGCCAAGAGCCTACACCCAGGAATGGCAGCTGTGACGGTGCATCCTCCACACTCAGTCACACCAGGAGCTCCTGTTG
Seq A exon
GTAAGACTCTTCTGCATGAAAAACCTGTGTGAACCCACAAGAGGTTCATCACTTAGGTCAAGGTCATATGGCTCCACGGCATTTTTTTTTTTTTTTTTTGCTAGAATGGGCCTTTCTGACTCATTCACTCACTTCGTTTTCATTATCCCAAGAAAGGCAGAAAGTGATGTATCCTAGACACTAAGAGGAGAGAAATTGGAGGCTGCTAGGAACTGACCAAGAGAGAAGGGTAAGGGTGGCTGGTTCCCAAGTCAGCAGGCATCCTGTGATGGTGTCCTGTCTGCAG
Seq C2 exon
GCCAAACTGTCAGCCCCAGGCCCTTCCCACCCATGCCGTGTGGCCCTGGGCAGGTGCCCTGTGATGTGTTGGGCTGTGTGGAGCAGGAACAGCTGTGTGATGGGAGGGAAGACTGTCTTGATGGATCCGATGAGCAGCACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.293
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=75.5)
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:
TCTCATCCCTGCTTCTGAGGG
R:
GTGCTGCTCATCGGATCCATC
Band lengths:
301-587
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