MmuINT1032241 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48458970-48459430:+
Coord C1 exon
chr6:48458970-48459166
Coord A exon
chr6:48459167-48459302
Coord C2 exon
chr6:48459303-48459430
Length
136 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGC
5' ss Score
4.78
3' ss Seq
ACAAAAGTACCGTTTTGCAGGTG
3' ss Score
5.74
Exon sequences
Seq C1 exon
GCACCCGGGTGCTGGTACAGCTGTCCCCCCACTTCCATGGTCGTGTGGCCGGGCTGTGCGGAAACTTTGATAGTGATGCCAGTAATGATCTGCGGAGTCGCCAAGGAGTCCTGGAGCCCACAGCAGAACTGACTGCGCATTCCTGGCGCCTCAATCCCCTGTGCCCTGAGCCAGGAGACCTGCCACATCCTTGTACC
Seq A exon
GTGAGCAGGACAGGGTAGCCAGAAGGGAGGGTGGATATACTAGCAGAGAGAGAGAGAGAGAGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGATCCACAAAAGTACCGTTTTGCAG
Seq C2 exon
GTGAATGCCCATCGGGCAAACTGGGCCCGGGCACGCTGTGAGGTGATATTGCAGCCAATCTTTGCCCCATGCCACACAGAGGTGCCCCCACAGCAGTACTATGAGTGGTGTGTGTACGATGCTTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:22
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=0.008
Domain overlap (PFAM):
C1:
PF0009420=VWD=PD(24.0=56.2)
A:
NA
C2:
PF087426=C8=PU(49.3=86.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGTAATGATCTGCGGAGT
R:
GCATCGTACACACACCACTCA
Band lengths:
242-378
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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