MmuINT0152988 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48496619-48497583:+
Coord C1 exon
chr6:48496619-48496665
Coord A exon
chr6:48496666-48497374
Coord C2 exon
chr6:48497375-48497583
Length
709 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
AGTGGCTGGTCTTCCTGCAGAGT
3' ss Score
8.23
Exon sequences
Seq C1 exon
CACCTGTCAAGGTGGAGCCTTCATCTGCTCCCTTACGGACTGTCAGG
Seq A exon
GTGAGATGTGGCTGTCCTTACCTCCCAAGCCAAGACTTTGCTCAGGGAAAGAGGGTCCTATCTACAACCCAGGCTAAGCTACTCGCTTTGGGAAATGGACCCCTTCCTGCCCTGAGCCCTAGCACACCCCACTCCGTAATCCCAGAGCACCCCGTGTGTCTTTTCTATTGCCAGTACAGTACATGCACACTGAGCCAGGCTACATGAGTGAAGCTAGGAATTAAATGCTTCCTGTTGAAGTCCAGGGGGGTGAGTGGAAAGGAGCTGTCTGGCTTGGAAAACTCCAGACCCTCAGCATTCAACTTCTGCTGCTGTCCACCTTTGCCACTCGGGGATCTGTAGATTCAGACATAGGTTTTGCAAATTCCGAAGCACAAATCCTGGCTGCTGAATGAAGGTGGGCAAGCTACCAGAACAAGTATAGACAGGAGACTGTCTCTGAGTTTCTAGCCAGCAGGCAGCACCCTTCTAATGTGGCAGAGTCCTGGAAGTGCAGAGGTGAGGTGGGCAAAAGTGGTGATAGAGTTAGGACTGTCTGGGCCTAGTGTTTGATGAATGGGTCAGAGGGAGAGGCATAGCTGATAGATGGCAGCTGGAGCCACGAGGGCAAAGGAAGAGGTCAGGTCAAGTGCCCAAGGCATGTCTAGTGGGGCGGGAGATCTAGGTTGGATCCAGAGCTGACAGACAGAAGTGGCTGGTCTTCCTGCAG
Seq C2 exon
AGTGCGCTCCTGGGGAAATATGGCAGCATGGGAAGCTGGGGCCTTGCGAGAAGACATGCCCGGAAATGAACATGACACAGGCTTGGAGCAACTGCACTGAGGCACAGGCTCCAGGCTGTGTGTGTCAGCTGGGGTACTTCCGCAGCCAGACAGGTCTCTGTGTTCCCGAAGACCACTGTGAATGTTGGCACCATGGGAGTCCCCATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:97
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:
NO
A:
NA
C2:
PF0182612=TIL=WD(100=84.3),PF0009313=VWC=PU(14.3=11.4)
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:
GGTGGAGCCTTCATCTGCT
R:
GACTCCCATGGTGCCAACATT
Band lengths:
238-947
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