MmuINT0152912 @ mm10
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48460771-48461692:+
Coord C1 exon
chr6:48460771-48461004
Coord A exon
chr6:48461005-48461470
Coord C2 exon
chr6:48461471-48461692
Length
466 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
TCCTCTCCTCTTGACTGCAGGGC
3' ss Score
8.65
Exon sequences
Seq C1 exon
GTTGTGCCACCTCAGTCTGTGGGGAGGGACAGATGTCTTGCCAGTCTGGCCACTGCCTGCCCCTGTCCCTGATCTGTGACGGGCAGGATGACTGTGGAGATGGCACAGATGAGCAAGGGTGCCTATGTCCCCATGGCTCTTTGGCCTGTGCTGATGGTCGCTGCCTACCACCTGCCCTGCTGTGTAATGGTCATCCTGACTGTCTGGATGCTGCAGATGAAGAGTCCTGTCTGG
Seq A exon
GTGAGGAGTCTCTGCCCTGCCTCCAGCCTTCTAGGAAGCCCCTCTCAGGGTCTAGATCCTGAAGTCCCCTGAGTATCTACCCCATTCTATGTCCGGTCTCCACTCATGAAGGTGGTACCTGTGAATGAATAAGTGGAGATCCCCAAAAGAGATAGAATAAGGGGGCAATCCCAGGAGCTGGATTGGTCAGTGGTTAAGAACACATGCTGCTCTTCAAGAAAAGCTGAAATTAGCTCCCAGCATCCACGCTGAACCTTACGACCACCTATAACTCCAGATCTAGGGGTTCTGACATGCTCTTCTGGCCTCCACATGTCCCTGTACACATGTAGCATACATGCACAGACACACACACGTAGCATACATGCACAGACACACACATGTAGCATACATGCACAGACACATACATTTTTTACGTCTTAAAAGGGGTGAATCTCAGGATCACCTCCTCTCCTCTTGACTGCAG
Seq C2 exon
GGCCTGTGAGCTGCATCTCTGGAGAGGTATCTTGTGTTGATGGCACTTGTGTTAGGACTATCCAGCTATGTGATGGAGTTTGGGACTGCCCAGATGGAGCTGATGAGGGGCCTAGCCACTGCTCTCTGCCTTCTCTGCCTACTCCTCCTGGGGGCATTGGGCAGAACCCTTCCACCAGTTCCCTGGATACAGCACCGAGTCCTGTGGGTAGTACCAGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797:ENSMUST00000169350:28
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=0.293
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=PD(2.6=1.3),PF0005713=Ldl_recept_a=WD(100=46.8),PF0005713=Ldl_recept_a=WD(100=45.6)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=52.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGACAGATGTCTTGCCAGT
R:
AGGAGTAGGCAGAGAAGGCAG
Band lengths:
356-822
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