MmuINT0152892 @ mm9
Intron Retention
Gene
ENSMUSG00000029797 | Sspo
Description
SCO-spondin [Source:MGI Symbol;Acc:MGI:2674311]
Coordinates
chr6:48448643-48450520:+
Coord C1 exon
chr6:48448643-48448773
Coord A exon
chr6:48448774-48450369
Coord C2 exon
chr6:48450370-48450520
Length
1596 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
AACCAGTCGCTCTTGCCCAGGAA
3' ss Score
2.84
Exon sequences
Seq C1 exon
AGGAGGAGCCAGTCTCCTGCAGGTACCTCACAGAACTCAGAAACCTCACCAAGGGTCCCTGCCACCTGGATCAGATAGAAGTGAGCTACTGCAGTGGACACTGCAGGTCCAGCACCAATGTCATGACTGAG
Seq A exon
GTGAGCTGGGGGCTGTTGTAACATTCCATGGGGTAGGTCGGCCAGTGACTCTGGGGCTCTTGACGCTATCTGAGGACCTAGGAAAAACCCAGAGACCGTGAGGAACATCATCCATTCTCATAGAGCTGACAGAACTGGGCCTATGGAGTGTCAGAGTCCTTCTCCGAGGTAGTGGTATACGCACATCCCCTGAGTATGTCTCTCGGCCATATTGTGTCCATCTAAGCTGATAAGCCAAGATGCCCACAAAGAAAGGAGGGCCAGACCCATCATGCTTACTGCAGGAGGGTATCCAGAGTCGCCCCACCACCCTGGGCTTTCCTTGTAATGTCTACACCTGAGCAGGCCCAGCATCAAGTTCTCTCTGCTTGCTCCCCTTGGACGCAGCTTCACCCCCTGATTTCCTCAGCTTCCAACCTGGAAAGCTGTAACTGGGACCACTAGCATCCCTTTGAATGGAGACCCGATCCTGACTCCCAGGACCTCACATCCATCCTTAAGTCCATTCCCTTCTGCTTCCACCACGCTGGGTTAGCAAGTGCCAGAGAACAATGGTGGTTCCCAGATGTTGCCCCTCAGCCTGCGCTGTGCTGCTGCTGGCCTGAGTGTCCCTGCCCTCCTGGGGATGCTTTCTCCAAACACATCTGGAACTTTTAAAAGACAAAGTAAAGAAAGAAAAAAGGAACAGTTAGGAGATGATAACCTTTGCCATTTTGAACTTGATACTGTATGAATGTCTGAGTTATTAGCTATACAAAGTGTTGTAGCTTGTCAAAAGACCCTCACCCACAAAGAGCACAGAAATCATCATCGTTGCAAAACGCATGAGGATTTTACTTATCCAAAGTGTTGGGGAGCCCCCTCTCAGCACGCAGGCTGGAGGAGAGACCCAGAACAAAGAAAGACACACTTTTTATAACTTTGTAAGGGCCGGATATAGGCACCAGGGTAGTTTGGCTTATTTTAATTGGTGTAGTCAATAACCTTTTTAGACATTGGTTGGTTTGTAGAGGGTGACTCTCATTTTGTCTGTCCTGAGGTTTTTAGTGTGAGGCAGGGCAGGGGAATTGTTAATCTTGTTTTGGAAGTTTAGTAATTTTGACCATTAAAACTATGTTTCTATATTTGTATGGTCAGCCAGCTTTTTATTTGACTCTGTACTTGGCCTGCTAGTTACAGTTTGGAAAGTCCTTTTGAAGGAGGAAGGTACTGGGTAGTCTTGAATTTATTTTGGATATTACAAAAGATTACAGGTAAACTTAAGTCACTATTGAGTTGCTCTGGAAGGGCAGCCCATTGTACTTAGGATCCCAACTGTGCACTTAGCAGTTTCACGCATGATTAGCCTGTTTCCATCTAGACGCCCTTAGGGCGGAAGCCACATCCTTACCCGATGCATCCATTCACTGGGGGTTCACATGTGCTGGGCTGGAGTGAAGAAAATGGACCTCTTGAGGAAGGGAGCTTGGGAGGCCAAACTGCCTTGGGAGTCCAGGACCGTTGGAATTTGGCCCTTCCTCTGGAAGGGAAAGACCAGGGAAAAGGAGGAAAACTCCATTTGGTTCCCTACGCACTAAACCAGTCGCTCTTGCCCAG
Seq C2 exon
GAACCCTACCTGCAGAGCCAGTGTGACTGCTGTAGCTACAGACTGGATCCGGACAGCCCCGTGCGGATCTTGAACCTCCTTTGCCCCGATGGCCACACAGAGCCAGTGGTGTTGCCAGTGATTCACAGCTGCCAGTGCAGTGCCTGTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029797-Sspo:NM_173428:101
Average complexity
IR-S
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:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCAGTCTCCTGCAGGTA
R:
ACTGGCAGCTGTGAATCACTG
Band lengths:
262-1858
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: