MmuINT0140042 @ mm10
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28164298-28164790:+
Coord C1 exon
chr17:28164298-28164402
Coord A exon
chr17:28164403-28164673
Coord C2 exon
chr17:28164674-28164790
Length
271 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
AGCTTCTCTTCTCCCTCTAGAGG
3' ss Score
9.37
Exon sequences
Seq C1 exon
AGTCAGAGAACGGTTTCACCGTGAGCTGTGGTACCCCGAGCCCTAAAGCTGCTCCAGCCCGAGTGATCCACTCTGGGAACAGCACCGTCTCCAGCTCCTGCCATG
Seq A exon
GTGAGCACCTGCCCAGAGTCCTCCTCTTCTCTGCCCCCACAGTTCTCCTCATCCCTGGCCGACTCACCCTCTACCTCCCTTGTTACTCTCTAACTCTCCAGCTTTGCTGCCAAGCTCCTCCTATCTTACCCCTCCTATCTGTTACCCTTGGCTTTCCTGATCCCACTCTCTAGCTAAACCTTACTGCTGAGCTCGGAGCCACCTCCCAGAGCAGGCCGTCCCCAGGGTCCCCAGGCCCTGGAGCTGTGCTGAGCTTCTCTTCTCCCTCTAG
Seq C2 exon
AGGCTGCAGTGCTGCCAGTCAAGCAGAGAGCCTCCTTCAAGATCAAGGATGCCAAATGTCGCCTGCATCTGCGAAACAAAGGCAAAGCCGAGGAGGCCAGCAGGATCCTGGGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677:ENSMUST00000043503:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.050
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCAGAGAACGGTTTCACC
R:
GGCCCCAGGATCCTGCTG
Band lengths:
220-491
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