MmuINT0140041 @ mm10
Intron Retention
Gene
ENSMUSG00000038677 | Scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:MGI Symbol;Acc:MGI:3045253]
Coordinates
chr17:28164045-28164402:+
Coord C1 exon
chr17:28164045-28164161
Coord A exon
chr17:28164162-28164297
Coord C2 exon
chr17:28164298-28164402
Length
136 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TGATAAGCCCCTTCTTTCAGAGT
3' ss Score
6.02
Exon sequences
Seq C1 exon
AGCCAGTGAAGTGTCAGAGCAGTCTTGGAGCCTCAAAAGCCATGCTTAGCTGCAATCGCTCGGGCAAGAAGGATACTTGTGCCCTGACCTGTCCCTCCCGGGCCCGGTTCTTGCCAG
Seq A exon
GTATGTGAGAGAGACGGGGTTCTGGGGAGAAGGGAGGGCAGACTGGCTGTTCAGCAGTGCCTCTGTTCCCCCGGGGTTCCTCCAACCATTGGGGGTTGAGAGGTGGGTCAGAGCTGTGATAAGCCCCTTCTTTCAG
Seq C2 exon
AGTCAGAGAACGGTTTCACCGTGAGCTGTGGTACCCCGAGCCCTAAAGCTGCTCCAGCCCGAGTGATCCACTCTGGGAACAGCACCGTCTCCAGCTCCTGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038677:ENSMUST00000043503:11
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=0.083
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=PD(10.6=12.5)
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:
GCCAGTGAAGTGTCAGAGCAG
R:
ATGGCAGGAGCTGGAGACG
Band lengths:
220-356
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